Discuss Newer Restraint Schemes for ABFE

paper/alchemical.bib

@@ -141,6 +141,35 @@ @incollection{aldeghi2019accurate
   publisher = {{Springer}}
 }
 
+@article{alibay2022evaluating,
+  title = {Evaluating the Use of Absolute Binding Free Energy in the Fragment Optimisation Process},
+  author = {Alibay, Irfan and Magarkar, Aniket and Seeliger, Daniel and Biggin, Philip Charles},
+  year = {2022},
+  month = sep,
+  journal = {Commun. Chem.},
+  volume = {5},
+  number = {1},
+  pages = {105},
+  issn = {2399-3669},
+  doi = {10.1038/s42004-022-00721-4},
+  urldate = {2022-11-29},
+  abstract = {Abstract                            Key to the fragment optimisation process within drug design is the need to accurately capture the changes in affinity that are associated with a given set of chemical modifications. Due to the weakly binding nature of fragments, this has proven to be a challenging task, despite recent advancements in leveraging experimental and computational methods. In this work, we evaluate the use of Absolute Binding Free Energy (ABFE) calculations in guiding fragment optimisation decisions, retrospectively calculating binding free energies for 59 ligands across 4 fragment elaboration campaigns. We first demonstrate that ABFEs can be used to accurately rank fragment-sized binders with an overall Spearman's r of 0.89 and a Kendall {$\tau$} of 0.67, although often deviating from experiment in absolute free energy values with an RMSE of 2.75\,kcal/mol. We then also show that in several cases, retrospective fragment optimisation decisions can be supported by the ABFE calculations. Comparing against cheaper endpoint methods, namely N               wat               -MM/GBSA, we find that ABFEs offer better ranking power and correlation metrics. Our results indicate that ABFE calculations can usefully guide fragment elaborations to maximise affinity.},
+  langid = {english}
+}
+
+@misc{alibay2021mdrestraintsgenerator,
+  title = {{{IAlibay}}/{{MDRestraintsGenerator}}: 0.1.0},
+  shorttitle = {{{IAlibay}}/{{MDRestraintsGenerator}}},
+  author = {Alibay, Irfan},
+  year = {2021},
+  month = mar,
+  doi = {10.5281/zenodo.4570556},
+  urldate = {2022-04-19},
+  abstract = {First initial release of the MDRestraintsGenerator code. This release will be the first zenodo entry for this repository. Note: this code is not feature complete and non-API stable.},
+  copyright = {Open Access},
+  howpublished = {Zenodo}
+}
+
 @misc{amber,
   title = {Amber {{Tutorials}}},
   file = {/Users/toni_brain/Zotero/storage/L65CLMNU/tutorials.html},
@@ -227,6 +256,21 @@ @article{basavapathruni2012conformational
   number = {6}
 }
 
+@article{baumann2023broadening,
+  title = {Broadening the {{Scope}} of {{Binding Free Energy Calculations Using}} a {{Separated Topologies Approach}}},
+  author = {Baumann, Hannah M. and Dybeck, Eric and McClendon, Christopher L. and Pickard, Frank C. and Gapsys, Vytautas and {P{\'e}rez-Benito}, Laura and Hahn, David F. and Tresadern, Gary and Mathiowetz, Alan M. and Mobley, David L.},
+  year = {2023},
+  month = aug,
+  journal = {J. Chem. Theory Comput.},
+  volume = {19},
+  number = {15},
+  pages = {5058--5076},
+  issn = {1549-9618, 1549-9626},
+  doi = {10.1021/acs.jctc.3c00282},
+  urldate = {2023-11-01},
+  langid = {english}
+}
+
 @article{beierlein2011simple,
   title = {A {{Simple QM}}/{{MM Approach}} for {{Capturing Polarization Effects}} in {{Protein}}-{{Ligand Binding Free Energy Calculations}}},
   author = {Beierlein, Frank R. and Michel, Julien and Essex, Jonathan W.},
@@ -572,6 +616,22 @@ @article{chen2018accurate
   number = {12}
 }
 
+@article{chen2023enhancing,
+  title = {Enhancing {{Hit Discovery}} in {{Virtual Screening}} through {{Absolute Protein}}--{{Ligand Binding Free-Energy Calculations}}},
+  author = {Chen, Wei and Cui, Di and Jerome, Steven V. and Michino, Mayako and Lenselink, Eelke B. and Huggins, David J. and Beautrait, Alexandre and Vendome, Jeremie and Abel, Robert and Friesner, Richard A. and Wang, Lingle},
+  year = {2023},
+  month = may,
+  journal = {J. Chem. Inf. Model.},
+  volume = {63},
+  number = {10},
+  pages = {3171--3185},
+  issn = {1549-9596, 1549-960X},
+  doi = {10.1021/acs.jcim.3c00013},
+  urldate = {2024-03-15},
+  langid = {english}
+}
+
+
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   title = {Replica Exchange and Expanded Ensemble Simulations as {{Gibbs}} Sampling: {{Simple}} Improvements for Enhanced Mixing},
   shorttitle = {Replica Exchange and Expanded Ensemble Simulations as {{Gibbs}} Sampling},
@@ -927,6 +987,22 @@ @article{eastman2017openmm
   number = {7}
 }
 
+@article{ebrahimi2022symmetry,
+  title = {Symmetry-{{Adapted Restraints}} for {{Binding Free Energy Calculations}}},
+  author = {Ebrahimi, Mina and H{\'e}nin, J{\'e}r{\^o}me},
+  year = {2022},
+  month = apr,
+  journal = {J. Chem. Theory Comput.},
+  volume = {18},
+  number = {4},
+  pages = {2494--2502},
+  issn = {1549-9618, 1549-9626},
+  doi = {10.1021/acs.jctc.1c01235},
+  urldate = {2022-06-21},
+  langid = {english}
+}
+
+
 @misc{efficient,
   title = {Efficient {{Round}}-{{Trip Time Optimization}} for {{Replica}}-{{Exchange Enveloping Distribution Sampling}} ({{RE}}-{{EDS}}) | {{Journal}} of {{Chemical Theory}} and {{Computation}}},
   file = {/Users/toni_brain/Zotero/storage/ID5AI2XX/acs.jctc.html},
@@ -1022,6 +1098,52 @@ @article{friesner2004glide
   number = {7}
 }
 
+@article{fu2017new,
+  title = {New {{Coarse Variables}} for the {{Accurate Determination}} of {{Standard Binding Free Energies}}},
+  author = {Fu, Haohao and Cai, Wensheng and H{\'e}nin, J{\'e}r{\^o}me and Roux, Beno{\^i}t and Chipot, Christophe},
+  year = {2017},
+  journal = {J. Chem. Theory Comput.},
+  volume = {13},
+  number = {11},
+  pages = {5173--5178},
+  issn = {1549-9618, 1549-9626},
+  doi = {10.1021/acs.jctc.7b00791},
+  urldate = {2022-06-21},
+  langid = {english}
+}
+
+@article{fu2021bfee2,
+  title = {{{BFEE2}}: {{Automated}}, {{Streamlined}}, and {{Accurate Absolute Binding Free-Energy Calculations}}},
+  shorttitle = {{{BFEE2}}},
+  author = {Fu, Haohao and Chen, Haochuan and Cai, Wensheng and Shao, Xueguang and Chipot, Christophe},
+  year = {2021},
+  month = may,
+  journal = {J. Chem. Inf. Model.},
+  volume = {61},
+  number = {5},
+  pages = {2116--2123},
+  issn = {1549-9596, 1549-960X},
+  doi = {10.1021/acs.jcim.1c00269},
+  urldate = {2022-06-23},
+  langid = {english}
+}
+
+@article{fu2022accurate,
+  title = {Accurate Determination of Protein:Ligand Standard Binding Free Energies from Molecular Dynamics Simulations},
+  shorttitle = {Accurate Determination of Protein},
+  author = {Fu, Haohao and Chen, Haochuan and Blazhynska, Marharyta and {Goulard Coderc de Lacam}, Emma and Szczepaniak, Florence and Pavlova, Anna and Shao, Xueguang and Gumbart, James C. and Dehez, Fran{\c c}ois and Roux, Beno{\^i}t and Cai, Wensheng and Chipot, Christophe},
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+  month = apr,
+  journal = {Nat. Protoc.},
+  volume = {17},
+  number = {4},
+  pages = {1114--1141},
+  issn = {1754-2189, 1750-2799},
+  doi = {10.1038/s41596-021-00676-1},
+  urldate = {2022-06-21},
+  langid = {english}
+}
+
 @article{fujitani2005direct,
   title = {Direct Calculation of the Binding Free Energies of {{FKBP}} Ligands},
   author = {Fujitani, Hideaki and Tanida, Yoshiaki and Ito, Masakatsu and Jayachandran, Guha and Snow, Christopher D. and Shirts, Michael R. and Sorin, Eric J. and Pande, Vijay S.},
@@ -1384,6 +1506,24 @@ @article{hedges2019biosimspace
   number = {43}
 }
 
+@article{hedges2023suite,
+  title = {A {{Suite}} of {{Tutorials}} for the {{BioSimSpace Framework}} for {{Interoperable Biomolecular Simulation}} [{{Article}} v1.0]},
+  author = {Hedges, Lester O. and Bariami, Sofia and Burman, Matthew and Clark, Finlay and Cossins, Benjamin P. and Hardie, Adele and Herz, Anna M. and Lukauskis, Dominykas and Mey, Antonia S. J. S. and Michel, Julien and Scheen, Jenke and Suruzhon, Miroslav and Woods, Christopher J. and Wu, Zhiyi},
+  year = {2023},
+  month = dec,
+  journal = {LiveCOMS},
+  volume = {5},
+  number = {1},
+  pages = {2375--2375},
+  issn = {2575-6524},
+  doi = {10.33011/livecoms.5.1.2375},
+  urldate = {2024-03-12},
+  abstract = {This tutorial serves as a getting-started guide for BioSimSpace (BSS), an interoperable molecular simulation framework, that allows simulations with different sets of molecular dynamics software packages. This tutorial will cover four main use cases for BioSimSpace. The introductory tutorial introduces the basic structure of BioSimSpace, how to use the API to access functionality, and how to write code for setting up and running standard molecular dynamics simulations. Three advanced use cases of BSS are then provided, describing how to set up and run a funnel metady- namics simulation, steered molecular dynamics, and relative or absolute alchemical binding free energy calculations.},
+  copyright = {Copyright (c) 2023 Lester O. Hedges, Sofia Bariami, Matthew Burman, Finlay Clark, Benjamin P. Cossins, Adele Hardie, Anna M. Herz, Dominykas Lukauskis, Antonia S. J. S.  Mey, Julien Michel, Jenke Scheen, Miroslav Suruzhon, Christopher J. Woods, Zhiyi Wu},
+  langid = {english},
+  keywords = {alchemical free energy}
+}
+
 @article{heinzelmann2017attachpullrelease,
   title = {Attach-{{Pull}}-{{Release Calculations}} of {{Ligand Binding}} and {{Conformational Changes}} on the {{First BRD4 Bromodomain}}},
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@@ -3302,6 +3442,20 @@ @article{rustenburg2016measuring
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 }
 
+@article{salari2018streamlined,
+  title = {A {{Streamlined}}, {{General Approach}} for {{Computing Ligand Binding Free Energies}} and {{Its Application}} to {{GPCR-Bound Cholesterol}}},
+  author = {Salari, Reza and Joseph, Thomas and Lohia, Ruchi and H{\'e}nin, J{\'e}r{\^o}me and Brannigan, Grace},
+  year = {2018},
+  month = dec,
+  volume = {14},
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+  issn = {1549-9618, 1549-9626},
+  doi = {10.1021/acs.jctc.8b00447},
+  journal = {J. Chem. Theory Comput.},
+  language = {en},
+  number = {12},
+}
+
 @article{salomon-ferrer2013overview,
   title = {An Overview of the {{Amber}} Biomolecular Simulation Package},
   author = {Salomon-Ferrer, Romelia and Case, David A. and Walker, Ross C.},
@@ -3335,6 +3489,24 @@ @article{salomon-ferrer2013routine
   number = {9}
 }
 
+@article{santiago-mcrae2023computing,
+  title = {Computing {{Absolute Binding Affinities}} by {{Streamlined Alchemical Free Energy Perturbation}} ({{SAFEP}}) [{{Article}} v1.0]},
+  author = {{Santiago-McRae}, Ezry and Ebrahimi, Mina and Sandberg, Jesse W. and Brannigan, Grace and H{\'e}nin, J{\'e}r{\^o}me},
+  year = {2023},
+  month = oct,
+  journal = {LiveCoMS},
+  volume = {5},
+  number = {1},
+  pages = {2067--2067},
+  issn = {2575-6524},
+  doi = {10.33011/livecoms.5.1.2067},
+  urldate = {2024-07-12},
+  abstract = {Free Energy Perturbation (FEP) is a powerful but challenging computational technique for estimating differences in free energy between two or more states. This document is intended both as a tutorial and as an adaptable protocol for computing free energies of binding using free energy perturbations in NAMD. We present the Streamlined Alchemical Free Energy Perturbation (SAFEP) framework. SAFEP shifts the computational frame of reference from the ligand to the binding site itself. This both simplifies the thermodynamic cycle and makes the approach more broadly applicable to superficial sites and other less common geometries. As a practical example, we give instructions for calculating the absolute binding free energy of phenol to lysozyme. We assume familiarity with standard procedures for setting up, running, and analyzing molecular dynamics simulations using NAMD and VMD. While simulation times will vary, the human tasks should take no more than 3 to 4 hours for a reader without previous training in free energy calculations or ex- perience with the VMD Colvars Dashboard. Sample data are provided for all key calculations both for comparison and readers' convenience.},
+  copyright = {Copyright (c) 2023 Ezry Santiago-McRae, Mina Ebrahimi, Jesse W. Sandberg, Grace Brannigan, J{\'e}r{\^o}me H{\'e}nin},
+  langid = {english},
+  keywords = {alchemy}
+}
+
 @article{sasmal2020sampling,
   title = {Sampling {{Conformational Changes}} of {{Bound Ligands Using Nonequilibrium Candidate Monte Carlo}} and {{Molecular Dynamics}}},
   author = {Sasmal, Sukanya and Gill, Samuel C. and Lim, Nathan M. and Mobley, David L.},

paper/manuscript.tex

@@ -769,7 +769,9 @@ \subsubsection{Absolute free energy calculations must handle the standard state
 
 Many choices of restraints involve selecting reference atoms.
 Again, in principle this choice is unimportant given adequate simulation time but practical considerations may be important.
-The choice is likely especially important with Boresch-style restraints, where some relative placements of reference atoms are likely to be numerically unstable; additionally, ligand reference atoms should likely be in a part of the molecule which defines the binding orientation well, rather than in a floppy solvent-exposed tail, for example.
+The choice is likely especially important with Boresch-style restraints, where some relative placements of reference atoms are likely to be numerically unstable; additionally, ligand reference atoms should likely be in a part of the molecule which defines the binding orientation well, rather than in a floppy solvent-exposed tail, for example. Several automated methods have been proposed to select anchor points for Boresch restraints, which typically involve analysing a simulation of the fully-interacting receptor-ligand complex~\cite{alibay2022evaluating, alibay2021mdrestraintsgenerator, baumann2023broadening, chen2023enhancing, hedges2023suite}.
+
+More recently, restrictive restraint schemes have been proposed that avoid relying on a few critical reference atoms. Instead, these aim to simplify restraint selection by using larger sets of atomic positions in the receptor and ligand. Fu et al. suggested restraining the six relative rigid-body degrees of freedom derived by finding the rotation of the ligand which minimises RMSD to a reference structure of the receptor-ligand complex (after accounting for rotation and translation of the receptor)~\cite{fu2017new}. Salari et al. proposed restraining the ``distance-from-bound-configuration'' (DBC) variable, which is the RMSD of ligand coordinates in the frame of reference of the binding site~\cite{salari2018streamlined, ebrahimi2022symmetry}. This may allow the binding pose to be closely preserved as the ligand intermolecular interactions are removed, but has the disadvantage of coupling the internal and relative external degrees of freedom of the receptor and ligand, preventing easy computation of the standard state correction. This necessitates an additional step where the DBC restraints are released to a single harmonic restraint. Both restraint schemes are implemented in open-source workflows~\cite{fu2021bfee2, fu2022accurate, santiago-mcrae2023computing}.
 
 \subsection{Absolute and relative calculations deal with some of the same issues}
 \subsubsection{Handling weak binders and high dissociation rates}\label{sec:weak-binders}