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A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing

https://doi.org/10.1002/prot.26176
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What this work says

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

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The Hungarian method for the assignment problem
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Structure-based computational analysis of protein binding sites for function and druggability prediction
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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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Binding site comparison for function prediction and pharmaceutical discovery
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Novel function discovery through sequence and structural data mining
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Evolutionary studies of ligand binding sites in proteins
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CATH – a hierarchic classification of protein domain structures
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DeeplyTough: Learning Structural Comparison of Protein Binding Sites
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Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach
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Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design
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Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe
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Pocket Similarity: Are α Carbons Enough?
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Fast Protein Binding Site Comparison via an Index-Based Screening Technology
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Cavities Tell More than Sequences: Exploring Functional Relationships of Proteases via Binding Pockets
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Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family
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Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein−Ligand Binding Sites
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The PDBbind Database: Methodologies and Updates
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The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery
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Structure to function of an α-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis
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Binding site characterization – similarity, promiscuity, and druggability
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FDA Approval of Remdesivir — A Step in the Right Direction
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Detecting evolutionary relationships across existing fold space, using sequence order-independent profile–profile alignments
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Fast screening of protein surfaces using geometric invariant fingerprints
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Structural basis for efficient phosphorylation of 3′-azidothymidine monophosphate by Escherichia coli thymidylate kinase
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High Resolution Structure of the Phosphohistidine-activated Form of Escherichia coli Cofactor-dependent Phosphoglycerate Mutase
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Rigid substructure search
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APoc: large-scale identification of similar protein pockets
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A Simplex Method for Function Minimization
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SCOP: a Structural Classification of Proteins database
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
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TM-align: a protein structure alignment algorithm based on the TM-score
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The Pfam protein families database
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SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison
inferredcites →https://doi.org/10.1093/nar/gku928openalex-snapshot
sc-PDB: a 3D-database of ligandable binding sites—10 years on
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KEGG as a reference resource for gene and protein annotation
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/10.1093/protein/13.3.149openalex-snapshot
Simplified amino acid alphabets for protein fold recognition and implications for folding
inferredcites →https://doi.org/10.1103/physreve.75.011920openalex-snapshot
Amino acid hydrophobicity and accessible surface area
inferredcites →https://doi.org/10.1126/science.abb4489openalex-snapshot
Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease
inferredcites →https://doi.org/10.1126/science.abc1560openalex-snapshot
Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir
inferredcites →https://doi.org/10.1137/s003614450242889openalex-snapshot
Optimization by Direct Search: New Perspectives on Some Classical and Modern Methods
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/10.1186/1471-2105-9-543openalex-snapshot
PocketMatch: A new algorithm to compare binding sites in protein structures
inferredcites →https://doi.org/10.1186/s12859-018-2109-2openalex-snapshot
Comparative assessment of strategies to identify similar ligand-binding pockets in proteins
inferredcites →https://doi.org/10.1186/s13321-015-0091-5openalex-snapshot
A fast topological analysis algorithm for large-scale similarity evaluations of ligands and binding pockets
inferredcites →https://doi.org/10.1186/s13321-016-0180-0openalex-snapshot
Mapping the 3D structures of small molecule binding sites
inferredcites →https://doi.org/10.1371/journal.pcbi.1003341openalex-snapshot
Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison
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Providing data science support for systems pharmacology and its implications to drug discovery
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.

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SiteMine: Large‐scale binding site similarity searching in protein structure databases
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Artificial Intelligence in Pharmaceutical Sciences
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SiteContext: A Web Server for Protein Binding Site Comparison
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MeCOM: A Method for Comparing Three-Dimensional Metalloenzyme Active Sites
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MAI-TargetFisher: A proteome-wide drug target prediction method synergetically enhanced by artificial intelligence and physical modeling
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Relating SARS-CoV-2 variants using cellular automata imaging
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Machine Learning for the Identification of Viral Attachment Machinery from Respiratory Virus Sequences
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CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction
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Method development for potential drug target identification and drug discovery
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Machine learning for the identification of respiratory viral attachment machinery from sequences data
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Relating SARS-CoV-2 Variants Using Cellular Automata Imaging
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A New Strategy for Multitarget Drug Discovery/Repositioning Through the Identification of Similar 3D Amino Acid Patterns Among Proteins Structures: The Case of Tafluprost and its Effects on Cardiac Ion Channels
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Estimating the Similarity between Protein Pockets
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Applications of Artificial Intelligence in Drug Target Discovery
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