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A Searchable Database for Comparing Protein−Ligand Binding Sites for the Analysis of Structure−Function Relationships
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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NADP-Dependent enzymes. I: Conserved stereochemistry of cofactor binding
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When fold is not important: A common structural framework for adenine and AMP binding in 12 unrelated protein families
inferredcites →https://doi.org/10.1002/j.1460-2075.1982.tb01276.xopenalex-snapshot
Distantly related sequences in the alpha‐ and beta‐subunits of ATP synthase, myosin, kinases and other ATP‐requiring enzymes and a common nucleotide binding fold.
inferredcites →https://doi.org/10.1002/pro.5560070507openalex-snapshot
Two “unrelated” families of ATP‐dependent enzymes share extensive structural similarities about their cofactor binding sites
inferredcites →https://doi.org/10.1002/prot.1093openalex-snapshot
Adenine recognition: A motif present in ATP‐, CoA‐, NAD‐, NADP‐, and FAD‐dependent proteins
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
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Crystal Structure ofEscherichia coliPhosphoenolpyruvate Carboxykinase: A New Structural Family with the P-loop Nucleoside Triphosphate Hydrolase Fold
inferredcites →https://doi.org/10.1006/jmbi.1996.0591openalex-snapshot
Protein Recognition of Adenylate: An Example of a Fuzzy Recognition Template
inferredcites →https://doi.org/10.1006/jmbi.1998.1844openalex-snapshot
Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution
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.2005.01.061openalex-snapshot
A Ligand-centric Analysis of the Diversity and Evolution of Protein–Ligand Relationships in E.coli
inferredcites →https://doi.org/10.1016/s0022-2836(03)00045-7openalex-snapshot
A Model for Statistical Significance of Local Similarities in Structure
inferredcites →https://doi.org/10.1016/s0022-2836(03)00882-9openalex-snapshot
Inferring Functional Relationships of Proteins from Local Sequence and Spatial Surface Patterns
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/s0968-0004(98)01254-7openalex-snapshot
Catalytic triads and their relatives
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Applications of Effective Core Potentials and Density Functional Theory to the Spin States of Iron Porphyrin
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The Relationship between the Sequence Identities of Alpha Helical Proteins in the PDB and the Molecular Similarities of Their Ligands
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Influenza Virus Neuraminidase Inhibitors: Generation and Comparison of Structure-Based and Common Feature Pharmacophore Hypotheses and Their Application in Virtual Screening
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Identification of protein functions from a molecular surface database, eF-site
inferredcites →https://doi.org/10.1038/372631a0openalex-snapshot
Protein superfamilles and domain superfolds
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The Journal Bioinformatics, key medium for computational biology
inferredcites →https://doi.org/10.1093/nar/21.6.1369openalex-snapshot
A study into the effects of protein binding on nucleotide conformation
inferredcites →https://doi.org/10.1093/nar/gkg500openalex-snapshot
Multiple sequence alignment with the Clustal series of programs
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Supporting Biocatalysis Research with Structural Bioinformatics
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.21933openalex-snapshot
Method for comparing the structures of protein ligand‐binding sites and application for predicting protein–drug interactions
inferred← citeshttps://doi.org/10.1002/prot.24205openalex-snapshot
Predicting enzymatic function from global binding site descriptors
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In Silico Target Druggability Assessment: From Structural to Systemic Approaches
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Structure-Based Chemogenomics: Analysis of Protein Family Landscapes
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Structure-Based Target Druggability Assessment
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Protein ligand interaction database (PLID)
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2015.12.004openalex-snapshot
Comparison of non-sequential sets of protein residues
inferred← citeshttps://doi.org/10.1016/j.ejcb.2011.06.003openalex-snapshot
Binding sites in membrane proteins – Diversity, druggability and prospects
inferred← citeshttps://doi.org/10.1016/j.sbi.2009.03.008openalex-snapshot
The sequence–structure relationship and protein function prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01398openalex-snapshot
DEPACT and PACMatch: A Workflow of Designing De Novo Protein Pockets to Bind Small Molecules
inferred← citeshttps://doi.org/10.1021/ci100210copenalex-snapshot
Pocket Similarity: Are α Carbons Enough?
inferred← citeshttps://doi.org/10.1021/ci900427bopenalex-snapshot
Pharmacophore Screening of the Protein Data Bank for Specific Binding Site Chemistry
inferred← citeshttps://doi.org/10.1021/jm0606589openalex-snapshot
In Silico-Guided Target Identification of a Scaffold-Focused Library: 1,3,5-Triazepan-2,6-diones as Novel Phospholipase A2 Inhibitors
inferred← citeshttps://doi.org/10.1021/jm8005977openalex-snapshot
The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery
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/10.1042/bst0350561openalex-snapshot
New opportunities for protease ligand-binding site comparisons using SitesBase
inferred← citeshttps://doi.org/10.1093/nar/gkq400openalex-snapshot
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2008.00762.xopenalex-snapshot
CREDO: A Protein–Ligand Interaction Database for Drug Discovery
inferred← citeshttps://doi.org/10.1186/1471-2105-12-s1-s35openalex-snapshot
Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites
inferred← citeshttps://doi.org/10.1186/1472-6807-8-45openalex-snapshot
Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites
inferred← citeshttps://doi.org/10.1186/1756-0500-4-17openalex-snapshot
Searching the protein structure database for ligand-binding site similarities using CPASS v.2
inferred← citeshttps://doi.org/10.1186/gb-2007-8-8-r176openalex-snapshot
Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000387openalex-snapshot
Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors
inferred← citeshttps://doi.org/10.1517/17425250802660467openalex-snapshot
Computational toxicology: an overview of the sources of data and of modelling methods
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Characterization, classification and alignment of protein-protein interfaces
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