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Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

https://doi.org/10.1021/ci4003602
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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/pro.5560070905openalex-snapshot
Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
inferredcites →https://doi.org/10.1002/prot.10146openalex-snapshot
Scoring residue conservation
inferredcites →https://doi.org/10.1002/prot.20088openalex-snapshot
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
inferredcites →https://doi.org/10.1002/prot.20264openalex-snapshot
Scoring function for automated assessment of protein structure template quality
inferredcites →https://doi.org/10.1002/prot.21780openalex-snapshot
Binding similarity network of ligand
inferredcites →https://doi.org/10.1002/prot.22572openalex-snapshot
Protein‐binding site prediction based on three‐dimensional protein modeling
inferredcites →https://doi.org/10.1002/prot.23165openalex-snapshot
BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures
inferredcites →https://doi.org/10.1002/prot.23174openalex-snapshot
Assessment of ligand‐binding residue predictions in CASP9
inferredcites →https://doi.org/10.1016/0022-2836(70)90057-4openalex-snapshot
A general method applicable to the search for similarities in the amino acid sequence of two proteins
inferredcites →https://doi.org/10.1016/0263-7855(92)80074-nopenalex-snapshot
POCKET: A computer graphies method for identifying and displaying protein cavities and their surrounding amino acids
inferredcites →https://doi.org/10.1016/0263-7855(95)00073-9openalex-snapshot
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
inferredcites →https://doi.org/10.1016/j.drudis.2010.05.015openalex-snapshot
Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery
inferredcites →https://doi.org/10.1016/j.jmb.2004.04.012openalex-snapshot
Recognition of Functional Sites in Protein Structures
inferredcites →https://doi.org/10.1016/j.jmb.2007.06.017openalex-snapshot
Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon
inferredcites →https://doi.org/10.1016/j.str.2012.03.009openalex-snapshot
Recognizing Protein-Ligand Binding Sites by Global Structural Alignment and Local Geometry Refinement
inferredcites →https://doi.org/10.1016/s0022-2836(02)00811-2openalex-snapshot
A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology
inferredcites →https://doi.org/10.1016/s0959-440x(03)00075-7openalex-snapshot
Ligand binding: functional site location, similarity and docking
inferredcites →https://doi.org/10.1016/s1093-3263(98)00002-3openalex-snapshot
LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
inferredcites →https://doi.org/10.1021/ci300178eopenalex-snapshot
Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design
inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
inferredcites →https://doi.org/10.1021/jm061277yopenalex-snapshot
Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance
inferredcites →https://doi.org/10.1021/jm801385dopenalex-snapshot
Binding Site Detection and Druggability Index from First Principles
inferredcites →https://doi.org/10.1038/332564a0openalex-snapshot
Dissecting the catalytic triad of a serine protease
inferredcites →https://doi.org/10.1073/pnas.0707684105openalex-snapshot
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
inferredcites →https://doi.org/10.1073/pnas.1101835108openalex-snapshot
Structural conservation of druggable hot spots in protein–protein interfaces
inferredcites →https://doi.org/10.1074/mcp.m400159-mcp200openalex-snapshot
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
inferredcites →https://doi.org/10.1093/bioinformatics/bti315openalex-snapshot
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
inferredcites →https://doi.org/10.1093/bioinformatics/btm270openalex-snapshot
Predicting functionally important residues from sequence conservation
inferredcites →https://doi.org/10.1093/bioinformatics/btq100openalex-snapshot
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
inferredcites →https://doi.org/10.1093/bioinformatics/btr331openalex-snapshot
Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction
inferredcites →https://doi.org/10.1093/bioinformatics/bts182openalex-snapshot
Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles
inferredcites →https://doi.org/10.1093/bioinformatics/btt024openalex-snapshot
APoc: large-scale identification of similar protein pockets
inferredcites →https://doi.org/10.1093/nar/gki524openalex-snapshot
TM-align: a protein structure alignment algorithm based on the TM-score
inferredcites →https://doi.org/10.1093/nar/gkj062openalex-snapshot
SitesBase: a database for structure-based protein-ligand binding site comparisons
inferredcites →https://doi.org/10.1093/nar/gkm839openalex-snapshot
LigASite a database of biologically relevant binding sites in proteins with known apo-structures
inferredcites →https://doi.org/10.1093/nar/gkq1021openalex-snapshot
The RCSB Protein Data Bank: redesigned web site and web services
inferredcites →https://doi.org/10.1126/science.1121018openalex-snapshot
The Impact of Structural Genomics: Expectations and Outcomes
inferredcites →https://doi.org/10.1186/1471-2105-10-168openalex-snapshot
Fpocket: An open source platform for ligand pocket detection
inferredcites →https://doi.org/10.1371/journal.pcbi.1000585openalex-snapshot
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
inferredcites →https://doi.org/10.1371/journal.pone.0010109openalex-snapshot
Binding-Site Assessment by Virtual Fragment Screening

What points at this work

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

inferred← citeshttps://doi.org/10.1002/jcc.25813openalex-snapshot
Stalis: A Computational Method for Template‐Based Ab Initio Ligand Design
inferred← citeshttps://doi.org/10.1002/pro.2890openalex-snapshot
G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design
inferred← citeshttps://doi.org/10.1007/978-1-0716-1665-9_3openalex-snapshot
Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods with a Focus on FunFOLD3
inferred← citeshttps://doi.org/10.1007/978-1-4939-1465-4_17openalex-snapshot
Methods for Predicting Protein–Ligand Binding Sites
inferred← citeshttps://doi.org/10.1007/978-1-4939-7015-5_8openalex-snapshot
G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures
inferred← citeshttps://doi.org/10.1016/j.sbi.2013.11.012openalex-snapshot
Binding site comparison for function prediction and pharmaceutical discovery
inferred← citeshttps://doi.org/10.1017/s003358352500006xopenalex-snapshot
Computational methods for binding site prediction on macromolecules
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01354openalex-snapshot
Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00561openalex-snapshot
CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01156openalex-snapshot
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00534openalex-snapshot
ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01744openalex-snapshot
RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00751openalex-snapshot
Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates
inferred← citeshttps://doi.org/10.1038/s41598-018-26497-zopenalex-snapshot
A Novel Geometry-Based Approach to Infer Protein Interface Similarity
inferred← citeshttps://doi.org/10.1093/bib/bbad459openalex-snapshot
Unraveling viral drug targets: a deep learning-based approach for the identification of potential binding sites
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv489openalex-snapshot
LIBRA: LIgand Binding site Recognition Application
inferred← citeshttps://doi.org/10.1093/glycob/cwaa062openalex-snapshot
A systematic analysis of protein–carbohydrate interactions in the Protein Data Bank
inferred← citeshttps://doi.org/10.1186/s12859-022-04995-2openalex-snapshot
A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions
inferred← citeshttps://doi.org/10.1186/s13321-018-0285-8openalex-snapshot
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure
inferred← citeshttps://doi.org/10.1186/s13321-024-00821-4openalex-snapshot
Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures
inferred← citeshttps://doi.org/10.1186/s13321-024-00923-zopenalex-snapshot
Comparative evaluation of methods for the prediction of protein–ligand binding sites
inferred← citeshttps://doi.org/10.6084/m9.figshare.21485795openalex-snapshot
Additional file 1 of A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions
inferred← citeshttps://doi.org/10.6084/m9.figshare.26693644openalex-snapshot
Additional file 1 of Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures
inferred← citeshttps://doi.org/10.64898/2026.07.10.737806openalex-snapshot
FUSED: A Functional Representation for Joint Structural and Elemental Analysis of Protein Ligand Binding Sites
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