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Fast Protein Binding Site Comparison via an Index-Based Screening Technology

https://doi.org/10.1021/ci300469h
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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.5560050603openalex-snapshot
Derivation of 3D coordinate templates for searching structural databases: Application to ser‐His‐Asp catalytic triads in the serine proteinases and lipases
inferredcites →https://doi.org/10.1002/prot.10339openalex-snapshot
A new bioinformatic approach to detect common 3D sites in protein structures
inferredcites →https://doi.org/10.1002/prot.20123openalex-snapshot
Towards a structural classification of phosphate binding sites in protein–nucleotide complexes: An automated all‐against‐all structural comparison using geometric matching
inferredcites →https://doi.org/10.1002/prot.21858openalex-snapshot
A simple and fuzzy method to align and compare druggable ligand‐binding sites
inferredcites →https://doi.org/10.1002/prot.21933openalex-snapshot
Method for comparing the structures of protein ligand‐binding sites and application for predicting protein–drug interactions
inferredcites →https://doi.org/10.1002/prot.22458openalex-snapshot
Structure is three to ten times more conserved than sequence—A study of structural response in protein cores
inferredcites →https://doi.org/10.1002/prot.23232openalex-snapshot
PDB‐scale analysis of known and putative ligand‐binding sites with structural sketches
inferredcites →https://doi.org/10.1007/bf00124464openalex-snapshot
Placement of medium-sized molecular fragments into active sites of proteins
inferredcites →https://doi.org/10.1007/s00203-010-0549-9openalex-snapshot
An overview of in silico protein function prediction
inferredcites →https://doi.org/10.1007/s10822-007-9103-5openalex-snapshot
TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time
inferredcites →https://doi.org/10.1016/j.jbiotec.2011.12.005openalex-snapshot
Structure-based computational analysis of protein binding sites for function and druggability prediction
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.2005.11.044openalex-snapshot
Fold Independent Structural Comparisons of Protein–Ligand Binding Sites for Exploring Functional Relationships
inferredcites →https://doi.org/10.1016/j.jmb.2006.04.024openalex-snapshot
From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase
inferredcites →https://doi.org/10.1016/j.sbi.2011.01.004openalex-snapshot
Structure-based systems biology for analyzing off-target binding
inferredcites →https://doi.org/10.1016/s0022-2836(02)00016-5openalex-snapshot
Enzyme Function Less Conserved than Anticipated
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(96)80058-3openalex-snapshot
Surprising similarities in structure comparison
inferredcites →https://doi.org/10.1021/ci100241yopenalex-snapshot
Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets
inferredcites →https://doi.org/10.1021/ci200324eopenalex-snapshot
NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats
inferredcites →https://doi.org/10.1021/ci300184xopenalex-snapshot
Comparison and Druggability Prediction of Protein–Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes
inferredcites →https://doi.org/10.1021/ci600253eopenalex-snapshot
A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application
inferredcites →https://doi.org/10.1021/ci9000212openalex-snapshot
Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds
inferredcites →https://doi.org/10.1021/ci900317xopenalex-snapshot
Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions
inferredcites →https://doi.org/10.1021/ci900349yopenalex-snapshot
Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein−Ligand Binding Sites
inferredcites →https://doi.org/10.1023/a:1011318527094openalex-snapshot
Identification of protein functions from a molecular surface database, eF-site
inferredcites →https://doi.org/10.1073/pnas.0900979106openalex-snapshot
Model structure of APOBEC3C reveals a binding pocket modulating ribonucleic acid interaction required for encapsidation
inferredcites →https://doi.org/10.1073/pnas.0906146106openalex-snapshot
Fast screening of protein surfaces using geometric invariant fingerprints
inferredcites →https://doi.org/10.1093/bib/3.3.252openalex-snapshot
The PRINTS database: A resource for identification of protein families
inferredcites →https://doi.org/10.1093/bib/3.3.265openalex-snapshot
PROSITE: A documented database using patterns and profiles as motif descriptors
inferredcites →https://doi.org/10.1093/bioinformatics/btg1086openalex-snapshot
Flexible structure alignment by chaining aligned fragment pairs allowing twists
inferredcites →https://doi.org/10.1093/bioinformatics/bti337openalex-snapshot
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
inferredcites →https://doi.org/10.1093/bioinformatics/btn263openalex-snapshot
Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
inferredcites →https://doi.org/10.1093/bioinformatics/btr120openalex-snapshot
sc-PDB: a database for identifying variations and multiplicity of ‘druggable’ binding sites in proteins
inferredcites →https://doi.org/10.1093/bioinformatics/btr432openalex-snapshot
Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling
inferredcites →https://doi.org/10.1093/bioinformatics/bts138openalex-snapshot
Fast protein binding site comparisons using visual words representation
inferredcites →https://doi.org/10.1093/nar/25.1.236openalex-snapshot
SCOP: a Structural Classification of Proteins database
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/28.1.228openalex-snapshot
Increased coverage of protein families with the Blocks Database servers
inferredcites →https://doi.org/10.1093/nar/gki414openalex-snapshot
ProFunc: a server for predicting protein function from 3D structure
inferredcites →https://doi.org/10.1093/nar/gkl273openalex-snapshot
PAST: fast structure-based searching in the PDB
inferredcites →https://doi.org/10.1093/nar/gkm351openalex-snapshot
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
inferredcites →https://doi.org/10.1093/nar/gks435openalex-snapshot
ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins
inferredcites →https://doi.org/10.1093/protein/gzg080openalex-snapshot
Common Structural Cliques: a tool for protein structure and function analysis
inferredcites →https://doi.org/10.1109/tcbb.2010.21openalex-snapshot
Image-Based Surface Matching Algorithm Oriented to Structural Biology
inferredcites →https://doi.org/10.1142/9781848163324_0006openalex-snapshot
BSAlign: A RAPID GRAPH-BASED ALGORITHM FOR DETECTING LIGAND-BINDING SITES IN PROTEIN STRUCTURES
inferredcites →https://doi.org/10.1186/1471-2105-11-47openalex-snapshot
BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server
inferredcites →https://doi.org/10.1186/1471-2105-9-543openalex-snapshot
PocketMatch: A new algorithm to compare binding sites in protein structures
inferredcites →https://doi.org/10.1186/1472-6807-8-45openalex-snapshot
Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites
inferredcites →https://doi.org/10.1371/journal.pcbi.0030217openalex-snapshot
In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators
inferredcites →https://doi.org/10.1371/journal.pcbi.1000423openalex-snapshot
Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis
inferredcites →https://doi.org/10.2174/157340908785747401openalex-snapshot
How to Measure the Similarity Between Protein Ligand-Binding Sites?

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9783527806539.ch6gopenalex-snapshot
Prediction, Analysis, and Comparison of Active Sites
inferred← citeshttps://doi.org/10.1002/minf.201300054openalex-snapshot
Towards the Next Generation of Computational Chemogenomics Tools
inferred← citeshttps://doi.org/10.1002/minf.201300082openalex-snapshot
Identification of Similar Binding Sites to Detect Distant Polypharmacology
inferred← citeshttps://doi.org/10.1002/prot.26176openalex-snapshot
A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing
inferred← citeshttps://doi.org/10.1007/7653_2018_18openalex-snapshot
Computational Studies on Natural Products for the Development of Multi-target Drugs
inferred← citeshttps://doi.org/10.1007/s10822-016-9940-1openalex-snapshot
mRAISE: an alternative algorithmic approach to ligand-based virtual screening
inferred← citeshttps://doi.org/10.1007/s10822-017-0011-zopenalex-snapshot
Ligand-based virtual screening under partial shape constraints
inferred← citeshttps://doi.org/10.1016/bs.armc.2017.08.001openalex-snapshot
Kinase-Centric Computational Drug Development
inferred← citeshttps://doi.org/10.1016/j.jbiotec.2017.06.004openalex-snapshot
From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library
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/10.1021/acs.jcim.5b00627openalex-snapshot
Identification and Visualization of Kinase-Specific Subpockets
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00118openalex-snapshot
Prediction of Protein Pairs Sharing Common Active Ligands Using Protein Sequence, Structure, and Ligand Similarity
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00832openalex-snapshot
Advances and Challenges in Computational Target Prediction
inferred← citeshttps://doi.org/10.1021/ci5005898openalex-snapshot
Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real
inferred← citeshttps://doi.org/10.1093/nar/gkaa235openalex-snapshot
ProteinsPlus: interactive analysis of protein–ligand binding interfaces
inferred← citeshttps://doi.org/10.1101/2025.01.09.632218openalex-snapshot
Improved Functional Classification of Hydrolases through Pairwise Structural Similarity of Reaction Cores
inferred← citeshttps://doi.org/10.1111/cbdd.12631openalex-snapshot
Considerations of Protein Subpockets in Fragment‐Based Drug Design
inferred← citeshttps://doi.org/10.1186/s13321-016-0180-0openalex-snapshot
Mapping the 3D structures of small molecule binding sites
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1014636openalex-snapshot
Metal binding site alignment enables network-driven discovery of recurrent geometries across sequence-divergent proteins and drug off-targets
inferred← citeshttps://doi.org/10.3390/ijms232012462openalex-snapshot
Estimating the Similarity between Protein Pockets
inferred← citeshttps://doi.org/10.4155/fmc.13.202openalex-snapshot
Predictive in silico Off-Target Profiling in Drug Discovery
inferred← citeshttps://doi.org/10.4155/fmc.14.3openalex-snapshot
Exploiting Structural Information for Drug-Target Assessment
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