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A novel approach to local similarity of protein binding sites substantially improves computational drug design results

https://doi.org/10.1002/prot.21487
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What this work says

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

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Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
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Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands
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Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites
inferredcites →https://doi.org/10.1002/prot.10026openalex-snapshot
Geometric and chemical patterns of interaction in protein–ligand complexes and their application in docking
inferredcites →https://doi.org/10.1002/prot.10115openalex-snapshot
Principles of docking: An overview of search algorithms and a guide to scoring functions
inferredcites →https://doi.org/10.1002/prot.10119openalex-snapshot
ConsDock: A new program for the consensus analysis of protein–ligand interactions
inferredcites →https://doi.org/10.1002/prot.10465openalex-snapshot
Improved protein–ligand docking using GOLD
inferredcites →https://doi.org/10.1002/prot.20149openalex-snapshot
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
inferredcites →https://doi.org/10.1006/jmbi.1994.1657openalex-snapshot
A Graph-theoretic Approach to the Identification of Three-dimensional Patterns of Amino Acid Side-chains in Protein Structures
inferredcites →https://doi.org/10.1006/jmbi.1995.0159openalex-snapshot
SCOP: A structural classification of proteins database for the investigation of sequences and structures
inferredcites →https://doi.org/10.1006/jmbi.1996.0477openalex-snapshot
A Fast Flexible Docking Method using an Incremental Construction Algorithm
inferredcites →https://doi.org/10.1007/s10822-005-0097-6openalex-snapshot
A very large diversity space of synthetically accessible compounds for use with drug design programs
inferredcites →https://doi.org/10.1016/j.bmcl.2005.03.068openalex-snapshot
Structure-based design of protein tyrosine phosphatase-1B inhibitors
inferredcites →https://doi.org/10.1016/j.cbpa.2003.11.001openalex-snapshot
Searching for functional sites in protein structures
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/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/s0022-2836(03)00045-7openalex-snapshot
A Model for Statistical Significance of Local Similarities in Structure
inferredcites →https://doi.org/10.1016/s0969-2126(98)00089-6openalex-snapshot
Protein folds and functions
inferredcites →https://doi.org/10.1016/s1074-5521(00)00104-6openalex-snapshot
Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator
inferredcites →https://doi.org/10.1016/s1367-5931(00)00217-9openalex-snapshot
High-throughput docking for lead generation
inferredcites →https://doi.org/10.1021/bi00010a003openalex-snapshot
Structures of Aromatic Inhibitors of Influenza Virus Neuraminidase
inferredcites →https://doi.org/10.1021/ci0503964openalex-snapshot
The Quest for Bioisosteric Replacements
inferredcites →https://doi.org/10.1021/ja038606lopenalex-snapshot
A Highly Potent Non-Nucleoside Adenosine Deaminase Inhibitor: Efficient Drug Discovery by Intentional Lead Hybridization
inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm020406hopenalex-snapshot
Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine
inferredcites →https://doi.org/10.1021/jm030161oopenalex-snapshot
Multiple Active Site Corrections for Docking and Virtual Screening
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm040015yopenalex-snapshot
SDOCKER: A Method Utilizing Existing X-ray Structures To Improve Docking Accuracy
inferredcites →https://doi.org/10.1023/a:1007907728892openalex-snapshot
QXP: Powerful, rapid computer algorithms for structure-based drug design
inferredcites →https://doi.org/10.1023/a:1008040531766openalex-snapshot
Combinatorial docking and combinatorial chemistry: Design of potent non-peptide thrombin inhibitors
inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
inferredcites →https://doi.org/10.1023/a:1020155510718openalex-snapshot
A review of protein-small molecule docking methods
inferredcites →https://doi.org/10.1023/a:1023866311551openalex-snapshot
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
inferredcites →https://doi.org/10.1023/b:jcam.0000005766.95985.7eopenalex-snapshot
A novel scoring function for molecular docking
inferredcites →https://doi.org/10.1023/b:jcam.0000046819.20241.16openalex-snapshot
PLASS: Protein-ligand affinity statistical score – a knowledge-based force-field model of interaction derived from the PDB
inferredcites →https://doi.org/10.1038/35093574openalex-snapshot
A tour of structural genomics
inferredcites →https://doi.org/10.1038/80784openalex-snapshot
From structure to function: approaches and limitations.
inferredcites →https://doi.org/10.1038/nature01256openalex-snapshot
The structure of the protein universe and genome evolution
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1093/bioinformatics/btg226openalex-snapshot
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis
inferredcites →https://doi.org/10.1093/bioinformatics/bti645openalex-snapshot
The SuMo server: 3D search for protein functional sites
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/28.1.254openalex-snapshot
The ASTRAL compendium for protein structure and sequence analysis
inferredcites →https://doi.org/10.1093/nar/gki482openalex-snapshot
SiteEngines: recognition and comparison of binding sites and protein-protein interfaces
inferredcites →https://doi.org/10.1107/s0108767389004678openalex-snapshot
Structural comparisons using restrained inhomogeneous transformations
inferredcites →https://doi.org/10.1110/ps.27401openalex-snapshot
The effect of substrate binding on the conformation and structural stability of Herpes simplex virus type 1 thymidine kinase
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms

What points at this work

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

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Pharmacophore inference and its application to computational drug discovery
inferred← citeshttps://doi.org/10.1002/minf.201300082openalex-snapshot
Identification of Similar Binding Sites to Detect Distant Polypharmacology
inferred← citeshttps://doi.org/10.1007/978-1-0716-4662-5_5openalex-snapshot
A Survey of Deep Learning Methods and Tools for Protein Binding Site Prediction
inferred← citeshttps://doi.org/10.1007/978-94-007-0881-5_8openalex-snapshot
Protein Binding Ligand Prediction Using Moments-Based Methods
inferred← citeshttps://doi.org/10.1016/j.drudis.2010.05.015openalex-snapshot
Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00601openalex-snapshot
Subpocket Similarity-Based Hit Identification for Challenging Targets: Application to the WDR Domain of LRRK2
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00158openalex-snapshot
Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c00422openalex-snapshot
A Computer Vision Approach to Align and Compare Protein Cavities: Application to Fragment-Based Drug Design
inferred← citeshttps://doi.org/10.1021/bk-2011-1076.ch005openalex-snapshot
A Computational Fragment Approach by Mining the Protein Data Bank: Library Design and Bioisosterism
inferred← citeshttps://doi.org/10.1021/ci3000776openalex-snapshot
Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement
inferred← citeshttps://doi.org/10.1021/ci8003094openalex-snapshot
Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity
inferred← citeshttps://doi.org/10.1093/bib/bbad390openalex-snapshot
Identifying local associations in biological time series: algorithms, statistical significance, and applications
inferred← citeshttps://doi.org/10.1093/bioinformatics/btp204openalex-snapshot
Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation
inferred← citeshttps://doi.org/10.1093/nar/gkt457openalex-snapshot
webPDBinder: a server for the identification of ligand binding sites on protein structures
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Maturation of the Translation Inhibitor Microcin C
inferred← citeshttps://doi.org/10.1134/s0026893314060028openalex-snapshot
NMR screening of potential inhibitors of methionine γ-lyase from Citrobacter freundii
inferred← citeshttps://doi.org/10.1186/1471-2105-13-s4-s17openalex-snapshot
Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities
inferred← citeshttps://doi.org/10.12691/ajmo-4-3-2openalex-snapshot
Docking and Ligand Binding Affinity: Uses and Pitfalls
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003554openalex-snapshot
Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine
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Analysis of HSP90-related folds with MED-SuMo classification approach
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Estimating the Similarity between Protein Pockets
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Exploiting Structural Information for Drug-Target Assessment
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Quantitative Structure-Activity Relationship Modeling and Bayesian Networks: Optimality of Naive Bayes Model
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