From 0d56d27581d841c266b6014ace0e7f573a8be9f9 Mon Sep 17 00:00:00 2001 From: Goran Giudetti Date: Sat, 16 Dec 2023 02:14:35 +0100 Subject: [PATCH] Uploaded models discussed in paper The yml files refer to models of 3CLpro in complex with different inhibitors. These are all described in this article: https://doi.org/10.1021/jacs.3c02229 and in the related SI --- data/models/ Carmofur_REAC.yml | 11 +++++++++++ data/models/Carmofur_IP.yml | 11 +++++++++++ data/models/Carmofur_PROD.yml | 11 +++++++++++ data/models/Nirmatrelvir_IP.yml | 11 +++++++++++ data/models/Nirmatrelvir_PROD.yml | 11 +++++++++++ data/models/Nirmatrelvir_REAC.yml | 11 +++++++++++ data/models/X77A_IP.yml | 11 +++++++++++ data/models/X77A_PROD.yml | 11 +++++++++++ data/models/X77A_REAC.yml | 11 +++++++++++ data/models/X77A_TI.yml | 11 +++++++++++ data/models/X77C_IP.yml | 11 +++++++++++ data/models/X77C_MC.yml | 11 +++++++++++ data/models/X77C_PROD.yml | 11 +++++++++++ data/models/X77C_REAC.yml | 11 +++++++++++ 14 files changed, 154 insertions(+) create mode 100644 data/models/ Carmofur_REAC.yml create mode 100644 data/models/Carmofur_IP.yml create mode 100644 data/models/Carmofur_PROD.yml create mode 100644 data/models/Nirmatrelvir_IP.yml create mode 100644 data/models/Nirmatrelvir_PROD.yml create mode 100644 data/models/Nirmatrelvir_REAC.yml create mode 100644 data/models/X77A_IP.yml create mode 100644 data/models/X77A_PROD.yml create mode 100644 data/models/X77A_REAC.yml create mode 100644 data/models/X77A_TI.yml create mode 100644 data/models/X77C_IP.yml create mode 100644 data/models/X77C_MC.yml create mode 100644 data/models/X77C_PROD.yml create mode 100644 data/models/X77C_REAC.yml diff --git a/data/models/ Carmofur_REAC.yml b/data/models/ Carmofur_REAC.yml new file mode 100644 index 0000000..ff85d88 --- /dev/null +++ b/data/models/ Carmofur_REAC.yml @@ -0,0 +1,11 @@ +name: Carmofur_REAC.pdb +description: Carmofur - Main Protease complex structure (REAC) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/Carmofur_REAC.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/Carmofur_IP.yml b/data/models/Carmofur_IP.yml new file mode 100644 index 0000000..ab64e04 --- /dev/null +++ b/data/models/Carmofur_IP.yml @@ -0,0 +1,11 @@ +name: Carmofur_IP.pdb +description: Carmofur - Main Protease complex structure (IP) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/Carmofur_IP.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/Carmofur_PROD.yml b/data/models/Carmofur_PROD.yml new file mode 100644 index 0000000..b918f24 --- /dev/null +++ b/data/models/Carmofur_PROD.yml @@ -0,0 +1,11 @@ +name: Carmofur_PROD.pdb +description: Carmofur - Main Protease complex structure (PROD) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/Carmofur_PROD.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/Nirmatrelvir_IP.yml b/data/models/Nirmatrelvir_IP.yml new file mode 100644 index 0000000..b1be336 --- /dev/null +++ b/data/models/Nirmatrelvir_IP.yml @@ -0,0 +1,11 @@ +name: Nirmatrelvir_IP.pdb +description: Nirmatrelvir - Main Protease complex structure (IP) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/Nirmatrelvir_IP.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/Nirmatrelvir_PROD.yml b/data/models/Nirmatrelvir_PROD.yml new file mode 100644 index 0000000..383c562 --- /dev/null +++ b/data/models/Nirmatrelvir_PROD.yml @@ -0,0 +1,11 @@ +name: Nirmatrelvir_PROD.pdb +description: Nirmatrelvir - Main Protease complex structure (PROD) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/Nirmatrelvir_PROD.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/Nirmatrelvir_REAC.yml b/data/models/Nirmatrelvir_REAC.yml new file mode 100644 index 0000000..420cc34 --- /dev/null +++ b/data/models/Nirmatrelvir_REAC.yml @@ -0,0 +1,11 @@ +name: Nirmatrelvir_REAC.pdb +description: Nirmatrelvir - Main Protease complex structure (REAC) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/Nirmatrelvir_REAC.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/X77A_IP.yml b/data/models/X77A_IP.yml new file mode 100644 index 0000000..917d89c --- /dev/null +++ b/data/models/X77A_IP.yml @@ -0,0 +1,11 @@ +name: X77A_IP.pdb +description: X77A - Main Protease complex structure (IP) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/X77A_IP.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/X77A_PROD.yml b/data/models/X77A_PROD.yml new file mode 100644 index 0000000..518527d --- /dev/null +++ b/data/models/X77A_PROD.yml @@ -0,0 +1,11 @@ +name: X77A_PROD.pdb +description: X77A - Main Protease complex structure (PROD) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/X77A_PROD.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/X77A_REAC.yml b/data/models/X77A_REAC.yml new file mode 100644 index 0000000..0c1c835 --- /dev/null +++ b/data/models/X77A_REAC.yml @@ -0,0 +1,11 @@ +name: X77A_REAC.pdb +description: X77A - Main Protease complex structure (REAC) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/X77A_REAC.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/X77A_TI.yml b/data/models/X77A_TI.yml new file mode 100644 index 0000000..10e03cb --- /dev/null +++ b/data/models/X77A_TI.yml @@ -0,0 +1,11 @@ +name: X77A_TI.pdb +description: X77A - Main Protease complex structure (TI) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/X77A_TI.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/X77C_IP.yml b/data/models/X77C_IP.yml new file mode 100644 index 0000000..931c66c --- /dev/null +++ b/data/models/X77C_IP.yml @@ -0,0 +1,11 @@ +name: X77C_IP.pdb +description: X77C - Main Protease complex structure (IP) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/X77C_IP.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/X77C_MC.yml b/data/models/X77C_MC.yml new file mode 100644 index 0000000..6127818 --- /dev/null +++ b/data/models/X77C_MC.yml @@ -0,0 +1,11 @@ +name: X77C_MC.pdb +description: X77C - Main Protease complex structure (MC) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/X77C_MC.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/X77C_PROD.yml b/data/models/X77C_PROD.yml new file mode 100644 index 0000000..1acbce8 --- /dev/null +++ b/data/models/X77C_PROD.yml @@ -0,0 +1,11 @@ +name: X77C_PROD.pdb +description: X77C - Main Protease complex structure (PROD) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/X77C_PROD.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229 diff --git a/data/models/X77C_REAC.yml b/data/models/X77C_REAC.yml new file mode 100644 index 0000000..ecdd939 --- /dev/null +++ b/data/models/X77C_REAC.yml @@ -0,0 +1,11 @@ +name: X77C_REAC.pdb +description: X77C - Main Protease complex structure (REAC) +url: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/X77C_REAC.pdb +pdbids: + - 7BUY +proteins: + - 3CLpro +creator: Bella Grigorenko and Igor Polyakov +institution: Lomonosov Moscow State University, Department of Chemistry +lab: Alexander V. Nemukhin research group +publication: https://doi.org/10.1021/jacs.3c02229