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Merging chemical and biological space: Structural mapping of enzyme binding pocket space

https://doi.org/10.1002/prot.22345
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What this work says

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

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Protein Structure Comparison by Alignment of Distance Matrices
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SCOP: A structural classification of proteins database for the investigation of sequences and structures
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Comparison of substructural epitopes in enzyme active sites using self-organizing maps
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Protein structure alignment
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[5] Rapid and sensitive sequence comparison with FASTP and FASTA
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Recognition of Functional Sites in Protein Structures
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Fold Independent Structural Comparisons of Protein–Ligand Binding Sites for Exploring Functional Relationships
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From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase
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pkn22 (alr2502) encoding a putative Ser/Thr kinase in the cyanobacterium Anabaena sp. PCC 7120 is induced by both iron starvation and oxidative stress and regulates the expression of isiA
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A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology
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A Model for Statistical Significance of Local Similarities in Structure
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CATH – a hierarchic classification of protein domain structures
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LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
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Structure-based screening and design in drug discovery
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Protein structure similarity clustering and natural product structure as guiding principles in drug discovery
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Unexpected Nanomolar Inhibition of Carbonic Anhydrase by COX-2-Selective Celecoxib: New Pharmacological Opportunities Due to Related Binding Site Recognition
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RETRACTED: A Priori Inference of Cross Reactivity for Drug-Targeted Kinases
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Global mapping of pharmacological space
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Relating protein pharmacology by ligand chemistry
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Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
inferredcites →https://doi.org/10.1093/bib/3.3.246openalex-snapshot
ProDom: Automated clustering of homologous domains
inferredcites →https://doi.org/10.1093/bioinformatics/16.6.566openalex-snapshot
DaliLite workbench for protein structure comparison
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SIMAP—The similarity matrix of proteins
inferredcites →https://doi.org/10.1093/nar/24.1.206openalex-snapshot
The FSSP database: fold classification based on structure-structure alignment of proteins
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/30.1.276openalex-snapshot
The Pfam Protein Families Database
inferredcites →https://doi.org/10.1093/nar/gkg068openalex-snapshot
The Protein Data Bank and structural genomics
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Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
inferredcites →https://doi.org/10.1093/nar/gkh039openalex-snapshot
SCOP database in 2004: refinements integrate structure and sequence family data
inferredcites →https://doi.org/10.1093/nar/gki024openalex-snapshot
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
inferredcites →https://doi.org/10.1093/nar/gki034openalex-snapshot
The ProDom database of protein domain families: more emphasis on 3D
inferredcites →https://doi.org/10.1093/protein/11.9.739openalex-snapshot
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
inferredcites →https://doi.org/10.1109/tcbb.2007.1024openalex-snapshot
Multiple Graph Alignment for the Structural Analysis of Protein Active Sites
inferredcites →https://doi.org/10.1110/ps.0368703openalex-snapshot
Identification of protein biochemical functions by similarity search using the molecular surface database eF‐site
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Effiziente Algorithmen zur Musterentdeckung in strukturierten Objekten mit Anwendungen im strukturbasierten Wirkstoffdesign
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The Nuclear Receptor Ligand-Binding Domain: A Family-Based Structure Analysis

What points at this work

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

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Acceleration of Binding Site Comparisons by Graph Partitioning
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Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method
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Pillar[5]arene-Derived endo-Functionalized Molecular Tube for Mimicking Protein–Ligand Interactions
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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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Detecting Drug Promiscuity Using Gaussian Ensemble Screening
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Cavities Tell More than Sequences: Exploring Functional Relationships of Proteases via Binding Pockets
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GES Polypharmacology Fingerprints: A Novel Approach for Drug Repositioning
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Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real
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Protein Pockets: Inventory, Shape, and Comparison
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Identification of the First Inhibitor of the GBP1:PIM1 Interaction. Implications for the Development of a New Class of Anticancer Agents against Paclitaxel Resistant Cancer Cells
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Similar interactions of natural products with biosynthetic enzymes and therapeutic targets could explain why nature produces such a large proportion of existing drugs
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