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Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990515)35:3<364::aid-prot11>3.0.co;2-4openalex-snapshot
Use of pair potentials across protein interfaces in screening predicted docked complexes
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19991201)37:4<565::aid-prot7>3.0.co;2-vopenalex-snapshot
Hydrophobicity at the surface of proteins
inferredcites →https://doi.org/10.1002/(sici)1097-0134(20000601)39:4<372::aid-prot100>3.0.co;2-qopenalex-snapshot
BiGGER: A new (soft) docking algorithm for predicting protein interactions
inferredcites →https://doi.org/10.1002/1097-0134(20010101)42:1<108::aid-prot110>3.0.co;2-oopenalex-snapshot
Protein-protein interfaces: Analysis of amino acid conservation in homodimers
inferredcites →https://doi.org/10.1002/1097-0134(20010501)43:2<89::aid-prot1021>3.0.co;2-hopenalex-snapshot
Residue frequencies and pairing preferences at protein-protein interfaces
inferredcites →https://doi.org/10.1002/cbic.200300581openalex-snapshot
Conserved Amino Acid Residues Correlating With Ketoreductase Stereospecificity in Modular Polyketide Synthases
inferredcites →https://doi.org/10.1002/prot.10085openalex-snapshot
Dissecting protein–protein recognition sites
inferredcites →https://doi.org/10.1002/prot.10092openalex-snapshot
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
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.10389openalex-snapshot
ZDOCK: An initial‐stage protein‐docking algorithm
inferredcites →https://doi.org/10.1002/prot.10390openalex-snapshot
A protein–protein docking benchmark
inferredcites →https://doi.org/10.1002/prot.10473openalex-snapshot
Combination of scoring functions improves discrimination in protein–protein docking
inferredcites →https://doi.org/10.1002/prot.1070openalex-snapshot
Protein docking using a genetic algorithm
inferredcites →https://doi.org/10.1002/prot.20145openalex-snapshot
Hydrophobic complementarity in protein–protein docking
inferredcites →https://doi.org/10.1002/prot.20560openalex-snapshot
Protein–protein docking benchmark 2.0: An update
inferredcites →https://doi.org/10.1002/prot.20575openalex-snapshot
Improving CAPRI predictions: Optimized desolvation for rigid‐body docking
inferredcites →https://doi.org/10.1006/jmbi.1996.0634openalex-snapshot
Hydrogen Bonding and Molecular Surface Shape Complementarity as a Basis for Protein Docking
inferredcites →https://doi.org/10.1006/jmbi.1996.0859openalex-snapshot
Determination of atomic desolvation energies from the structures of crystallized proteins
inferredcites →https://doi.org/10.1006/jmbi.1996.0868openalex-snapshot
Novel knowledge-based mean force potential at atomic level
inferredcites →https://doi.org/10.1006/jmbi.1997.0987openalex-snapshot
Electrostatic complementarity at protein/protein interfaces 1 1Edited by B. Honig
inferredcites →https://doi.org/10.1006/jmbi.1997.1203openalex-snapshot
Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1006/jmbi.1997.1234openalex-snapshot
Analysis of protein-protein interaction sites using surface patches 1 1Edited by G.Von Heijne
inferredcites →https://doi.org/10.1006/jmbi.1998.2439openalex-snapshot
The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht
inferredcites →https://doi.org/10.1006/jmbi.2001.5075openalex-snapshot
Degenerate interfaces in antigen-antibody complexes
inferredcites →https://doi.org/10.1016/0022-2836(91)80222-gopenalex-snapshot
Protein docking and complementarity
inferredcites →https://doi.org/10.1016/0263-7855(95)00073-9openalex-snapshot
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
inferredcites →https://doi.org/10.1016/j.crvi.2004.03.006openalex-snapshot
On proteins, grids, correlations, and docking
inferredcites →https://doi.org/10.1016/j.jmb.2004.02.040openalex-snapshot
ProMate: A Structure Based Prediction Program to Identify the Location of Protein–Protein Binding Sites
inferredcites →https://doi.org/10.1016/j.sbi.2004.04.006openalex-snapshot
A structural perspective on protein–protein interactions
inferredcites →https://doi.org/10.1016/j.str.2004.04.009openalex-snapshot
Protein-Protein Interactions
inferredcites →https://doi.org/10.1016/j.tibtech.2004.01.006openalex-snapshot
Protein–protein docking: is the glass half-full or half-empty?
inferredcites →https://doi.org/10.1016/s0021-9258(17)46181-3openalex-snapshot
The structure of protein-protein recognition sites.
inferredcites →https://doi.org/10.1016/s0022-2836(02)00030-xopenalex-snapshot
On the Role of Electrostatic Interactions in the Design of Protein–Protein Interfaces
inferredcites →https://doi.org/10.1016/s0022-2836(03)00670-3openalex-snapshot
Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
inferredcites →https://doi.org/10.1016/s0959-440x(00)00065-8openalex-snapshot
Electrostatic aspects of protein–protein interactions
inferredcites →https://doi.org/10.1016/s0959-440x(02)00285-3openalex-snapshot
Prediction of protein–protein interactions by docking methods
inferredcites →https://doi.org/10.1016/s0959-440x(96)80061-3openalex-snapshot
Computational methods for biomolecular docking
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/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/jm0100279openalex-snapshot
Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System
inferredcites →https://doi.org/10.1073/pnas.0136888100openalex-snapshot
Insufficiently dehydrated hydrogen bonds as determinants of protein interactions
inferredcites →https://doi.org/10.1073/pnas.181147798openalex-snapshot
Protein docking along smooth association pathways
inferredcites →https://doi.org/10.1073/pnas.89.6.2195openalex-snapshot
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.
inferredcites →https://doi.org/10.1073/pnas.93.1.13openalex-snapshot
Principles of protein-protein interactions.
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/nar/gkh039openalex-snapshot
SCOP database in 2004: refinements integrate structure and sequence family data
inferredcites →https://doi.org/10.1093/proeng/gzg014openalex-snapshot
Flexibility analysis of enzyme active sites by crystallographic temperature factors
inferredcites →https://doi.org/10.1093/proeng/gzg035openalex-snapshot
A protein–protein docking algorithm dependent on the type of complexes
inferredcites →https://doi.org/10.1093/protein/14.2.105openalex-snapshot
Protein docking using continuum electrostatics and geometric fit
inferredcites →https://doi.org/10.1093/protein/gzh021openalex-snapshot
A novel method for scoring of docked protein complexes using predicted protein-protein binding sites
inferredcites →https://doi.org/10.1110/ps.0236203openalex-snapshot
Improved amino acid flexibility parameters
inferredcites →https://doi.org/10.1110/ps.03348304openalex-snapshot
An accurate, residue‐level, pair potential of mean force for folding and binding based on the distance‐scaled, ideal‐gas reference state
inferredcites →https://doi.org/10.1110/ps.041081905openalex-snapshot
Assessing predictions of protein–protein interaction: The CAPRI experiment
inferredcites →https://doi.org/10.1110/ps.12901openalex-snapshot
Electrostatic contributions to protein–protein interactions: Fast energetic filters for docking and their physical basis
inferredcites →https://doi.org/10.1110/ps.26002openalex-snapshot
Electrostatics in protein–protein docking
inferredcites →https://doi.org/10.1110/ps.2830102openalex-snapshot
Protein–protein docking with multiple residue conformations and residue substitutions
inferredcites →https://doi.org/10.1110/ps.8.3.603openalex-snapshot
Comparison of protein–protein interactions in serine protease‐inhibitor and antibody‐antigen complexes: Implications for the protein docking problem
inferredcites →https://doi.org/10.1142/s0219720005001429openalex-snapshot
A QUANTITATIVE ANALYSIS OF INTERFACIAL AMINO ACID CONSERVATION IN PROTEIN-PROTEIN HETERO COMPLEXES
inferredcites →https://doi.org/10.1529/biophysj.104.058768openalex-snapshot
Optimal Clustering for Detecting Near-Native Conformations in Protein Docking
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/ddr.20402openalex-snapshot
Applications of machine learning and computational intelligence to drug discovery and development
inferred← citeshttps://doi.org/10.1002/jcc.21837openalex-snapshot
PROCOS: Computational analysis of protein–protein complexes
inferred← citeshttps://doi.org/10.1002/pmic.201100217openalex-snapshot
Feature‐based classification of native and non‐native protein–protein interactions: Comparing supervised and semi‐supervised learning approaches
inferred← citeshttps://doi.org/10.1002/prot.22415openalex-snapshot
Automated site preparation in physics‐based rescoring of receptor ligand complexes
inferred← citeshttps://doi.org/10.1002/prot.22436openalex-snapshot
Combining interface core and whole interface descriptors in postscan processing of protein‐protein docking models
inferred← citeshttps://doi.org/10.1002/prot.22550openalex-snapshot
PIE—Efficient filters and coarse grained potentials for unbound protein–protein docking
inferred← citeshttps://doi.org/10.1002/prot.23223openalex-snapshot
Optimized grid‐based protein–protein docking as a global search tool followed by incorporating experimentally derivable restraints
inferred← citeshttps://doi.org/10.1002/prot.24314openalex-snapshot
Ranking multiple docking solutions based on the conservation of inter‐residue contacts
inferred← citeshttps://doi.org/10.1002/prot.24370openalex-snapshot
DockRank: Ranking docked conformations using partner‐specific sequence homology‐based protein interface prediction
inferred← citeshttps://doi.org/10.1002/prot.24479openalex-snapshot
PAIRpred: Partner‐specific prediction of interacting residues from sequence and structure
inferred← citeshttps://doi.org/10.1007/s10930-021-10031-8openalex-snapshot
Protein–Protein Docking: Past, Present, and Future
inferred← citeshttps://doi.org/10.1016/j.sbi.2010.02.001openalex-snapshot
Accounting for conformational changes during protein–protein docking
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00336openalex-snapshot
Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue
inferred← citeshttps://doi.org/10.1021/ci100490wopenalex-snapshot
Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation
inferred← citeshttps://doi.org/10.1021/ct400508sopenalex-snapshot
Protein–Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes
inferred← citeshttps://doi.org/10.1109/bibm.2010.5706560openalex-snapshot
An accurate classification of native and non-native protein-protein interactions using supervised and semi-supervised learning approaches
inferred← citeshttps://doi.org/10.1371/journal.pone.0017695openalex-snapshot
CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK
inferred← citeshttps://doi.org/10.2174/157340909787580863openalex-snapshot
Computational Intelligence Methods for Docking Scores
inferred← citeshttps://doi.org/10.31274/etd-180810-4308openalex-snapshot
Sequence homology based protein-protein interacting residue predictions and the applications in ranking docked conformations
inferred← citeshttps://doi.org/10.32469/10355/37826openalex-snapshot
Understanding structure, function, and evolution of protein-protein interactions by computational modeling and analysis
inferred← citeshttps://doi.org/10.3762/bjoc.12.267openalex-snapshot
Computational methods in drug discovery
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