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Consensus scoring for enriching near‐native structures from protein–protein docking decoys

https://doi.org/10.1002/prot.22252
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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/prot.10389openalex-snapshot
ZDOCK: An initial‐stage protein‐docking algorithm
inferredcites →https://doi.org/10.1002/prot.1099openalex-snapshot
Prediction of protein interaction sites from sequence profile and residue neighbor list
inferredcites →https://doi.org/10.1002/prot.20238openalex-snapshot
Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores
inferredcites →https://doi.org/10.1002/prot.20551openalex-snapshot
Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
inferredcites →https://doi.org/10.1002/prot.20560openalex-snapshot
Protein–protein docking benchmark 2.0: An update
inferredcites →https://doi.org/10.1002/prot.20570openalex-snapshot
Scoring docking models with evolutionary information
inferredcites →https://doi.org/10.1002/prot.20576openalex-snapshot
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
inferredcites →https://doi.org/10.1002/prot.20634openalex-snapshot
Refinement of unbound protein docking studies using biological knowledge
inferredcites →https://doi.org/10.1002/prot.20842openalex-snapshot
WHISCY: What information does surface conservation yield? Application to data‐driven docking
inferredcites →https://doi.org/10.1002/prot.21373openalex-snapshot
ZRANK: Reranking protein docking predictions with an optimized energy function
inferredcites →https://doi.org/10.1002/prot.21498openalex-snapshot
A simple reference state makes a significant improvement in near‐native selections from structurally refined docking decoys
inferredcites →https://doi.org/10.1002/prot.21502openalex-snapshot
Integrating statistical pair potentials into protein complex prediction
inferredcites →https://doi.org/10.1002/prot.21804openalex-snapshot
Docking and scoring protein complexes: CAPRI 3rd Edition
inferredcites →https://doi.org/10.1006/jmbi.1997.1233openalex-snapshot
Prediction of protein-protein interaction sites using patch analysis 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.2001.4870openalex-snapshot
Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein 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.jmb.2006.01.001openalex-snapshot
Efficient Restraints for Protein–Protein Docking by Comparison of Observed Amino Acid Substitution Patterns with those Predicted from Local Environment
inferredcites →https://doi.org/10.1016/j.sbi.2006.03.003openalex-snapshot
High-resolution protein–protein docking
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/10.1073/pnas.89.22.10915openalex-snapshot
Amino acid substitution matrices from protein blocks.
inferredcites →https://doi.org/10.1093/bioinformatics/btg371openalex-snapshot
ClusPro: an automated docking and discrimination method for the prediction of protein complexes
inferredcites →https://doi.org/10.1093/bioinformatics/btm323openalex-snapshot
Interaction-site prediction for protein complexes: a critical assessment
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/gkl454openalex-snapshot
Protein binding site prediction using an empirical scoring function
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.04941505openalex-snapshot
Physicochemical and residue conservation calculations to improve the ranking of protein–protein docking solutions

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9781394167258.ch9openalex-snapshot
Protein Redesign and Engineering Using Machine Learning
inferred← citeshttps://doi.org/10.1002/cpch.27openalex-snapshot
Overview of Methods and Strategies for Conducting Virtual Small Molecule Screening
inferred← citeshttps://doi.org/10.1002/jcc.25874openalex-snapshot
GalaxyTongDock: Symmetric and asymmetric ab initio protein–protein docking web server with improved energy parameters
inferred← citeshttps://doi.org/10.1002/jmr.1165openalex-snapshot
Scoring optimisation of unbound protein–protein docking including protein binding site predictions
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
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Sampling and scoring: A marriage made in heaven
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Solvent‐accessible surface area: How well can be applied to hot‐spot detection?
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Prediction of protein oligomer structures using GALAXY in CASP13
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Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38‐45
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Modeling Protein Complexes and Molecular Assemblies Using Computational Methods
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Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties
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Protein Structure Prediction
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A comparative study of AutoDock and PMF scoring performances, and SAR of 2-substituted pyrazolotriazolopyrimidines and 4-substituted pyrazolopyrimidines as potent xanthine oxidase inhibitors
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Drug Repurposing and Multi-Target Therapies
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Current applications of biomolecules in artificial intelligence and machine learning
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A deep attention model for wide-genome protein-peptide binding affinity prediction at a sequence level
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Accounting for conformational changes during protein–protein docking
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HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes
inferred← citeshttps://doi.org/10.1021/acs.jproteome.2c00020openalex-snapshot
PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein–Peptide and Protein–Protein Binding Affinity
inferred← citeshttps://doi.org/10.1021/ci100353eopenalex-snapshot
Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein−Protein Docking
inferred← citeshttps://doi.org/10.1039/c8mo00089aopenalex-snapshot
PredCSO: an ensemble method for the prediction of S-sulfenylation sites in proteins
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Boosting Prediction Performance of Protein–Protein Interaction Hot Spots by Using Structural Neighborhood Properties
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx822openalex-snapshot
Computational identification of binding energy hot spots in protein–RNA complexes using an ensemble approach
inferred← citeshttps://doi.org/10.1093/nar/gkr317openalex-snapshot
PRUNE and PROBE--two modular web services for protein-protein docking
inferred← citeshttps://doi.org/10.1101/617506openalex-snapshot
DeepInterface: Protein-protein interface validation using 3D Convolutional Neural Networks
inferred← citeshttps://doi.org/10.1186/s12859-015-0572-6openalex-snapshot
DOCKSCORE: a webserver for ranking protein-protein docked poses
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Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach
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Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions
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CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK
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Prediction of Ligand Binding Using an Approach Designed to Accommodate Diversity in Protein-Ligand Interactions
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Accurate prediction of functional effects for variants by combining gradient tree boosting with optimal neighborhood properties
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Thorough Assessment of Machine Learning Techniques for Predicting Protein-Nucleic Acid Binding Hot Spots
inferred← citeshttps://doi.org/10.3389/fmolb.2020.559005openalex-snapshot
Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein–Protein Docking Poses
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XGBPRH: Prediction of Binding Hot Spots at Protein–RNA Interfaces Utilizing Extreme Gradient Boosting
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Machine Learning Approaches for Protein–Protein Interaction Hot Spot Prediction: Progress and Comparative Assessment
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Flexible Protein-Protein Docking
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