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Pharmacophore Screening of the Protein Data Bank for Specific Binding Site Chemistry

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What this work says

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

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Computational approaches to identifying and characterizing protein binding sites for ligand design

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Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design

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A new bioinformatic approach to detect common 3D sites in protein structures

inferredcites →https://doi.org/10.1002/prot.21092openalex-snapshot

Comparison of protein active site structures for functional annotation of proteins and drug design

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Basic Local Alignment Search Tool

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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

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Molecular Mechanism of AHSP-Mediated Stabilization of α-Hemoglobin

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Structural Basis for the Methylation State-Specific Recognition of Histone H4-K20 by 53BP1 and Crb2 in DNA Repair

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Chk1 Is a Histone H3 Threonine 11 Kinase that Regulates DNA Damage-Induced Transcriptional Repression

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

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A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology

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Molecular Basis of Phosphorylation-Induced Activation of the NADPH Oxidase

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Malignant Brain Tumor Repeats

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LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

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Structural Mechanism of the Bromodomain of the Coactivator CBP in p53 Transcriptional Activation

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Recombinant Kringle IV-10 Modules of Human Apolipoprotein(a): Structure, Ligand Binding Modes, and Biological Relevance

inferredcites →https://doi.org/10.1021/bi9917378openalex-snapshot

Solution Structure and Dynamics of the Plasminogen Kringle 2−AMCHA Complex: 31-Helix in Homologous Domains,

inferredcites →https://doi.org/10.1021/ci050359copenalex-snapshot

A Searchable Database for Comparing Protein−Ligand Binding Sites for the Analysis of Structure−Function Relationships

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/jm00053a018openalex-snapshot

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds

inferredcites →https://doi.org/10.1021/jm00053a019openalex-snapshot

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds

inferredcites →https://doi.org/10.1021/jm00125a025openalex-snapshot

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure

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/jm8005977openalex-snapshot

The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery

inferredcites →https://doi.org/10.1023/a:1008124202956openalex-snapshot

Fast prediction and visualization of protein binding pockets with PASS

inferredcites →https://doi.org/10.1038/nature05971openalex-snapshot

Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity

inferredcites →https://doi.org/10.1038/nature06034openalex-snapshot

Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression

inferredcites →https://doi.org/10.1038/nsmb.1384openalex-snapshot

The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules

inferredcites →https://doi.org/10.1038/nsmb1116openalex-snapshot

Molecular recognition of histone H3 by the WD40 protein WDR5

inferredcites →https://doi.org/10.1038/nsmb1338openalex-snapshot

How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers

inferredcites →https://doi.org/10.1074/mcp.m400159-mcp200openalex-snapshot

Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes

inferredcites →https://doi.org/10.1089/omi.2009.0045openalex-snapshot

MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction

inferredcites →https://doi.org/10.1093/bioinformatics/19.1.163openalex-snapshot

ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information

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/bti645openalex-snapshot

The SuMo server: 3D search for protein functional sites

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/nar/gkg512openalex-snapshot

CASTp: Computed Atlas of Surface Topography of proteins

inferredcites →https://doi.org/10.1093/nar/gkh054openalex-snapshot

SURFACE: a database of protein surface regions for functional annotation

inferredcites →https://doi.org/10.1093/nar/gkl897openalex-snapshot

FireDB--a database of functionally important residues from proteins of known structure

inferredcites →https://doi.org/10.1159/000123041openalex-snapshot

FKBP Family Proteins: Immunophilins with Versatile Biological Functions

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Functional annotation by identification of local surface similarities: a novel tool for structural genomics

inferredcites →https://doi.org/10.1186/1471-2105-8-475openalex-snapshot

Predicting gene ontology functions from protein's regional surface structures

inferredcites →https://doi.org/10.1186/1471-2105-9-s2-s2openalex-snapshot

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures

inferredcites →https://doi.org/10.1186/1472-6807-6-19openalex-snapshot

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.

inferredcites →https://doi.org/10.1186/1752-153x-1-7openalex-snapshot

PocketPicker: analysis of ligand binding-sites with shape descriptors

What points at this work

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

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2/3D Pharmacophore Definitions and Their Application

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2/3D Pharmacophore definitions and their application

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The role of the histone demethylase KDM4A in cancer

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Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

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Exploring Cocrystallized Aromatic Cage Binders to Target Histone Methylation Reader Proteins

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TASK Channels Pharmacology: New Challenges in Drug Design

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Prediction of Active Site Cleft Using Support Vector Machines

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Drug-like Density: A Method of Quantifying the “Bindability” of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data Bank

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Small-Molecule Ligands of Methyl-Lysine Binding Proteins

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Heteroatom Incorporation Effect in σ- and π-Electron Systems: The sEDA(II) and pEDA(II) Descriptors

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Self-Organizing Fuzzy Graphs for Structure-Based Comparison of Protein Pockets

inferred← citeshttps://doi.org/10.1039/c1md00210dopenalex-snapshot

From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling

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Supramolecular hosts that recognize methyllysines and disrupt the interaction between a modified histone tail and its epigenetic reader protein

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Molecular modelling of cation–π interactions

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Writing and Rewriting the Epigenetic Code of Cancer Cells: From Engineered Proteins to Small Molecules

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Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites

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Receptor-based pharmacophore tool for design and development of next-generation drugs

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Discovery of Novel TASK-3 Channel Blockers Using a Pharmacophore-Based Virtual Screening

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