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@article{ostberg_analysis_2013,
series = {Enzymology and {Molecular} {Biology} of {Carbonyl} {Metabolism} 16},
title = {Analysis of mammalian alcohol dehydrogenase 5 ({ADH}5): {Characterisation} of rat {ADH}5 with comparisons to the corresponding human variant},
volume = {202},
issn = {0009-2797},
shorttitle = {Analysis of mammalian alcohol dehydrogenase 5 ({ADH}5)},
doi = {10.1016/j.cbi.2012.11.002},
abstract = {Alcohol dehydrogenase 5 (ADH5) is a member of the mammalian alcohol dehydrogenase family of yet undefined functions. ADH5 was first identified at the DNA level in human and deer mouse. A rat alcohol dehydrogenase structure of similar type has been isolated at the cDNA level using human ADH5 as a screening probe, where the rat cDNA structure displayed several atypical properties. mRNA for rat ADH5 was found in multiple tissues, especially in the kidney. In vitro translation experiments indicated that rat ADH5 is expressed as efficiently as ADH1 and furthermore, rat ADH5 was readily expressed in COS cells fused to Green Fluorescent Protein. However, no soluble ADH5 protein could be heterologously expressed in Escherichia coli cells with expression systems successfully used for other mammalian ADHs, including fused to glutathione-S-transferase. Molecular modelling of the enzyme indicated that the protein does not fold in a productive way, which can be the explanation why no stable and active ADH5 has been isolated. These results indicate that ADH5, while readily expressed at the mRNA level, does not behave similarly to other mammalian ADHs investigated. The results, in vitro and in silico, suggest an unstable ADH5 structure, which can explain for why no active and stable protein can be isolated. Further possibilities are conceivable: the ADH5 protein may have to interact with a stabiliser, or the gene is actually a pseudogene.},
number = {1–3},
urldate = {2014-10-02},
journal = {Chem. Biol. Interact.},
author = {Östberg, Linus J. and Strömberg, Patrik and Hedberg, Jesper J. and Persson, Bengt and Höög, Jan-Olov},
month = feb,
year = {2013},
keywords = {ADH classes, Alcohol Dehydrogenase, Enzyme family, Molecular modelling, Protein expression},
pages = {97--103}
}
@misc{munroe_xkcd_2017,
type = {Webcomic},
title = {xkcd},
copyright = {CC BY-NC 2.5},
shorttitle = {xkcd},
url = {https://xkcd.com/1605/},
language = {English},
urldate = {2017-03-22},
journal = {xkcd: DNA},
author = {Munroe, Randall},
month = mar,
year = {2017}
}
@article{altchul_basic_1990,
title = {Basic {Local} {Alignment} {Search} {Tool}},
volume = {215},
journal = {J. Mol. Biol.},
author = {Altchul, SF and Gish, W and Miller, W and Myers, EW and Lipman, DJ},
year = {1990},
pages = {403--410}
}
@article{thompson_balibase_2005,
title = {{BAliBASE} 3.0: latest developments of the multiple sequence alignment benchmark},
volume = {61},
issn = {1097-0134},
shorttitle = {{BAliBASE} 3.0},
doi = {10.1002/prot.20527},
abstract = {Multiple sequence alignment is one of the cornerstones of modern molecular biology. It is used to identify conserved motifs, to determine protein domains, in 2D/3D structure prediction by homology and in evolutionary studies. Recently, high-throughput technologies such as genome sequencing and structural proteomics have lead to an explosion in the amount of sequence and structure information available. In response, several new multiple alignment methods have been developed that improve both the efficiency and the quality of protein alignments. Consequently, the benchmarks used to evaluate and compare these methods must also evolve. We present here the latest release of the most widely used multiple alignment benchmark, BAliBASE, which provides high quality, manually refined, reference alignments based on 3D structural superpositions. Version 3.0 of BAliBASE includes new, more challenging test cases, representing the real problems encountered when aligning large sets of complex sequences. Using a novel, semiautomatic update protocol, the number of protein families in the benchmark has been increased and representative test cases are now available that cover most of the protein fold space. The total number of proteins in BAliBASE has also been significantly increased from 1444 to 6255 sequences. In addition, full-length sequences are now provided for all test cases, which represent difficult cases for both global and local alignment programs. Finally, the BAliBASE Web site (http://www-bio3d-igbmc.u-strasbg.fr/balibase) has been completely redesigned to provide a more user-friendly, interactive interface for the visualization of the BAliBASE reference alignments and the associated annotations.},
language = {eng},
number = {1},
journal = {Proteins},
author = {Thompson, Julie D. and Koehl, Patrice and Ripp, Raymond and Poch, Olivier},
month = oct,
year = {2005},
pmid = {16044462},
keywords = {Amino Acid Sequence, Benchmarking, Databases, Protein, Internet, Molecular Sequence Data, Protein Folding, Proteins, Protein Structure, Quaternary, Sequence Alignment, Software, Structural Homology, Protein},
pages = {127--136}
}
@article{katoh_mafft_2013,
title = {{MAFFT} multiple sequence alignment software version 7: improvements in performance and usability},
volume = {30},
issn = {1537-1719},
shorttitle = {{MAFFT} multiple sequence alignment software version 7},
doi = {10.1093/molbev/mst010},
abstract = {We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.},
language = {eng},
number = {4},
journal = {Mol. Biol. Evol.},
author = {Katoh, Kazutaka and Standley, Daron M.},
month = apr,
year = {2013},
pmid = {23329690},
pmcid = {PMC3603318},
keywords = {Algorithms, Amino Acid Sequence, Base Sequence, DNA, Fungal, DNA, Ribosomal, DNA, Ribosomal Spacer, Fungi, Humans, Models, Genetic, Molecular Sequence Data, Phylogeny, Protein Structure, Tertiary, Quality Improvement, Ribonucleases, Ribosome Subunits, Small, Bacterial, RNA, Bacterial, Sequence Alignment, Software},
pages = {772--780}
}
@article{jornvall_alcohol_2015,
series = {17th {International} {Workshop} on the {Enzymology} and {Molecular} {Biology} of {Carbonyl} {Metabolism}},
title = {Alcohol dehydrogenase, {SDR} and {MDR} structural stages, present update and altered era},
volume = {234},
issn = {0009-2797},
doi = {10.1016/j.cbi.2014.10.017},
abstract = {It is now about half a century since molecular research on alcohol dehydrogenase (ADH), short-chain dehydrogenase/reductase (SDR) and medium-chain dehydrogenase/reductase (MDR) started. During this time, at least four stages of research can be distinguished, which led to many ADH, SDR and MDR structures from which their origins could be traced. An introductory summary of these stages is given, followed by a current update on the now known structures, including the present pattern of mammalian MDR–ADH enzymes into six classes and their evolutionary relationships. In spite of the wide spread in evolutionary changes from the “constant” class III to the more “variable” other classes, the change in class V (only confirmed as a transcript in humans) and class VI (absent in humans) are also restricted. Such spread in variability is visible also in other dehydrogenases, but not always so restricted in other co-evolving proteins we have studied. Finally, the shift in era of present ADH research is highlighted, as well as levels of likely future continuation.},
urldate = {2015-04-27},
journal = {Chem. Biol. Interact.},
author = {Jörnvall, Hans and Landreh, Michael and Östberg, Linus J.},
month = jun,
year = {2015},
keywords = {Alcohol dehydrogenase (ADH), Enzymogenesis, Evolution, Gene duplication, Medium-chain dehydrogenase/reductase (MDR), Short-chain dehydrogenase/reductase (SDR)},
pages = {75--79}
}
@article{sakurai_quantitative_2007,
title = {Quantitative structure-activity relationship analysis and molecular dynamics simulation to functionally validate nonsynonymous polymorphisms of human {ABC} transporter {ABCB}1 ({P}-glycoprotein/{MDR}1)},
volume = {46},
journal = {Biochemistry},
author = {Sakurai, A. and Onishi, Y. and Hirano, H. and Seigneuret, M. and Obanayama, K. and Kim, G. and Liew, E. L. and Sakaeda, T. and Yoshiura, K. and Niikawa, N. and Sakurai, M. and Ishikawa, T.},
year = {2007},
pages = {7678--7693}
}
@article{chen_enzymatic_1991,
title = {Enzymatic properties of the protein encoded by newly cloned human alcohol dehydrogenase {ADH}6 gene},
volume = {181},
issn = {0006-291X},
doi = {10.1016/0006-291X(91)91253-9},
abstract = {Five non-allelic genes which encode five types of alcohol dehydrogenase subunits have been identified in humans. An additional gene (ADH6) and cDNA, whose coding sequences were not highly analogous to any of the known alcohol dehydrogenase subunits, were recently cloned (Yasunami et al., Proc. Natl. Acad. Sci. USA 88, 7610–7614, 1991). The full-length ADH6 cDNA was expressed in the E.coli expression system and in the invitro translation system of rabbit reticulocytes. The protein produced had its isoelectric point at pH 8.6, optimum pH at pH 10, and a lower Km for benzylalcohol than for ethanol and propanol. These characteristics are compatible to the properties of μ- or σ-alcohol dehydrogenase isozyme existing in human stomach, indicating that ADH6 gene encodes the μ- or σ-alcohol dehydrogenase subunit.},
number = {2},
urldate = {2013-08-26},
journal = {Biochem. Biophys. Res. Commun.},
author = {Chen, Cheng-Sheng and Yoshida, Akira},
month = dec,
year = {1991},
pages = {743--747},
file = {ScienceDirect Full Text PDF:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/W64D95AV/Chen and Yoshida - 1991 - Enzymatic properties of the protein encoded by new.pdf:application/pdf;ScienceDirect Snapshot:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/3ZJWMIPA/0006291X91912539.html:text/html}
}
@article{liu_rapid_2009,
title = {Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees},
volume = {324},
issn = {1095-9203},
doi = {10.1126/science.1171243},
abstract = {Inferring an accurate evolutionary tree of life requires high-quality alignments of molecular sequence data sets from large numbers of species. However, this task is often difficult, slow, and idiosyncratic, especially when the sequences are highly diverged or include high rates of insertions and deletions (collectively known as indels). We present SATé (simultaneous alignment and tree estimation), an automated method to quickly and accurately estimate both DNA alignments and trees with the maximum likelihood criterion. In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies.},
language = {eng},
number = {5934},
journal = {Science},
author = {Liu, Kevin and Raghavan, Sindhu and Nelesen, Serita and Linder, C. Randal and Warnow, Tandy},
month = jun,
year = {2009},
pmid = {19541996},
keywords = {Algorithms, Automation, Computer Simulation, DNA, Evolution, Molecular, Likelihood Functions, Phylogeny, Sequence Alignment, Software},
pages = {1561--1564}
}
@article{webb_comparative_2016,
title = {Comparative {Protein} {Structure} {Modeling} {Using} {MODELLER}},
volume = {54},
issn = {1934-340X},
doi = {10.1002/cpbi.3},
abstract = {Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley \& Sons, Inc.},
language = {eng},
journal = {Curr Protoc Bioinformatics},
author = {Webb, Benjamin and Sali, Andrej},
month = jun,
year = {2016},
pmid = {27322406},
pmcid = {PMC5031415},
keywords = {comparative modeling, ModBase, MODELLER, protein fold, protein structure, structure prediction},
pages = {5.6.1--5.6.37}
}
@article{estonius_alcohol_1996,
title = {Alcohol dehydrogenase in human tissues: localisation of transcripts coding for five classes of the enzyme},
volume = {397},
issn = {0014-5793},
shorttitle = {Alcohol dehydrogenase in human tissues},
abstract = {Tissue distribution of the five identified classes of human alcohol dehydrogenase was studied by assessment of mRNA levels in 23 adult and four fetal tissues. Alcohol dehydrogenase of class I was found in most tissues, brain and placenta excluded, but expression levels among tissues differed widely. The distribution pattern of class III transcripts was consistent with those of housekeeping enzymes while, in contrast, class IV transcripts were found only in stomach. Transcripts of multiple length were detected for most classes and were due to different gene products arising through the use of different poly-A signals or transcription from different gene loci. Both class II and class V showed a pattern of liver-enriched expression. However, low mRNA levels were detected also in stomach, pancreas and small intestine for class II, and in fetal kidney and small intestine for class V. Significantly higher levels of class V transcripts were present in fetal liver when compared with levels in adult liver, which suggests that human class V is a predominantly fetal alcohol dehydrogenase.},
language = {eng},
number = {2-3},
journal = {FEBS Lett.},
author = {Estonius, M. and Svensson, S. and Höög, J-O},
month = nov,
year = {1996},
pmid = {8955375},
keywords = {Alcohol Dehydrogenase, Blotting, Northern, Brain, Cloning, Molecular, Digestive System, Female, Genitalia, Humans, Kidney, Liver, Lymphoid Tissue, Male, Organ Specificity, Placenta, RNA, Messenger, Tissue Distribution},
pages = {338--342}
}
@article{altschul_gapped_1997,
title = {Gapped {BLAST} and {PSI}-{BLAST}: a new generation of protein database search programs},
volume = {25},
issn = {0305-1048},
shorttitle = {Gapped {BLAST} and {PSI}-{BLAST}},
doi = {10.1093/nar/25.17.3389},
number = {17},
urldate = {2017-01-27},
journal = {Nucl Acids Res},
author = {Altschul, Stephen F. and Madden, Thomas L. and Schäffer, Alejandro A. and Zhang, Jinghui and Zhang, Zheng and Miller, Webb and Lipman, David J.},
month = sep,
year = {1997},
pages = {3389--3402}
}
@article{sali_comparative_1993,
title = {Comparative protein modelling by satisfaction of spatial restraints},
volume = {234},
issn = {0022-2836},
doi = {10.1006/jmbi.1993.1626},
abstract = {We describe a comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures. The three-dimensional (3D) model is obtained by optimally satisfying spatial restraints derived from the alignment and expressed as probability density functions (pdfs) for the features restrained. For example, the probabilities for main-chain conformations of a modelled residue may be restrained by its residue type, main-chain conformation of an equivalent residue in a related protein, and the local similarity between the two sequences. Several such pdfs are obtained from the correlations between structural features in 17 families of homologous proteins which have been aligned on the basis of their 3D structures. The pdfs restrain C alpha-C alpha distances, main-chain N-O distances, main-chain and side-chain dihedral angles. A smoothing procedure is used in the derivation of these relationships to minimize the problem of a sparse database. The 3D model of a protein is obtained by optimization of the molecular pdf such that the model violates the input restraints as little as possible. The molecular pdf is derived as a combination of pdfs restraining individual spatial features of the whole molecule. The optimization procedure is a variable target function method that applies the conjugate gradients algorithm to positions of all non-hydrogen atoms. The method is automated and is illustrated by the modelling of trypsin from two other serine proteinases.},
language = {eng},
number = {3},
journal = {J. Mol. Biol.},
author = {Sali, A. and Blundell, T. L.},
month = dec,
year = {1993},
pmid = {8254673},
keywords = {Amino Acid Sequence, Animals, Enzymes, Humans, Kallikreins, Mathematics, Models, Theoretical, Molecular Sequence Data, Pancreatic Elastase, Probability, Protein Conformation, Proteins, Sequence Homology, Amino Acid, Software, Thermodynamics, Tissue Kallikreins, Trypsin},
pages = {779--815}
}
@article{jones_genthreader:_1999,
title = {{GenTHREADER}: an efficient and reliable protein fold recognition method for genomic sequences},
volume = {287},
number = {4},
journal = {J. Mol. Biol.},
author = {Jones, DT},
year = {1999},
pages = {797--815}
}
@article{chenna_multiple_2003,
title = {Multiple sequence alignment with the {Clustal} series of programs},
volume = {31},
journal = {Nucleic Acids Res.},
author = {Chenna, R. and Sugawara, H. and Koike, T. and Lopez, R. and Gibson, T. J. and Higgins, D. G. and Thompson, J. D},
year = {2003},
pages = {3497--3500}
}
@article{hoog_mammalian_2011,
title = {Mammalian alcohol dehydrogenases – {A} comparative investigation at gene and protein levels},
volume = {191},
issn = {0009-2797},
shorttitle = {Enzymology and {Molecular} {Biology} of {Carbonyl} {Metabolism} 15th {International} {Meeting} on {Enzymology} and {Molecular} {Biology} of {Carbonyl} {Metabolism}},
doi = {10.1016/j.cbi.2011.01.028},
abstract = {Mammalian alcohol dehydrogenase (ADH) can be divided into six classes, ADH1–ADH6, according to primary structure and function, where the classes are further subdivided into isozymes and allelic forms. With the increasing amount of available genomic data a general pattern is possible to trace within the mammalian ADH gene and protein families. The transcriptional order for the ADH genes in all mammalian genomes is the same (ADH4–ADH1–ADH6–ADH5–ADH2–ADH3), but the cluster is found on different chromosomes in different species. However, in primates only ADH1–ADH5 are present, where the loss of ADH6 may have occurred simultaneously as the split into ADH1 isoforms. ADH3, also denoted glutathione-dependent formaldehyde dehydrogenase and S-nitrosoglutathione reductase, is identified as the last gene in the ADH transcriptional order, but several pseudogenes for ADH3 have been traced at other chromosomes. The flanking genes outside the ADH genome are similar or identical for all species showing that a larger DNA region has been duplicated and further evolved. However, the only entirely completed ADH genomes are those from primates and rodents.
The latest identified ADH forms, ADH5 (class V) and ADH6 (class VI), are truly different classes and both are very diverged in contrast to ADH3, which is the most conserved class of all ADHs. ADH5 and ADH6 have been identified at the gene and transcriptional levels only, and their functions are still an enigma.},
number = {1–3},
urldate = {2013-08-26},
journal = {Chem. Biol. Interact.},
author = {Höög, Jan-Olov and Östberg, Linus J.},
month = may,
year = {2011},
keywords = {Alcohol Dehydrogenase, Gene cluster, Isoforms, Mammalian gene family, Protein family},
pages = {2--7},
file = {ScienceDirect Full Text PDF:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/8HZC5UQC/Höög and Östberg - 2011 - Mammalian alcohol dehydrogenases – A comparative i.pdf:application/pdf;ScienceDirect Snapshot:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/PJ29XCTX/S0009279711000524.html:text/html}
}
@article{b._hess_p-lincs:_2008,
title = {P-{LINCS}: {A} {Parallel} {Linear} {Constraint} {Solver} for molecular simulation},
volume = {4},
author = {{B. Hess}},
year = {2008},
pages = {116--122}
}
@article{wang_pubchem_2017,
title = {{PubChem} {BioAssay}: 2017 update},
volume = {45},
issn = {0305-1048},
shorttitle = {{PubChem} {BioAssay}},
doi = {10.1093/nar/gkw1118},
abstract = {PubChem's BioAssay database (https://pubchem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research. To facilitate data discovery, PubChem is integrated with all other databases at NCBI. In this work, we provide an update for the PubChem BioAssay database describing several recent development including added sources of research data, redesigned BioAssay record page, new BioAssay classification browser and new features in the Upload system facilitating data sharing.},
number = {Database issue},
urldate = {2017-03-30},
journal = {Nucleic Acids Res},
author = {Wang, Yanli and Bryant, Stephen H. and Cheng, Tiejun and Wang, Jiyao and Gindulyte, Asta and Shoemaker, Benjamin A. and Thiessen, Paul A. and He, Siqian and Zhang, Jian},
month = jan,
year = {2017},
pmid = {27899599},
pmcid = {PMC5210581},
pages = {D955--D963},
file = {PubMed Central Full Text PDF:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/HS3RRVPB/Wang et al. - 2017 - PubChem BioAssay 2017 update.pdf:application/pdf}
}
@article{svensson_structural_1998,
title = {Structural and functional divergence of class {II} alcohol dehydrogenase},
volume = {251},
issn = {1432-1033},
doi = {10.1046/j.1432-1327.1998.2510236.x},
abstract = {cDNAs coding for class II alcohol dehydrogenase were isolated from a rabbit-liver cDNA library. Deduced amino acid sequences show that isozymic forms of rabbit class II alcohol dehydrogenase exist, with a positional identity of 88.4 \%. A high variability in structure of class II alcohol dehydrogenase between the species is also reflected in function. The rabbit II-1 isozyme shows common characteristics with the human enzyme, but has a lower Km value for ethanol, 4.2 mM. The II-2 isozyme shows restriction for aliphatic alcohols longer than pentanol. For shorter alcohols the II-2 form has similar Km values as the II-1 isozyme, 5.5 mM for ethanol, but is a low activity variant with a 10-fold decrease in kcat values compared with II-1. Nevertheless, II-2 has a higher specificity for benzoquinone than II-1 due to a lower Km value, 80 μM compared with 1 mM, and is in this sense more like the human class II enzyme. In addition a rabbit class III alcohol dehydrogenase cDNA was isolated that encodes a typical class III enzyme/glutathione-dependent formaldehyde dehydrogenase. The finding of isozymic forms of class II alcohol dehydrogenase is in line with the evolution of the system of medium-chain alcohol dehydrogenases with different enzymes, different classes and different isozymes and further underline the complexity of the entire mammalian alcohol dehydrogenase system.},
language = {en},
number = {1-2},
urldate = {2015-11-27},
journal = {European Journal of Biochemistry},
author = {Svensson, Stefan and Hedberg, Jesper J. and Höög, Jan-Olov},
month = jan,
year = {1998},
keywords = {Alcohol Dehydrogenase, cDNA sequence, isozyme, recombinant protein, substrate specificity.},
pages = {236--243}
}
@article{danielsson_enzymogenesis:_1992,
title = {"{Enzymogenesis}": classical liver alcohol dehydrogenase origin from the glutathione-dependent formaldehyde dehydrogenase line},
volume = {89},
issn = {0027-8424},
shorttitle = {"{Enzymogenesis}"},
abstract = {Analysis of the activity and structure of lower vertebrate alcohol dehydrogenases reveals that relationships between the classical liver and yeast enzymes need not be continuous. Both the ethanol activity of class I-type alcohol dehydrogenase (alcohol:NAD+ oxidoreductase, EC 1.1.1.1) and the glutathione-dependent formaldehyde activity of the class III-type enzyme [formaldehyde:NAD+ oxidoreductase (glutathione-formylating), EC 1.2.1.1] are present in liver down to at least the stage of bony fishes (cod liver: ethanol activity, 3.4 units/mg of protein in one enzyme; formaldehyde activity, 4.5 units/mg in the major form of another enzyme). Structural analysis of the latter protein reveals it to be a typical class III enzyme, with limited variation from the mammalian form and therefore with stable activity and structure throughout much of the vertebrate lineage. In contrast, the classical alcohol dehydrogenase (the class I enzyme) appears to be the emerging form, first in activity and later also in structure. The class I activity is present already in the piscine line, whereas the overall structural-type enzyme is not observed until amphibians and still more recent vertebrates. Consequently, the class I/III duplicatory origin appears to have arisen from a functional class III form, not a class I form. Therefore, ethanol dehydrogenases from organisms existing before this duplication have origins separate from those leading to the "classical" liver alcohol dehydrogenases. The latter now often occur in isozyme forms from further gene duplications and have a high rate of evolutionary change. The pattern is, however, not simple and we presently find in cod the first evidence for isozymes also within a class III alcohol dehydrogenase. Overall, the results indicate that both of these classes of vertebrate alcohol dehydrogenase are important and suggest a protective metabolic function for the whole enzyme system.},
language = {eng},
number = {19},
journal = {Proc. Natl. Acad. Sci. U.S.A.},
author = {Danielsson, O. and Jörnvall, H.},
month = oct,
year = {1992},
pmid = {1409630},
pmcid = {PMC50103},
keywords = {Alcohol Dehydrogenase, Aldehyde Oxidoreductases, Amino Acid Sequence, Animals, Chromatography, Affinity, Chromatography, DEAE-Cellulose, Fishes, Glutathione, Humans, Isoenzymes, Liver, Molecular Sequence Data, Sequence Homology, Amino Acid},
pages = {9247--9251}
}
@article{berendsen_gromacs:_1995,
title = {{GROMACS}: {A} message-passing parallel molecular dynamics implementation},
volume = {91},
journal = {Comp. Phys. Comm.},
author = {Berendsen, H J C and van der Spoel, D and van Drunen, R},
year = {1995},
pages = {43--56}
}
@article{soler_effects_2013,
title = {Effects of {Knots} on {Protein} {Folding} {Properties}},
volume = {8},
doi = {10.1371/journal.pone.0074755},
abstract = {This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism) via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may affect key aspects of folding kinetics. In this regard, we found clear evidence for a functional advantage of knots: knots enhance kinetic stability because a knotted protein unfolds at a distinctively slower rate than its unknotted counterpart. However, an increase in knot deepness does not necessarily lead to more effective changes in folding properties. In this regard, a terminus with a non-trivial conformation (e.g. hairpin) can have a more dramatic effect in enhancing kinetic stability than knot depth. Nevertheless, our results suggest that the probability of the denatured ensemble to keep knotted is higher for proteins with deeper knots, indicating that knot depth plays a role in determining the topology of the denatured state. Refolding simulations starting from denatured knotted conformations show that not every knot is able to nucleate folding and further indicate that the formation of the knotting loop is a key event in the folding of knotted trefoils. They also show that there are specific native contacts within the knotted core that are crucial to keep a native knotting loop in denatured conformations which otherwise have no detectable structure. The study of the knotting mechanism reveals that the threading of the knotting loop generally occurs towards late folding in conformations that exhibit a significant degree of structural consolidation.},
number = {9},
urldate = {2013-09-12},
journal = {PLoS ONE},
author = {Soler, Miguel A. and Faísca, Patrícia F. N.},
month = sep,
year = {2013},
pages = {e74755},
file = {PLoS Snapshot:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/65MKK9PF/Soler and Faísca - 2013 - Effects of Knots on Protein Folding Properties.html:text/html}
}
@article{krissinel_secondary-structure_2004,
title = {Secondary-structure matching ({SSM}), a new tool for fast protein structure alignment in three dimensions},
volume = {D60},
journal = {Acta Cryst},
author = {Krissinel, E and Henrick, K},
year = {2004},
pages = {2256--2268}
}
@article{f_c_bernstein_protein_1977,
title = {The {Protein} {Data} {Bank}: {A} {Computer}-based {Archival} {File} {For} {Macromolecular} {Structures}},
volume = {112},
journal = {J. of. Mol. Biol.},
author = {{F C Bernstein} and {T. F. Koetzle} and {G. J. Williams} and {E. E. Meyer Jr} and {M. D. Brice} and {J. R. Rodgers} and {O. Kennard} and {T. Shimanouchi} and {M. Tasumi}},
year = {1977},
pages = {535}
}
@article{nordling_molecular_2008,
title = {Molecular dynamics studies of alpha-helix stability in fibril-forming peptides},
volume = {22},
journal = {J Comput Aided Mol Des},
author = {Nordling, E. and Kallberg, Y. and Johansson, J. and Persson, B},
year = {2008},
pages = {53--58}
}
@incollection{eswar_current_2006,
title = {Current {Protocols} in {Bioinformatics}},
publisher = {John Wiley \& Sons, Inc},
author = {Eswar, N and Marti-Renom, M. A. and Webb, B. and Madhusudhan, M. S. and Eramian, D. and Shen, M. and Pieper, U. and Sali, A.},
year = {2006},
pages = {Supplement 15, 5.6.1--5.6.30}
}
@article{zhang_template-based_2007,
title = {Template-based modeling and free modeling by {I}-{TASSER} in {CASP}7},
volume = {69},
number = {S8},
journal = {Proteins: Structure, Function, and Bioinformatics},
author = {Zhang, Yang},
year = {2007},
pages = {108--17}
}
@article{wu_structural_2008,
title = {Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase {PTGR}2},
volume = {16},
issn = {0969-2126},
doi = {10.1016/j.str.2008.09.007},
abstract = {PTGR2 catalyzes an NADPH-dependent reduction of the conjugated alpha,beta-unsaturated double bond of 15-keto-PGE(2), a key step in terminal inactivation of prostaglandins and suppression of PPARgamma-mediated adipocyte differentiation. Selective inhibition of PTGR2 may contribute to the improvement of insulin sensitivity with fewer side effects. PTGR2 belongs to the medium-chain dehydrogenase/reductase superfamily. The crystal structures reported here reveal features of the NADPH binding-induced conformational change in a LID motif and a polyproline type II helix which are critical for the reaction. Mutation of Tyr64 and Tyr259 significantly reduces the rate of catalysis but increases the affinity to substrate, confirming the structural observations. Besides targeting cyclooxygenase, indomethacin also inhibits PTGR2 with a binding mode similar to that of 15-keto-PGE(2). The LID motif becomes highly disordered upon the binding of indomethacin, indicating plasticity of the active site. This study has implications for the rational design of inhibitors of PTGR2.},
language = {eng},
number = {11},
journal = {Structure},
author = {Wu, Yu-Hauh and Ko, Tzu-Ping and Guo, Rey-Ting and Hu, Su-Ming and Chuang, Lee-Ming and Wang, Andrew H.-J.},
month = nov,
year = {2008},
pmid = {19000823},
keywords = {Alcohol Dehydrogenase, Amino Acid Sequence, Animals, Catalysis, Dinoprostone, Guinea Pigs, Humans, Indomethacin, Kinetics, Mice, Models, Molecular, Molecular Conformation, Molecular Sequence Data, Niacinamide, Protein Binding, Sequence Alignment, Sequence Homology, Amino Acid},
pages = {1714--1723}
}
@article{skwark_pconsc:_2013,
title = {{PconsC}: combination of direct information methods and alignments improves contact prediction},
volume = {29},
issn = {1367-4811},
shorttitle = {{PconsC}},
doi = {10.1093/bioinformatics/btt259},
abstract = {SUMMARY: Recently, several new contact prediction methods have been published. They use (i) large sets of multiple aligned sequences and (ii) assume that correlations between columns in these alignments can be the results of indirect interaction. These methods are clearly superior to earlier methods when it comes to predicting contacts in proteins. Here, we demonstrate that combining predictions from two prediction methods, PSICOV and plmDCA, and two alignment methods, HHblits and jackhmmer at four different e-value cut-offs, provides a relative improvement of 20\% in comparison with the best single method, exceeding 70\% correct predictions for one contact prediction per residue.
AVAILABILITY: The source code for PconsC along with supplementary data is freely available at http://c.pcons.net/
CONTACT: [email protected]
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
language = {eng},
number = {14},
journal = {Bioinformatics},
author = {Skwark, Marcin J. and Abdel-Rehim, Abbi and Elofsson, Arne},
month = jul,
year = {2013},
pmid = {23658418},
keywords = {Algorithms, Protein Conformation, Proteins, Sequence Alignment, Sequence Analysis, Protein},
pages = {1815--1816}
}
@article{molotkov_distinct_2002,
title = {Distinct retinoid metabolic functions for alcohol dehydrogenase genes {Adh}1 and {Adh}4 in protection against vitamin {A} toxicity or deficiency revealed in double null mutant mice},
volume = {277},
issn = {0021-9258},
doi = {10.1074/jbc.M112039200},
abstract = {The ability of class I alcohol dehydrogenase (ADH1) and class IV alcohol dehydrogenase (ADH4) to metabolize retinol to retinoic acid is supported by genetic studies in mice carrying Adh1 or Adh4 gene disruptions. To differentiate the physiological roles of ADH1 and ADH4 in retinoid metabolism we report here the generation of an Adh1/4 double null mutant mouse and its comparison to single null mutants. We demonstrate that loss of both ADH1 and ADH4 does not have additive effects, either for production of retinoic acid needed for development or for retinol turnover to minimize toxicity. During gestational vitamin A deficiency Adh4 and Adh1/4 mutants exhibit completely penetrant postnatal lethality by day 15 and day 24, respectively, while 60\% of Adh1 mutants survive to adulthood similar to wild-type. Following administration of a 50-mg/kg dose of retinol to examine retinol turnover, Adh1 and Adh1/4 mutants exhibit similar 10-fold decreases in retinoic acid production, whereas Adh4 mutants have only a slight decrease. LD(50) studies indicate a large increase in acute retinol toxicity for Adh1 mutants, a small increase for Adh4 mutants, and an intermediate increase for Adh1/4 mutants. Chronic retinol supplementation during gestation resulted in 65\% postnatal lethality in Adh1 mutants, whereas only approximately 5\% for Adh1/4 and Adh4 mutants. These studies indicate that ADH1 provides considerable protection against vitamin A toxicity, whereas ADH4 promotes survival during vitamin A deficiency, thus demonstrating largely non-overlapping functions for these enzymes in retinoid metabolism.},
language = {eng},
number = {16},
journal = {J. Biol. Chem.},
author = {Molotkov, Andrei and Deltour, Louise and Foglio, Mario H. and Cuenca, Arnold E. and Duester, Gregg},
month = apr,
year = {2002},
pmid = {11836246},
pmcid = {PMC2832706},
keywords = {Alcohol Dehydrogenase, Animals, Chromatography, High Pressure Liquid, Female, Genetic Vectors, Genotype, Heterozygote, Male, Mice, Mice, Transgenic, Models, Genetic, Mutation, Time Factors, Tretinoin, Vitamin A, Vitamin A Deficiency},
pages = {13804--13811}
}
@article{miinalainen_characterization_2003,
title = {Characterization of 2-enoyl thioester reductase from mammals. {An} ortholog of {YBR}026p/{MRF}1'p of the yeast mitochondrial fatty acid synthesis type {II}},
volume = {278},
issn = {0021-9258},
doi = {10.1074/jbc.M302851200},
abstract = {A data base search with YBR026c/MRF1', which encodes trans-2-enoyl thioester reductase of the intramitochondrial fatty acid synthesis (FAS) type II in yeast (Torkko, J. M., Koivuranta, K. T., Miinalainen, I. J., Yagi, A. I., Schmitz, W., Kastaniotis, A. J., Airenne, T. T., Gurvitz, A., and Hiltunen, K. J. (2001) Mol. Cell. Biol. 21, 6243-6253), revealed the clone AA393871 (HsNrbf-1, nuclear receptor binding factor 1) in human EST data bank. Expression of HsNrbf-1, tagged C-terminally with green fluorescent protein, in HeLa cells, resulted in a punctated fluorescence signal, superimposable with the MitoTracker Red dye. Wild-type polypeptide was immunoisolated from the extract of bovine heart mitochondria. Recombinant HsNrbf-1p reduces trans-2-enoyl-CoA to acyl-CoA with chain length from C6 to C16 in an NADPH-dependent manner with preference to medium chain length substrate. Furthermore, expression of HsNRBF-1 in the ybr026cDelta yeast strain restored mitochondrial respiratory function allowing growth on glycerol. These findings provide evidence that Nrbf-1ps act as a mitochondrial 2-enoyl thioester reductase, and mammalian cells may possess bacterial type fatty acid synthetase (FAS type II) in mitochondria, in addition to FAS type I in the cytoplasm.},
language = {eng},
number = {22},
journal = {J. Biol. Chem.},
author = {Miinalainen, Ilkka J. and Chen, Zhi-Jun and Torkko, Juha M. and Pirilä, Päivi L. and Sormunen, Raija T. and Bergmann, Ulrich and Qin, Yong-Mei and Hiltunen, J. Kalervo},
month = may,
year = {2003},
pmid = {12654921},
keywords = {Amino Acid Sequence, Animals, Base Sequence, Cattle, DNA Primers, Fatty Acid Desaturases, HeLa Cells, Humans, Microscopy, Fluorescence, Mitochondria, Heart, Molecular Sequence Data, NADH, NADPH Oxidoreductases, Oxidoreductases Acting on CH-CH Group Donors, Saccharomyces cerevisiae, Sequence Homology, Amino Acid},
pages = {20154--20161}
}
@article{ostberg_computational_2016,
title = {Computational studies of human class {V} alcohol dehydrogenase - the odd sibling},
volume = {17},
issn = {1471-2091},
doi = {10.1186/s12858-016-0072-y},
abstract = {All known attempts to isolate and characterize mammalian class V alcohol dehydrogenase (class V ADH), a member of the large ADH protein family, at the protein level have failed. This indicates that the class V ADH protein is not stable in a non-cellular environment, which is in contrast to all other human ADH enzymes. In this report we present evidence, supported with results from computational analyses performed in combination with earlier in vitro studies, why this ADH behaves in an atypical way.},
urldate = {2017-01-19},
journal = {BMC Biochemistry},
author = {Östberg, Linus J. and Persson, Bengt and Höög, Jan-Olov},
year = {2016},
keywords = {Alcohol Dehydrogenase, Mutational pressure, Pseudoenzyme, Sequence analysis, Structural calculations},
pages = {16}
}
@article{wu_protein_2003,
title = {The {Protein} {Information} {Resource}},
volume = {31},
issn = {0305-1048},
doi = {10.1093/nar/gkg040},
number = {1},
urldate = {2017-03-24},
journal = {Nucleic Acids Res},
author = {Wu, Cathy H. and Yeh, Lai-Su L. and Huang, Hongzhan and Arminski, Leslie and Castro-Alvear, Jorge and Chen, Yongxing and Hu, Zhangzhi and Kourtesis, Panagiotis and Ledley, Robert S. and Suzek, Baris E. and Vinayaka, C. R. and Zhang, Jian and Barker, Winona C.},
month = jan,
year = {2003},
pages = {345--347},
file = {Full Text PDF:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/P7GFEQ79/Wu et al. - 2003 - The Protein Information Resource.pdf:application/pdf;Snapshot:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/IHKTKJM3/gkg040.html:text/html}
}
@article{persson_characteristics_1991,
title = {Characteristics of short-chain alcohol dehydrogenases and related enzymes},
volume = {200},
issn = {0014-2956},
abstract = {Different short-chain dehydrogenases are distantly related, constituting a protein family now known from at least 20 separate enzymes characterized, but with extensive differences, especially in the C-terminal third of their sequences. Many of the first known members were prokaryotic, but recent additions include mammalian enzymes from placenta, liver and other tissues, including 15-hydroxyprostaglandin, 17 beta-hydroxysteroid and 11 beta-hydroxysteroid dehydrogenases. In addition, species variants, isozyme-like multiplicities and mutants have been reported for several of the structures. Alignments of the different enzymes reveal large homologous parts, with clustered similarities indicating regions of special functional/structural importance. Several of these derive from relationships within a common type of coenzyme-binding domain, but central-chain patterns of similarity go beyond this domain. Total residue identities between enzyme pairs are typically around 25\%, but single forms deviate more or less (14-58\%). Only six of the 250-odd residues are strictly conserved and seven more are conserved in all but single cases. Over one third of the conserved residues are glycine, showing the importance of conformational and spatial restrictions. Secondary structure predictions, residue distributions and hydrophilicity profiles outline a common, N-terminal coenzyme-binding domain similar to that of other dehydrogenases, and a C-terminal domain with unique segments and presumably individual functions in each case. Strictly conserved residues of possible functional interest are limited, essentially only three polar residues. Asp64, Tyr152 and Lys156 (in the numbering of Drosophila alcohol dehydrogenase), but no histidine or cysteine residue like in the completely different, classical medium-chain alcohol dehydrogenase family. Asp64 is in the suggested coenzyme-binding domain, whereas Tyr152 and Lys156 are close to the center of the protein chain, at a putative inter-domain, active-site segment. Consequently, the overall comparisons suggest the possibility of related mechanisms and domain properties for different members of the short-chain family.},
language = {eng},
number = {2},
journal = {Eur. J. Biochem.},
author = {Persson, B. and Krook, M. and Jörnvall, H.},
month = sep,
year = {1991},
pmid = {1889416},
keywords = {Alcohol Dehydrogenase, Amino Acid Sequence, Binding Sites, Coenzymes, Isoenzymes, Molecular Sequence Data, Sequence Alignment, Sequence Homology, Nucleic Acid},
pages = {537--543}
}
@article{ferrari_soft_2004,
title = {Soft {Docking} and multiple receptor conformation in virtual screening},
volume = {47},
journal = {J. Med. Chem},
author = {Ferrari, A M and Wei, B Q and Costantino, L and Shoichet, B K},
year = {2004},
pages = {5076--5084}
}
@article{hellgren_enrichment_2010,
title = {Enrichment of ligands with molecular dockings and subsequent characterization for human alcohol dehydrogenase},
volume = {67},
number = {17},
journal = {Cell. Mol. Life. Sci.},
author = {Hellgren, Mikko and Carlsson, Jonas and Östberg, Linus J and Staab, Claudia A and Persson, Bengt and Höög, Jan-Olov},
year = {2010},
pages = {3005--15}
}
@article{kleiger_gxxxg_2002,
title = {{GXXXG} and {GXXXA} {Motifs} {Stabilize} {FAD} and {NAD}({P})-binding {Rossmann} {Folds} {Through} {C$\alpha$}–{H}⋯{O} {Hydrogen} {Bonds} and van der {Waals} {Interactions}},
volume = {323},
issn = {0022-2836},
doi = {10.1016/S0022-2836(02)00885-9},
abstract = {Here we present evidence that domains in soluble proteins containing either the GXXXG or GXXXA motif are stabilized by the interaction of a $\beta$-strand with the following $\alpha$-helix. As an example, we characterized a $\beta$-strand–helix interaction from the FAD or NAD(P)-binding Rossmann fold. The Rossmann fold is one of the three most highly represented folds in the Protein Data Bank (PDB). A subset of the proteins that adopt the Rossmann fold also bind to nucleotide cofactors such as FAD and NAD(P) and function as oxidoreductases. These Rossmann folds can often be identified by the short amino acid sequence motif, GX1–2GXXG. Here, we present evidence that in addition to this sequence motif, Rossmann folds that bind FAD and NAD(P) also typically contain either GXXXG or GXXXA motifs, where the first glycyl residue of these motifs and the third glycyl residue of the GX1–2GXXG motif are the same residue. These two motifs appear to stabilize the Rossmann fold: the first glycyl residue of either the GXXXG or GXXXA motif contacts the carbonyl oxygen atom from the first glycyl residue of the GX1–2GXXG motif consistent with the formation of a C$\alpha$–H⋯O hydrogen bond. In addition, both the glycyl and alanyl residues of the GXXXG or GXXXA motifs form van der Waals interactions with either a valine or isoleucine residue located either seven or eight residues further back along the polypeptide chain from the first glycine of the GXXXG or GXXXA motifs. Therefore, we combine both the GX1–2GXXG and GXXXG/A motifs into an extended motif, V/IXGX1–2GXXGXXXG/A, that is more strongly indicative than previously described motifs of Rossmann folds that bind FAD or NAD(P). The V/IXGX1–2GXXGXXXG/A motif can be used to search genomic sequence data and to annotate the function of proteins containing the motif as oxidoreductases, including proteins of previously unknown function.},
number = {1},
urldate = {2017-03-06},
journal = {Journal of Molecular Biology},
author = {Kleiger, Gary and Eisenberg, David},
month = oct,
year = {2002},
keywords = {FAD-binding, hydrogen bond, NAD(P)-binding, Rossmann fold, sequence motif},
pages = {69--76},
file = {ScienceDirect Full Text PDF:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/II98RM8N/Kleiger and Eisenberg - 2002 - GXXXG and GXXXA Motifs Stabilize FAD and NAD(P)-bi.pdf:application/pdf;ScienceDirect Snapshot:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/BMXKZUVC/Kleiger and Eisenberg - 2002 - GXXXG and GXXXA Motifs Stabilize FAD and NAD(P)-bi.html:text/html}
}
@article{abagyan_biased_1994,
title = {Biased probability {Monte} {Carlo} conformational searches and electrostatic calculations for peptides and proteins},
volume = {235},
journal = {J. Mol. Biol.},
author = {Abagyan, R and Totrov, M},
year = {1994},
pages = {983--1002}
}
@article{lassmann_kalign2:_2009,
title = {Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features},
volume = {37},
issn = {1362-4962},
shorttitle = {Kalign2},
doi = {10.1093/nar/gkn1006},
abstract = {In the growing field of genomics, multiple alignment programs are confronted with ever increasing amounts of data. To address this growing issue we have dramatically improved the running time and memory requirement of Kalign, while maintaining its high alignment accuracy. Kalign version 2 also supports nucleotide alignment, and a newly introduced extension allows for external sequence annotation to be included into the alignment procedure. We demonstrate that Kalign2 is exceptionally fast and memory-efficient, permitting accurate alignment of very large numbers of sequences. The accuracy of Kalign2 compares well to the best methods in the case of protein alignments while its accuracy on nucleotide alignments is generally superior. In addition, we demonstrate the potential of using known or predicted sequence annotation to improve the alignment accuracy. Kalign2 is freely available for download from the Kalign web site (http://msa.sbc.su.se/).},
language = {eng},
number = {3},
journal = {Nucleic Acids Res.},
author = {Lassmann, Timo and Frings, Oliver and Sonnhammer, Erik L. L.},
month = feb,
year = {2009},
pmid = {19103665},
pmcid = {PMC2647288},
keywords = {Reproducibility of Results, Sequence Alignment, Sequence Analysis, Protein, Sequence Analysis, RNA, Software, Time Factors},
pages = {858--865}
}
@book{noauthor_molsoft_2012,
title = {Molsoft {L}.{L}.{C}.: {Publications}},
year = {2012}
}
@article{hu_identification_2002,
title = {Identification and characterization of a novel {Nogo}-interacting mitochondrial protein ({NIMP})},
volume = {81},
issn = {0022-3042},
abstract = {Nogo is a potent inhibitor of regeneration following spinal cord injury. To develop a better understanding of the mechanisms responsible for regenerative failure we used a yeast two-hybrid approach to try and identify proteins that interact with Nogo. We identified a novel mitochondrial protein designated Nogo-interacting mitochondrial protein (NIMP) in a screen of an adult human brain cDNA library. This interaction was confirmed by co-immunoprecipitation in both brain tissue (endogenous) and transfected HEK293T cells (overexpressed). In support of these studies we demonstrate that Nogo interacts with the UQCRC1 and UQCRC2 components of complex III, within the mitochondrial respiratory chain. The mitochondrial localization of NIMP was evidenced by confocal image analysis and western blot analysis of isolated mitochondria. NIMP is highly conserved and ubiquitously expressed in mitochondria-enriched tissues. Within the CNS, NIMP-like immunoreactivity is present in neurons and astrocytes. These data suggest that NIMP is a novel mitochondrial protein that interacts with Nogo. The interaction of Nogo with mitochondrial proteins may provide insight into the mechanisms for Nogo-induced inhibition of neurite growth.},
language = {eng},
number = {1},
journal = {J. Neurochem.},
author = {Hu, Wen-Hui and Hausmann, Oliver N. and Yan, Ming-Shan and Walters, Winston M. and Wong, Paul K. Y. and Bethea, John R.},
month = apr,
year = {2002},
pmid = {12067236},
keywords = {Animals, Carrier Proteins, Cattle, Cell Line, Conserved Sequence, COS Cells, Electron Transport Complex III, Humans, Macromolecular Substances, Mice, Mitochondria, Mitochondrial Proteins, Molecular Sequence Data, Myelin Proteins, Nerve Regeneration, Nogo Proteins, Organ Specificity, Protein Binding, Protein Subunits, Recombinant Fusion Proteins, RNA, Messenger, Sequence Alignment, Sequence Homology, Amino Acid, Two-Hybrid System Techniques},
pages = {36--45}
}
@article{desiere_peptideatlas_2006,
title = {The {PeptideAtlas} project},
volume = {34},
issn = {0305-1048, 1362-4962},
doi = {10.1093/nar/gkj040},
abstract = {The completion of the sequencing of the human genome and the concurrent, rapid development of high-throughput proteomic methods have resulted in an increasing need for automated approaches to archive proteomic data in a repository that enables the exchange of data among researchers and also accurate integration with genomic data. PeptideAtlas (http://www.peptideatlas.org/) addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. A meaningful comparison of data across different experiments generated by different groups using different types of instruments is enabled by the implementation of a uniform analytic process. This uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications. The raw data from many diverse proteomic experiments are made available in the associated PeptideAtlas repository in several formats. Here we present a summary of our process and details about the Human, Drosophila and Yeast PeptideAtlas builds.},
language = {en},
number = {suppl 1},
urldate = {2014-12-11},
journal = {Nucl. Acids Res.},
author = {Desiere, Frank and Deutsch, Eric W. and King, Nichole L. and Nesvizhskii, Alexey I. and Mallick, Parag and Eng, Jimmy and Chen, Sharon and Eddes, James and Loevenich, Sandra N. and Aebersold, Ruedi},
month = jan,
year = {2006},
pmid = {16381952},
pages = {D655--D658}
}
@article{levinthal_how_1969,
title = {How to fold graciously},
journal = {Mossbauer Spectroscopy in Biological Systems},
author = {Levinthal, Cyrus},
year = {1969},
pages = {22}
}
@incollection{bolton_pubchem:_2008,
title = {{PubChem}: {Integrated} {Platform} of {Small} {Molecules} and {Biological} {Activities}},
volume = {4},
booktitle = {Annual {Reports} in {Computational} {Chemistry}},
author = {Bolton, E and Wang, Y and Thiessen, P A and Bryant, S H},
month = apr,
year = {2008}
}
@article{wierenga_prediction_1986,
title = {Prediction of the occurrence of the {ADP}-binding $\beta$$\alpha$$\beta$-fold in proteins, using an amino acid sequence fingerprint},
volume = {187},
issn = {0022-2836},
doi = {10.1016/0022-2836(86)90409-2},
abstract = {An amino acid sequence “fingerprint” has been derived that can be used to test if a particular sequence will fold into a$\beta$$\alpha$$\beta$-unit with ADP-binding properties. It was deduced from a careful analysis of the known three-dimensional structures of ADP-binding $\beta$$\alpha$$\beta$-folds. This fingerprint is in fact a set of 11 rules describing the type of amino acid that should occur at a specific position in a peptide fragment. The total length of this fingerprint varies between 29 and 31 residues. By checking against all possible sequences in a database, it appeared that every peptide, which exactly follows this fingerprint, does indeed fold into an ADP-binding $\beta$$\alpha$$\beta$-unit.},
number = {1},
urldate = {2017-03-06},
journal = {Journal of Molecular Biology},
author = {Wierenga, Rik K. and Terpstra, Peter and Hol, Wim G. J.},
month = jan,
year = {1986},
pages = {101--107}
}
@article{hedlund_subdivision_2010,
title = {Subdivision of the {MDR} superfamily of medium-chain dehydrogenases/reductases through iterative hidden {Markov} model refinement},
volume = {11},
issn = {1471-2105},
doi = {10.1186/1471-2105-11-534},
abstract = {BACKGROUND: The Medium-chain Dehydrogenases/Reductases (MDR) form a protein superfamily whose size and complexity defeats traditional means of subclassification; it currently has over 15000 members in the databases, the pairwise sequence identity is typically around 25\%, there are members from all kingdoms of life, the chain-lengths vary as does the oligomericity, and the members are partaking in a multitude of biological processes. There are profile hidden Markov models (HMMs) available for detecting MDR superfamily members, but none for determining which MDR family each protein belongs to. The current torrential influx of new sequence data enables elucidation of more and more protein families, and at an increasingly fine granularity. However, gathering good quality training data usually requires manual attention by experts and has therefore been the rate limiting step for expanding the number of available models.
RESULTS: We have developed an automated algorithm for HMM refinement that produces stable and reliable models for protein families. This algorithm uses relationships found in data to generate confident seed sets. Using this algorithm we have produced HMMs for 86 distinct MDR families and 34 of their subfamilies which can be used in automated annotation of new sequences. We find that MDR forms with 2 Zn2+ ions in general are dehydrogenases, while MDR forms with no Zn2+ in general are reductases. Furthermore, in Bacteria MDRs without Zn2+ are more frequent than those with Zn2+, while the opposite is true for eukaryotic MDRs, indicating that Zn2+ has been recruited into the MDR superfamily after the initial life kingdom separations. We have also developed a web site http://mdr-enzymes.org that provides textual and numeric search against various characterised MDR family properties, as well as sequence scan functions for reliable classification of novel MDR sequences.
CONCLUSIONS: Our method of refinement can be readily applied to create stable and reliable HMMs for both MDR and other protein families, and to confidently subdivide large and complex protein superfamilies. HMMs created using this algorithm correspond to evolutionary entities, making resolution of overlapping models straightforward. The implementation and support scripts for running the algorithm on computer clusters are available as open source software, and the database files underlying the web site are freely downloadable. The web site also makes our findings directly useful also for non-bioinformaticians.},
language = {eng},
journal = {BMC Bioinformatics},
author = {Hedlund, Joel and Jörnvall, Hans and Persson, Bengt},
year = {2010},
pmid = {20979641},
keywords = {Algorithms, Cluster Analysis, Computational Biology, Databases, Protein, Markov Chains, Oxidoreductases, Sequence Alignment},
pages = {534}
}
@article{simons_assembly_1997,
title = {Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and {Bayesian} scoring functions},
volume = {268},
issn = {0022-2836},
doi = {10.1006/jmbi.1997.0959},
abstract = {We explore the ability of a simple simulated annealing procedure to assemble native-like structures from fragments of unrelated protein structures with similar local sequences using Bayesian scoring functions. Environment and residue pair specific contributions to the scoring functions appear as the first two terms in a series expansion for the residue probability distributions in the protein database; the decoupling of the distance and environment dependencies of the distributions resolves the major problems with current database-derived scoring functions noted by Thomas and Dill. The simulated annealing procedure rapidly and frequently generates native-like structures for small helical proteins and better than random structures for small beta sheet containing proteins. Most of the simulated structures have native-like solvent accessibility and secondary structure patterns, and thus ensembles of these structures provide a particularly challenging set of decoys for evaluating scoring functions. We investigate the effects of multiple sequence information and different types of conformational constraints on the overall performance of the method, and the ability of a variety of recently developed scoring functions to recognize the native-like conformations in the ensembles of simulated structures.},
language = {eng},
number = {1},
journal = {J. Mol. Biol.},
author = {Simons, K. T. and Kooperberg, C. and Huang, E. and Baker, D.},
month = apr,
year = {1997},
pmid = {9149153},
keywords = {Bayes Theorem, Computer Simulation, Databases, Factual, Models, Molecular, Models, Statistical, Peptide Fragments, Protein Folding, Proteins, Protein Structure, Tertiary, Sequence Homology, Amino Acid},
pages = {209--225}
}
@article{altschul_basic_1990,
title = {Basic local alignment search tool},
volume = {215},
issn = {0022-2836},
doi = {10.1016/S0022-2836(05)80360-2},
abstract = {A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.},
language = {eng},
number = {3},
journal = {J. Mol. Biol.},
author = {Altschul, S. F. and Gish, W. and Miller, W. and Myers, E. W. and Lipman, D. J.},
month = oct,
year = {1990},
pmid = {2231712},
keywords = {Algorithms, Amino Acid Sequence, Base Sequence, Databases, Factual, Mutation, Sensitivity and Specificity, Sequence Homology, Nucleic Acid, Software},
pages = {403--410}
}
@article{staab_medium-_2008,
title = {Medium- and short-chain dehydrogenase/reductase gene and protein families : {Dual} functions of alcohol dehydrogenase 3: implications with focus on formaldehyde dehydrogenase and {S}-nitrosoglutathione reductase activities},
volume = {65},
issn = {1420-9071},
shorttitle = {Medium- and short-chain dehydrogenase/reductase gene and protein families},
doi = {10.1007/s00018-008-8592-2},
abstract = {Alcohol dehydrogenase 3 (ADH3) is highly conserved, ubiquitously expressed in mammals and involved in essential cellular pathways. A large active site pocket entails special substrate specificities: shortchain alcohols are poor substrates, while medium-chain alcohols and particularly the glutathione adducts S-hydroxymethylglutathione (HMGSH) and S-nitrosoglutathione (GSNO) are efficiently converted under concomitant use of NAD(+)/NADH. By oxidation of HMGSH, the spontaneous glutathione adduct of formaldehyde, ADH3 is implicated in the detoxification of formaldehyde. Through the GSNO reductase activity, ADH3 can affect the transnitrosation equilibrium between GSNO and S-nitrosated proteins, arguing for an important role in NO homeostasis. Recent findings suggest that ADH3-mediated GSNO reduction and subsequent product formation responds to redox states in terms of NADH availability and glutathione levels. Finally, a dual function of ADH3 is discussed in view of its potential implications for asthma.},
language = {eng},
number = {24},
journal = {Cell. Mol. Life Sci.},
author = {Staab, C. A. and Hellgren, M. and Höög, J.-O.},
month = dec,
year = {2008},
pmid = {19011746},
keywords = {Alcohol Dehydrogenase, Aldehyde Oxidoreductases, Animals, Humans, Multigene Family, Organ Specificity, Oxidation-Reduction, S-nitrosoglutathione},
pages = {3950--3960}
}
@article{carlsson_folding_2010,
title = {A folding study on {IAPP} ({Islet} {Amyloid} {Polypeptide}) using molecular dynamics simulations},
journal = {Manuscript},
author = {Carlsson, J. and Shariatpanahi, A. V. and Schultz, S. W. and Westermark, G. T. and Persson, B},
year = {2010}
}
@article{carlsson_structural_2011,
title = {A structural model of human steroid 11-beta-hydroxylase, {CYP}11B1, used to predict consequences of mutations},
journal = {Manuscript},
author = {Carlsson, J. and Wedell, A. and Persson, B.},
year = {2011}
}
@article{boratyn_domain_2012,
title = {Domain enhanced lookup time accelerated {BLAST}},
volume = {7},
issn = {1745-6150},
doi = {10.1186/1745-6150-7-12},
abstract = {BACKGROUND: BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific score matrix (PSSM) for searching the database in round i + 1. Biegert and Söding developed Context-sensitive BLAST (CS-BLAST), which combines information from searching the sequence database with information derived from a library of short protein profiles to achieve better homology detection than PSI-BLAST, which builds its PSSMs from scratch.
RESULTS: We describe a new method, called domain enhanced lookup time accelerated BLAST (DELTA-BLAST), which searches a database of pre-constructed PSSMs before searching a protein-sequence database, to yield better homology detection. For its PSSMs, DELTA-BLAST employs a subset of NCBI's Conserved Domain Database (CDD). On a test set derived from ASTRAL, with one round of searching, DELTA-BLAST achieves a ROC5000 of 0.270 vs. 0.116 for CS-BLAST. The performance advantage diminishes in iterated searches, but DELTA-BLAST continues to achieve better ROC scores than CS-BLAST.
CONCLUSIONS: DELTA-BLAST is a useful program for the detection of remote protein homologs. It is available under the "Protein BLAST" link at http://blast.ncbi.nlm.nih.gov.},
language = {eng},
journal = {Biol. Direct},
author = {Boratyn, Grzegorz M. and Schäffer, Alejandro A. and Agarwala, Richa and Altschul, Stephen F. and Lipman, David J. and Madden, Thomas L.},
month = apr,
year = {2012},
pmid = {22510480},
pmcid = {PMC3438057},
keywords = {Algorithms, Computational Biology, Databases, Protein, Internet, Protein Structure, Tertiary, Reproducibility of Results, ROC Curve, Search Engine, Sensitivity and Specificity, Sequence Alignment, Sequence Analysis, Protein, Sequence Homology, Amino Acid, Software, Time Factors},
pages = {12}
}
@article{estonius_distribution_1993,
title = {Distribution of alcohol and sorbitol dehydrogenases. {Assessment} of {mRNA} species in mammalian tissues},
volume = {215},
issn = {0014-2956},
abstract = {The tissue distribution of mRNA of alcohol dehydrogenases of classes I, II and III, and sorbitol dehydrogenase, was studied. mRNA from 19 different rat tissues was purified and analyzed by Northern blots, utilizing cDNA probes specific for the four dehydrogenases. Class-I alcohol-dehydrogenase mRNA was shown to be of widespread occurrence, detectable in all tissues including brain, but with pronounced differences in amounts. Hybridization revealed the pattern of occurrence of class-II alcohol-dehydrogenase mRNA to be unique, with transcripts only in the liver, duodenum, kidney, stomach, spleen and testis. Abundant levels of class-III alcohol-dehydrogenase (glutathione-dependent formaldehyde dehydrogenase) mRNA were present in all tissues analyzed, reflecting the general need for scavenging of formaldehyde in physiological cytoprotection. Sorbitol dehydrogenase mRNA was detected in all tissues except small intestine, in agreement with sorbitol resorbtion by passive diffusion in this tissue. In addition, evidence for a sex-specific expression, in the liver, of class-II alcohol dehydrogenase was obtained.},
language = {eng},
number = {2},
journal = {Eur. J. Biochem.},
author = {Estonius, M. and Danielsson, O. and Karlsson, C. and Persson, H. and Jörnvall, H. and Höög, J-O},
month = jul,
year = {1993},
pmid = {8344317},
keywords = {Alcohol Dehydrogenase, Amino Acid Sequence, Animals, Base Sequence, Blotting, Northern, DNA, Female, L-Iditol 2-Dehydrogenase, Male, Molecular Sequence Data, Nucleic Acid Hybridization, Rats, Rats, Sprague-Dawley, RNA, Messenger, Tissue Distribution, Transcription, Genetic},
pages = {497--503}
}
@book{steinbach_introduction_2005,
title = {Introduction to macromolecular simulation},
author = {Steinbach, Peter J},
month = aug,
year = {2005},
note = {Published: Retrieved January 23, 2010 from http://cmm.cit.nih.gov/intro\_simulation}
}
@article{moult_critical_2011,
title = {Critical assessment of methods of protein structure prediction ({CASP})—round {IX}},
volume = {79},
number = {S10},
journal = {Proteins: Structure, Function, and Bioinformatics},
author = {Moult, John and Fidelis, Krzysztof and Kryshtafovych, Andriy and Tramontano, Anna},
year = {2011},
pages = {1--207}
}
@article{nemethy_energy_1992,
title = {Energy parameters in polypeptides. 10. {Improved} geometrical parameters and nonbonded interactions for use in the {ECEPP}/3 algorithm, with application to proline-containing peptides},
volume = {96},
number = {15},
journal = {J. Phys. Chem.},
author = {Nemethy, George and Gibson, Kenneth D and Palmer, Kathleen A and Yoon, Chang No and Paterlini, Germana and Zagari, Adriana and Rumsey, Shirley and Scheraga, Harold A},
year = {1992},
pages = {6472--6484}
}
@book{baldi_bioinformatics:_1998,
address = {Cambridge},
title = {Bioinformatics: the {Machine} {Learning} {Aproach}},
publisher = {MIT Press},
author = {Baldi, Pierre and Brunak, Søren},
year = {1998}
}
@article{ncbi_resource_coordinators_database_2016,
title = {Database resources of the {National} {Center} for {Biotechnology} {Information}},
volume = {44},
issn = {0305-1048},
doi = {10.1093/nar/gkv1290},
abstract = {The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.},
number = {Database issue},
urldate = {2017-03-24},
journal = {Nucleic Acids Res},
author = {{NCBI Resource Coordinators}},
month = jan,
year = {2016},
pmid = {26615191},
pmcid = {PMC4702911},
pages = {D7--D19},
file = {PubMed Central Full Text PDF:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/NAGMB8KA/2016 - Database resources of the National Center for Biot.pdf:application/pdf}
}
@article{porte_three-dimensional_2009,
title = {Three-dimensional structure and enzymatic function of proapoptotic human p53-inducible quinone oxidoreductase {PIG}3},
volume = {284},
issn = {1083-351X},
doi = {10.1074/jbc.M109.001800},
abstract = {Tumor suppressor p53 regulates the expression of p53-induced genes (PIG) that trigger apoptosis. PIG3 or TP53I3 is the only known member of the medium chain dehydrogenase/reductase superfamily induced by p53 and is used as a proapoptotic marker. Although the participation of PIG3 in the apoptotic pathway is proven, the protein and its mechanism of action were never characterized. We analyzed human PIG3 enzymatic function and found NADPH-dependent reductase activity with ortho-quinones, which is consistent with the classification of PIG3 in the quinone oxidoreductase family. However, the activity is much lower than that of zeta-crystallin, a better known quinone oxidoreductase. In addition, we report the crystallographic structure of PIG3, which allowed the identification of substrate- and cofactor-binding sites, with residues fully conserved from bacteria to human. Tyr-59 in zeta-crystallin (Tyr-51 in PIG3) was suggested to participate in the catalysis of quinone reduction. However, kinetics of Tyr/Phe and Tyr/Ala mutants of both enzymes demonstrated that the active site Tyr is not catalytic but may participate in substrate binding, consistent with a mechanism based on propinquity effects. It has been proposed that PIG3 contribution to apoptosis would be through oxidative stress generation. We found that in vitro activity and in vivo overexpression of PIG3 accumulate reactive oxygen species. Accordingly, an inactive PIG3 mutant (S151V) did not produce reactive oxygen species in cells, indicating that enzymatically active protein is necessary for this function. This supports that PIG3 action is through oxidative stress produced by its enzymatic activity and provides essential knowledge for eventual control of apoptosis.},
language = {eng},
number = {25},
journal = {J. Biol. Chem.},
author = {Porté, Sergio and Valencia, Eva and Yakovtseva, Evgenia A. and Borràs, Emma and Shafqat, Naeem and Debreczeny, Judit E. and Pike, Ashley C. W. and Oppermann, Udo and Farrés, Jaume and Fita, Ignacio and Parés, Xavier},
month = jun,
year = {2009},
pmid = {19349281},
pmcid = {PMC2719357},
keywords = {Amino Acid Sequence, apoptosis, Binding Sites, Catalytic Domain, Crystallography, X-Ray, Humans, Intracellular Signaling Peptides and Proteins, In Vitro Techniques, Kinetics, Models, Molecular, Molecular Sequence Data, Mutagenesis, Site-Directed, NADP, Phylogeny, Protein Structure, Quaternary, Proto-Oncogene Proteins, reactive oxygen species, Recombinant Proteins, Sequence Homology, Amino Acid, Tumor Suppressor Protein p53, Tyrosine},
pages = {17194--17205}
}
@misc{noauthor_research_nodate,
title = {The {Research} {Collaboratory} for {Structural} {Bioinformatics} {PDB}},
url = {http://www.rcsb.org/pdb/}
}
@article{yang_paml_2007,
title = {{PAML} 4: phylogenetic analysis by maximum likelihood},
volume = {24},
issn = {0737-4038},
shorttitle = {{PAML} 4},
doi = {10.1093/molbev/msm088},
abstract = {PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).},
language = {eng},
number = {8},
journal = {Mol. Biol. Evol.},
author = {Yang, Ziheng},
month = aug,
year = {2007},
pmid = {17483113},
keywords = {Animals, Computer Simulation, Genetic Variation, Likelihood Functions, Models, Genetic, Phylogeny, Selection, Genetic, Software, Species Specificity},
pages = {1586--1591}
}
@article{ohta_synonymous_1995,
title = {Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory},
volume = {40},
issn = {0022-2844},
abstract = {The nearly neutral theory of molecular evolution predicts larger generation-time effects for synonymous than for nonsynonymous substitutions. This prediction is tested using the sequences of 49 single-copy genes by calculating the average and variance of synonymous and nonsynonymous substitutions in mammalian star phylogenies (rodentia, artiodactyla, and primates). The average pattern of the 49 genes supports the prediction of the nearly neutral theory, with some notable exceptions. The nearly neutral theory also predicts that the variance of the evolutionary rate is larger than the value predicted by the completely neutral theory. This prediction is tested by examining the dispersion index (ratio of the variance to the mean), which is positively correlated with the average substitution number. After weighting by the lineage effects, this correlation almost disappears for nonsynonymous substitutions, but not quite so for synonymous substitutions. After weighting, the dispersion indices of both synonymous and nonsynonymous substitutions still exceed values expected under the simple Poisson process. The results indicate that both the systematic bias in evolutionary rate among the lineages and the episodic type of rate variation are contributing to the large variance. The former is more significant to synonymous substitutions than to nonsynonymous substitutions. Isochore evolution may be similar to synonymous substitutions. The rate and pattern found here are consistent with the nearly neutral theory, such that the relative contributions of drift and selection differ between the two types of substitutions. The results are also consistent with Gillespie's episodic selection theory.},
language = {eng},
number = {1},
journal = {J. Mol. Evol.},
author = {Ohta, T.},
month = jan,
year = {1995},
pmid = {7714912},
keywords = {Animals, Biological Evolution, Mammals, Models, Theoretical},
pages = {56--63}
}
@article{abagyan_icm_1994,
title = {{ICM} — a new method for protein modeling and design. {Applications} to docking and structure prediction from the distorted native conformation},
volume = {15},
journal = {J. Comput. Chem.},
author = {Abagyan, R. and Totrov, M. and Kuznetsov, D.N.},
year = {1994},
pages = {488--506}
}
@article{nordling_medium-chain_2002,
title = {Medium-chain dehydrogenases/reductases ({MDR}). {Family} characterizations including genome comparisons and active site modeling},
volume = {269},
issn = {0014-2956},
abstract = {Completed eukaryotic genomes were screened for medium-chain dehydrogenases/reductases (MDR). In the human genome, 23 MDR forms were found, a number that probably will increase, because the genome is not yet fully interpreted. Partial sequences already indicate that at least three further members exist. Within the MDR superfamily, at least eight families were distinguished. Three families are formed by dimeric alcohol dehydrogenases (ADH; originally detected in animals/plants), cinnamyl alcohol dehydrogenases (originally detected in plants) and tetrameric alcohol dehydrogenases (originally detected in yeast). Three further families are centred around forms initially detected as mitochondrial respiratory function proteins, acetyl-CoA reductases of fatty acid synthases, and leukotriene B4 dehydrogenases. The two remaining families with polyol dehydrogenases (originally detected as sorbitol dehydrogenase) and quinone reductases (originally detected as zeta-crystallin) are also distinct but with variable sequences. The most abundant families in the human genome are the dimeric ADH forms and the quinone oxidoreductases. The eukaryotic patterns are different from those of Escherichia coli. The different families were further evaluated by molecular modelling of their active sites as to geometry, hydrophobicity and volume of substrate-binding pockets. Finally, sequence patterns were derived that are diagnostic for the different families and can be used in genome annotations.},
language = {eng},
number = {17},
journal = {Eur J Biochem},
author = {Nordling, Erik and Jörnvall, Hans and Persson, Bengt},
month = sep,
year = {2002},
pmid = {12199705},
keywords = {Amino Acid Motifs, Binding Sites, Crystallins, Evolution, Molecular, Genome, Human, Humans, Models, Molecular, Oxidoreductases, Phylogeny, Quinone Reductases},
pages = {4267--4276}
}
@article{jain_infrastructure_2009,
title = {Infrastructure for the life sciences: design and implementation of the {UniProt} website},
volume = {10},
journal = {BMC Bioinformatics},
author = {Jain, E and Bairoch, A and Duvaud, S and Phan, I and Redaschi, N and Suzek, B E and Martin, M J and McGarvey, P and Gasteiger, E},
year = {2009},
pages = {136}
}
@article{cardozo_homology_1995,
title = {Homology modeling by the {ICM} method},
volume = {23},
issn = {0887-3585},
doi = {10.1002/prot.340230314},
abstract = {Five models have been built by the ICM method for the Comparative Modeling section of the Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. The targets have homologous proteins with known three-dimensional structure with sequence identity ranging from 25 to 77\%. After alignment of the target sequence with the related three-dimensional structure, the modeling procedure consists of two subproblems: side-chain prediction and loop prediction. The ICM method approaches these problems with the following steps: (1) a starting model is created based on the homologous structure with the conserved portion fixed and the nonconserved portion having standard covalent geometry and free torsion angles; (2) the Biased Probability Monte Carlo (BPMC) procedure is applied to search the subspaces of either all the nonconservative side-chain torsion angles or torsion angles in a loop backbone and surrounding side chains. A special algorithm was designed to generate low-energy loop deformations. The BPMC procedure globally optimizes the energy function consisting of ECEPP/3 and solvation energy terms. Comparison of the predictions with the NMR or crystallographic solutions reveals a high proportion of correctly predicted side chains. The loops were not correctly predicted because imprinted distortions of the backbone increased the energy of the near-native conformation and thus made the solution unrecognizable. Interestingly, the energy terms were found to be reliable and the sampling of conformational space sufficient. The implications of this finding for the strategies of future comparative modeling are discussed.},
language = {eng},
number = {3},
journal = {Proteins},
author = {Cardozo, T. and Totrov, M. and Abagyan, R.},
month = nov,
year = {1995},
pmid = {8710833},
keywords = {Antibodies, Anti-Idiotypic, Bacterial Proteins, Computer Graphics, Computer Simulation, Cytochrome P-450 Enzyme System, Databases, Factual, Helix-Turn-Helix Motifs, Mixed Function Oxygenases, Models, Molecular, Monte Carlo Method, Muramidase, Nucleoside-Diphosphate Kinase, Phosphoenolpyruvate Sugar Phosphotransferase System, Protein Conformation, Proteins, Protein Structure, Secondary, Protein Structure, Tertiary, Receptors, Retinoic Acid, Sequence Alignment, Sequence Homology, Amino Acid},
pages = {403--414}
}
@article{eklund_structural_1976,
title = {Structural comparisons of mammalian, yeast and bacillar alcohol dehydrogenases},
volume = {102},
issn = {0022-2836},
language = {eng},
number = {1},
journal = {J. Mol. Biol.},
author = {Eklund, H. and Brändén, C. I. and Jörnvall, H.},
month = mar,
year = {1976},
pmid = {775100},
keywords = {Alcohol Oxidoreductases, Amino Acids, Amino Acid Sequence, Binding Sites, Biological Evolution, Geobacillus stearothermophilus, Liver, Models, Molecular, Protein Binding, Protein Conformation, Saccharomyces cerevisiae, Species Specificity},
pages = {61--73}
}
@article{pronk_gromacs_2013,
title = {{GROMACS} 4.5: {A} high-throughput and highly parallel open source molecular simulation toolkit},
volume = {29},
issn = {1367-4811},
shorttitle = {{GROMACS} 4.5},
doi = {10.1093/bioinformatics/btt055},
abstract = {MOTIVATION: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources.
RESULTS: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.
AVAILABILITY: GROMACS is an open source and free software available from http://www.gromacs.org.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
language = {eng},
number = {7},
journal = {Bioinformatics},
author = {Pronk, Sander and Páll, Szilárd and Schulz, Roland and Larsson, Per and Bjelkmar, Pär and Apostolov, Rossen and Shirts, Michael R and Smith, Jeremy C and Kasson, Peter M and van der Spoel, David and Hess, Berk and Lindahl, Erik},
month = apr,
year = {2013},
pmid = {23407358},
pages = {845--854}
}
@article{jornvall_short-chain_1995,
title = {Short-chain dehydrogenases/reductases ({SDR})},
volume = {34},
issn = {0006-2960},
abstract = {Short-chain dehydrogenases/reductases (SDR) constitute a large protein family. Presently, at least 57 characterized, highly different enzymes belong to this family and typically exhibit residue identities only at the 15-30\% level, indicating early duplicatory origins and extensive divergence. In addition, another family of 22 enzymes with extended protein chains exhibits part-chain SDR relationships and represents enzymes of no less than three EC classes. Furthermore, subforms and species variants are known of both families. In the combined SDR superfamily, only one residue is strictly conserved and ascribed a crucial enzymatic function (Tyr 151 in the numbering system of human NAD(+)-linked prostaglandin dehydrogenase). Such a function for this Tyr residue in SDR enzymes in general is supported also by chemical modifications, site-directed mutagenesis, and an active site position in those tertiary structures that have been characterized. A lysine residue four residues downstream is also largely conserved. A model for catalysis is available on the basis of these two residues. Binding of the coenzyme, NAD(H) or NADP(H), is in the N-terminal part of the molecules, where a common GlyXXXGlyXGly pattern occurs. Two SDR enzymes established by X-ray crystallography show a one-domain subunit with seven to eight beta-strands. Conformational patterns are highly similar, except for variations in the C-terminal parts. Additional structures occur in the family with extended chains. Some of the SDR molecules are known under more than one name, and one of the enzymes has been shown to be susceptible to native, chemical modification, producing reduced Schiff base adducts with pyruvate and other metabolic keto derivatives. Most SDR enzymes are dimers and tetramers. In those analyzed, the area of major subunit contacts involves two long alpha-helices (alpha E, alpha F) in similar and apparently strong subunit interactions. Future possibilities include verification of the proposed reaction mechanism and tracing of additional relationships, perhaps also with other protein families. Short-chain dehydrogenases illustrate the value of comparisons and diversified research in generating unexpected discoveries.},
language = {eng},
number = {18},
journal = {Biochemistry},
author = {Jörnvall, H. and Persson, B. and Krook, M. and Atrian, S. and Gonzàlez-Duarte, R. and Jeffery, J. and Ghosh, D.},
month = may,
year = {1995},
pmid = {7742302},
keywords = {Amino Acid Sequence, Animals, Models, Molecular, Molecular Sequence Data, Mutagenesis, Site-Directed, Oxidoreductases, Phylogeny, Protein Conformation, Sequence Alignment},
pages = {6003--6013}
}
@article{bussi_canonical_2007,
title = {Canonical sampling through velocity rescaling},
volume = {126},
journal = {J. Chem. Phys.},
author = {Bussi, G and Donadio, D and Parrinello, M},
year = {2007},
pages = {014101}
}
@article{leaver-fay_rosetta3:_2011,
title = {{ROSETTA}3: an object-oriented software suite for the simulation and design of macromolecules},
volume = {487},
journal = {Methods Enzymol},
author = {Leaver-Fay, A. and Tyka, M. and Lewis, S.M. and Lange, O.F. and Thompson, J. and Jacak, R. and Kaufman, K. and Renfrew, P.D. and Smith, C.A. and Sheffler, W. and others},
year = {2011},
pages = {545--574}
}
@misc{noauthor_adh6_nodate,
type = {Database},
title = {{ADH}6 in {PeptideAtlas}},
urldate = {2014-11-06},
journal = {PeptideAtlas}
}
@article{kim_pubchem_2016,
title = {{PubChem} {Substance} and {Compound} databases},
volume = {44},
issn = {0305-1048},
doi = {10.1093/nar/gkv951},
abstract = {PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the US National Institutes of Health (NIH). For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database. This paper provides an overview of the PubChem Substance and Compound databases, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. It also gives a brief description of PubChem3D, a resource derived from theoretical three-dimensional structures of compounds in PubChem, as well as PubChemRDF, Resource Description Framework (RDF)-formatted PubChem data for data sharing, analysis and integration with information contained in other databases.},
number = {Database issue},
urldate = {2017-03-30},
journal = {Nucleic Acids Res},
author = {Kim, Sunghwan and Thiessen, Paul A. and Bolton, Evan E. and Chen, Jie and Fu, Gang and Gindulyte, Asta and Han, Lianyi and He, Jane and He, Siqian and Shoemaker, Benjamin A. and Wang, Jiyao and Yu, Bo and Zhang, Jian and Bryant, Stephen H.},
month = jan,
year = {2016},
pmid = {26400175},
pmcid = {PMC4702940},
pages = {D1202--D1213},
file = {PubMed Central Full Text PDF:/home/talavis/.zotero/zotero/etop8sp2.default/zotero/storage/ZZ296VBF/Kim et al. - 2016 - PubChem Substance and Compound databases.pdf:application/pdf}
}
@article{carlsson_investigation_2009,