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Geometric and chemical patterns of interaction in protein–ligand complexes and their application in docking

https://doi.org/10.1002/prot.10026
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1096-987x(19970715)18:9<1175::aid-jcc6>3.0.co;2-oopenalex-snapshot
Critical evaluation of search algorithms for automated molecular docking and database screening
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19980215)30:3<321::aid-prot11>3.0.co;2-hopenalex-snapshot
Characterization of receptors with a new negative image: Use in molecular docking and lead optimization
inferredcites →https://doi.org/10.1002/pro.5560030202openalex-snapshot
Crystal structure of cholera toxin B‐pentamer bound to receptor G M1 pentasaccharide
inferredcites →https://doi.org/10.1002/pro.5560050406openalex-snapshot
Prediction of protein complexes using empirical free energy functions
inferredcites →https://doi.org/10.1002/prot.340180111openalex-snapshot
Molecular surface representations by sparse critical points
inferredcites →https://doi.org/10.1006/jmbi.1996.0311openalex-snapshot
X-SITE: Use of Empirically Derived Atomic Packing Preferences to Identify Favourable Interaction Regions in the Binding Sites of Proteins
inferredcites →https://doi.org/10.1006/jmbi.1996.0868openalex-snapshot
Novel knowledge-based mean force potential at atomic level
inferredcites →https://doi.org/10.1016/0022-2836(82)90153-xopenalex-snapshot
A geometric approach to macromolecule-ligand interactions
inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot
VMD: Visual molecular dynamics
inferredcites →https://doi.org/10.1023/a:1007934413448openalex-snapshot
IsoStar: A library of information about nonbonded interactions
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/protein/6.7.723openalex-snapshot
Matching chemistry and shape in molecular docking
inferredcites →https://doi.org/10.1126/science.257.5073.1078openalex-snapshot
Structure-Based Strategies for Drug Design and Discovery

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/minf.202100248openalex-snapshot
Data Mining Meets Machine Learning: A Novel ANN‐based Multi‐body Interaction Docking Scoring Function (MBI‐score) Based on Utilizing Frequent Geometric and Chemical Patterns of Interfacial Atoms in Native Protein‐ligand Complexes
inferred← citeshttps://doi.org/10.1002/prot.10484openalex-snapshot
Analysis of protein structures reveals regions of rare backbone conformation at functional sites
inferred← citeshttps://doi.org/10.1002/prot.21487openalex-snapshot
A novel approach to local similarity of protein binding sites substantially improves computational drug design results
inferred← citeshttps://doi.org/10.1007/s00214-007-0346-yopenalex-snapshot
Exploring the potential energy surfaces of association of NO with aminoacids and related organic functional groups: the role of entropy of association
inferred← citeshttps://doi.org/10.1016/j.theochem.2007.05.036openalex-snapshot
Theoretical affinity order among flavonoids and amino acid residues: An approach to understand flavonoid–protein interactions
inferred← citeshttps://doi.org/10.1021/ci800125kopenalex-snapshot
Information Theory-Based Scoring Function for the Structure-Based Prediction of Protein−Ligand Binding Affinity
inferred← citeshttps://doi.org/10.1021/ci900358zopenalex-snapshot
Quantum Chemical Associations Ligand−Residue: Their Role to Predict Flavonoid Binding Sites in Proteins
inferred← citeshttps://doi.org/10.1023/a:1023866311551openalex-snapshot
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
inferred← citeshttps://doi.org/10.1023/a:1023868309253openalex-snapshot
On the molecular interaction between lactoferrin and the dye Red HE-3B. A novel approach for docking a charged and highly flexible molecule to protein surfaces
inferred← citeshttps://doi.org/10.1039/9781849735377-00223openalex-snapshot
Accounting for Target Flexibility During Ligand–Receptor Docking
inferred← citeshttps://doi.org/10.1039/c1cp21140dopenalex-snapshot
Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function
inferred← citeshttps://doi.org/10.1074/jbc.m311693200openalex-snapshot
Structure and Molecular Interactions of a Unique Antitumor Antibody Specific for N-Glycolyl GM3
inferred← citeshttps://doi.org/10.1109/icise.2010.5688942openalex-snapshot
An effective method of electrostatic potential calculation on protein binding site
inferred← citeshttps://doi.org/10.1109/tcbb.2009.31openalex-snapshot
Evaluation of Geometric Complementarity between Molecular Surfaces Using Compactly Supported Radial Basis Functions
inferred← citeshttps://doi.org/10.1186/1471-2105-8-310openalex-snapshot
Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms
inferred← citeshttps://doi.org/10.3390/molecules28020692openalex-snapshot
Identifying Potential Molecular Targets in Fungi Based on (Dis)Similarities in Binding Site Architecture with Proteins of the Human Pharmacolome
inferred← citeshttps://doi.org/10.3851/imp1716openalex-snapshot
Structural Basis for a New Mechanism of Inhibition of H I V-1 Integrase Identified by Fragment Screening and Structure-Based Design
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