PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow (Q111078487)

2

object named as

Rachel Cavill

0 references

Chris T. Evelo

3

object named as

Chris Evelo

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Egon Willighagen

Journal of Cheminformatics

4

object named as

Egon Willighagen

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language of work or name

English

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publication date

28 February 2022

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published in

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volume

14

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cites work

The PDBbind database: methodologies and updates

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The Protein Data Bank

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UniProt: the Universal Protein knowledgebase

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ClinVar: improving access to variant interpretations and supporting evidence.

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SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

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volume

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ChEMBL: a large-scale bioactivity database for drug discovery

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BioJava: an open-source framework for bioinformatics in 2012

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Complex heatmaps reveal patterns and correlations in multidimensional genomic data.

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The FoldX web server: an online force field

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Open Babel: An open chemical toolbox

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Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?

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subject has role

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

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Biomolecules in the computer: Jmol to the rescue

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The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics

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StructMAn: annotation of single-nucleotide polymorphisms in the structural context

5 April 2022

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In silico analysis and molecular dynamics simulation of human superoxide dismutase 3 (SOD3) genetic variants

3 May 2022

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Performance of protein stability predictors.

3 May 2022

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MicroScale Thermophoresis: Interaction analysis and beyond

3 May 2022

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Improving the Accuracy of Protein-Ligand Binding Affinity Prediction by Deep Learning Models: Benchmark and Model

3 May 2022

1 reference

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PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants

3 May 2022

1 reference

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topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association

3 May 2022

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Genetic variation in human drug-related genes.

3 May 2022

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Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

3 May 2022

1 reference

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Label-free microscale thermophoresis discriminates sites and affinity of protein-ligand binding

3 May 2022

1 reference

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

3 May 2022

1 reference

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The SAAPdb web resource: a large-scale structural analysis of mutant proteins.

3 May 2022

1 reference

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Identification and in silico analysis of functional SNPs of human TAGAP protein: A comprehensive study.

3 May 2022

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Comparative Assessment of Scoring Functions: The CASF-2016 Update

3 May 2022

1 reference

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Principles governing Mg, Ca, and Zn binding and selectivity in proteins.

3 May 2022

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LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

3 May 2022

1 reference

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In silico profiling and structural insights of missense mutations in RET protein kinase domain by molecular dynamics and docking approach

3 May 2022

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SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

3 May 2022

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Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2.

3 May 2022

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In silico screening of deleterious single nucleotide polymorphisms (SNPs) and molecular dynamics simulation of disease associated mutations in gene responsible for oculocutaneous albinism type 6 (OCA 6) disorder

3 May 2022

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1001 Ways to run AutoDock Vina for virtual screening

3 May 2022

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Genetics and variable drug response

3 May 2022

1 reference

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Pharmacogenetics and human genetic polymorphisms

3 May 2022

1 reference

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Comparison of simple potential functions for simulating liquid water

3 May 2022

1 reference

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Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes.

3 May 2022

1 reference

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Identification and characterization of functional single nucleotide polymorphisms (SNPs) in Axin 1 gene: a molecular dynamics approach.

3 May 2022

1 reference

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PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks

3 May 2022

1 reference

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Computational protein-ligand docking and virtual drug screening with the AutoDock suite

3 May 2022

1 reference

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Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?

3 May 2022

1 reference

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SNPs3D: candidate gene and SNP selection for association studies.

3 May 2022

1 reference

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MSV3d: database of human MisSense Variants mapped to 3D protein structure

3 May 2022

1 reference

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Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene

3 May 2022

1 reference

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G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures

3 May 2022

1 reference

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Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details.

3 May 2022

1 reference

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Accurate prediction of functional, structural, and stability changes in PITX2 mutations using in silico bioinformatics algorithms.

3 May 2022

1 reference

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Discovering high-affinity ligands for proteins: SAR by NMR

3 May 2022

1 reference

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JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-021-00573-5

SNP2Structure: A Public and Versatile Resource for Mapping and Three-Dimensional Modeling of Missense SNPs on Human Protein Structures

3 May 2022

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coliSNP database server mapping nsSNPs on protein structures.

3 May 2022

1 reference

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Integrating in silico prediction methods, molecular docking, and molecular dynamics simulation to predict the impact of ALK missense mutations in structural perspective

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-021-00573-5

Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins

3 May 2022

1 reference

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Solution NMR Spectroscopy in Target-Based Drug Discovery

3 May 2022

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In silico analysis of PFN1 related to amyotrophic lateral sclerosis.

3 May 2022

1 reference

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Protein-ligand binding affinity determination by the waterLOGSY method: An optimised approach considering ligand rebinding.

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-021-00573-5

A machine learning approach towards the prediction of protein-ligand binding affinity based on fundamental molecular properties

3 May 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-021-00573-5