Protein-ligand affinity change upon mutation
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Protein-ligand affinity change upon mutation
metasource: Fairsharing.org
version: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Platinum
metasource: Fairsharing.org
version: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
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Protein-ligand affinity change upon mutation
metasource: Fairsharing.orgversion: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Platinum
metasource: Fairsharing.orgversion: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
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Protein-ligand affinity change upon mutation
metasource: Fairsharing.orgversion: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Platinum
metasource: Fairsharing.orgversion: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
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Platinum is a manually curated, literature-derived database comprising over 1,000 mutations which for the first time associates experimental information on changes in protein-ligand affinity with the three-dimensional structures of the complex.
Description
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Platinum is a manually curated, literature-derived database comprising over 1,000 mutations which for the first time associates experimental information on changes in protein-ligand affinity with the three-dimensional structures of the complex.
metasource: Fairsharing.orgversion: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The ability to understand and predict the effects of mutations on protein–ligand affinities and their roles in the emergence of resistance would significantly aid treatment and drug design strategies. In order to study and understand the impacts of missense mutations on the interaction of ligands with the proteome, we have developed Platinum (http://structure.bioc.cam.ac.uk/platinum). This manually curated, literature-derived database, comprising over 1000 mutations, associates for the first time experimental information on changes in affinity with three-dimensional structures of protein–ligand complexes. To minimize differences arising from experimental techniques and to directly compare binding affinities, Platinum considers only changes measured by the same group and with the same amino-acid sequence used for structure determination, providing a direct link between protein structure, how a ligand binds and how mutations alter the affinity of the ligand of the protein. In order to account for additional consequences of the mutations, the predicted effects of single point mutations on protein stability (1) and protein-protein affinity (2) in the three-dimensional structure were calculated when a wild-type PDB structure was available.We believe Platinum will be an invaluable resource for understanding the effects of mutations that give rise to drug resistance, a major problem emerging in pandemics including those caused by the influenza virus, in infectious diseases such as tuberculosis, in cancer and in many other life-threatening illnesses.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://structure.bioc.cam.ac.uk/platinumWebpage
More detailed information about this field from each metasource.
http://structure.bioc.cam.ac.uk/platinum
metasource: Fairsharing.orgversion: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes
PMID: 25324307
metasource: Fairsharing.org
version: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gku966
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes
PMID: 25324307
metasource: Fairsharing.org
version: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gku966
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes
PubMed citations: 41.
41 articles citing: Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes
Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. PMID:35189634
PremPLI: a machine learning model for predicting the effects of missense mutations on protein-ligand interactions. PMID:34799678
mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions. PMID:33893812
How quickly can we predict trimethoprim resistance using alchemical free energy methods? PMID:33178416
Genomics, Computational Biology and Drug Discovery for Mycobacterial Infections: Fighting the Emergence of Resistance. PMID:33101362
Systems Biology and Experimental Model Systems of Cancer. PMID:33086677
Recent advances in user-friendly computational tools to engineer protein function. PMID:32743637
mmCSM-AB: guiding rational antibody engineering through multiple point mutations. PMID:32432715
Predicting the impacts of mutations on protein-ligand binding affinity based on molecular dynamics simulations and machine learning methods. PMID:32153730
Improvement in predicting drug sensitivity changes associated with protein mutations using a molecular dynamics based alchemical mutation method. PMID:32034220
Prediction of impacts of mutations on protein structure and interactions: SDM, a statistical approach, and mCSM, using machine learning. PMID:31693276
MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. PMID:31679514
ProCarbDB: a database of carbohydrate-binding proteins. PMID:31598690
Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches. PMID:31482130
Understanding the impacts of missense mutations on structures and functions of human cancer-related genes: A preliminary computational analysis of the COSMIC Cancer Gene Census. PMID:31323058
Empirical ways to identify novel Bedaquiline resistance mutations in AtpE. PMID:31141524
mCSM-PPI2: predicting the effects of mutations on protein-protein interactions. PMID:31114883
Synthesis and Structure-Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH. PMID:31055147
Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation. PMID:30648154
Kinact: a computational approach for predicting activating missense mutations in protein kinases. PMID:29788456
RosettaLigandEnsemble: A Small-Molecule Ensemble-Driven Docking Approach. PMID:29732444
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. PMID:29718330
Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection. PMID:29547094
Familial STAG2 germline mutation defines a new human cohesinopathy. PMID:29263825
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. PMID:29254494
SDHA related tumorigenesis: a new case series and literature review for variant interpretation and pathogenicity. PMID:28546994
SDM: a server for predicting effects of mutations on protein stability. PMID:28525590
Rational design of non-resistant targeted cancer therapies. PMID:28436422
Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance. PMID:28408471
mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions. PMID:28383703
Protein-Ligand Scoring with Convolutional Neural Networks. PMID:28368587
LibME-automatic extraction of 3D ligand-binding motifs for mechanistic analysis of protein-ligand recognition. PMID:28255540
Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures. PMID:27964945
mutLBSgeneDB: mutated ligand binding site gene DataBase. PMID:27907895
The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis. PMID:27726334
Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis. PMID:27704782
Variation in Human Cytochrome P-450 Drug-Metabolism Genes: A Gateway to the Understanding of Plasmodium vivax Relapses. PMID:27467145
mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance. PMID:27384129
mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures. PMID:27216816
In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity. PMID:26797105
pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures. PMID:25860834 - http://dx.doi.org/10.1093/nar/gku966
Tags:
Tags
More detailed information about this field from each metasource.
mutation analysis
metasource: Fairsharing.org
version: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
mutation analysis
metasource: Fairsharing.orgversion: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein structure
metasource: Fairsharing.orgversion: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: Platinum; Protein-ligand affinity change upon mutation; DOI: https://doi.org/10.25504/FAIRsharing.51r558; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
structure databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
mutation analysis protein interaction protein structure small molecule structure
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