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A simple reference state makes a significant improvement in near‐native selections from structurally refined docking decoys

https://doi.org/10.1002/prot.21498
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What this work says

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

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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex
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Effective energy function for proteins in solution
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Examination of shape complementarity in docking of Unbound proteins
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Protein docking using spherical polar Fourier correlations
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BiGGER: A new (soft) docking algorithm for predicting protein interactions
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Discriminating between homodimeric and monomeric proteins in the crystalline state
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Discriminating between homodimeric and monomeric proteins in the crystalline state
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DARWIN: A program for docking flexible molecules
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Residue frequencies and pairing preferences at protein-protein interfaces
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CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
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An all atom force field for simulations of proteins and nucleic acids
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Bayesian statistical analysis of protein side‐chain rotamer preferences
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Modeling of protein interactions in genomes
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Principles of docking: An overview of search algorithms and a guide to scoring functions
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Stability of macromolecular complexes
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Guided docking: First step to locate potential binding sites
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CAPRI: A Critical Assessment of PRedicted Interactions
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A soft docking algorithm for predicting the structure of antibody‐antigen complexes
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Protein–protein docking predictions for the CAPRI experiment
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Evaluation of the third solvent clusters fitting procedure for the prediction of protein–protein interactions based on the results at the CAPRI blind docking study
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ZDOCK: An initial‐stage protein‐docking algorithm
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A protein–protein docking benchmark
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Weighted geometric docking: Incorporating external information in the rotation‐translation scan
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Assessment of blind predictions of protein–protein interactions: Current status of docking methods
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RDOCK: Refinement of rigid‐body protein docking predictions
inferredcites →https://doi.org/10.1002/prot.10473openalex-snapshot
Combination of scoring functions improves discrimination in protein–protein docking
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Effective scoring function for protein sequence design
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Protein docking using a genetic algorithm
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A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding
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.20556openalex-snapshot
Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side‐chain flexibility
inferredcites →https://doi.org/10.1002/prot.20559openalex-snapshot
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
inferredcites →https://doi.org/10.1002/prot.20561openalex-snapshot
Approaching the CAPRI challenge with an efficient geometry‐based docking
inferredcites →https://doi.org/10.1002/prot.20573openalex-snapshot
Development and testing of an automated approach to protein docking
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
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Protein‐protein recognition analyzed by docking simulation
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Determination of atomic desolvation energies from the structures of crystallized proteins
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.1997.1519openalex-snapshot
Rapid refinement of protein interfaces incorporating solvation: application to the docking problem
inferredcites →https://doi.org/10.1006/jmbi.1998.2152openalex-snapshot
A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions
inferredcites →https://doi.org/10.1006/jmbi.1998.2401openalex-snapshot
Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton
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The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht
inferredcites →https://doi.org/10.1016/0022-2836(78)90302-9openalex-snapshot
Computer analysis of protein-protein interaction
inferredcites →https://doi.org/10.1016/j.sbi.2006.02.002openalex-snapshot
Flexible protein–protein docking
inferredcites →https://doi.org/10.1016/j.sbi.2006.03.003openalex-snapshot
High-resolution protein–protein docking
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/s0006-3495(03)74997-2openalex-snapshot
Development of Unified Statistical Potentials Describing Protein-Protein Interactions
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(02)00285-3openalex-snapshot
Prediction of protein–protein interactions by docking methods
inferredcites →https://doi.org/10.1016/s0959-440x(02)00286-5openalex-snapshot
Protein–protein association kinetics and protein docking
inferredcites →https://doi.org/10.1016/s0959-440x(03)00064-2openalex-snapshot
Genome-wide studies of protein–protein interaction
inferredcites →https://doi.org/10.1021/ja9621760openalex-snapshot
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
inferredcites →https://doi.org/10.1021/ja984102popenalex-snapshot
Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model
inferredcites →https://doi.org/10.1021/jp984217fopenalex-snapshot
The GROMOS Biomolecular Simulation Program Package
inferredcites →https://doi.org/10.1073/pnas.181147798openalex-snapshot
Protein docking along smooth association pathways
inferredcites →https://doi.org/10.1073/pnas.97.19.10383openalex-snapshot
Native protein sequences are close to optimal for their structures
inferredcites →https://doi.org/10.1093/bioinformatics/btl524openalex-snapshot
Inherent limitations in protein–protein docking procedures
inferredcites →https://doi.org/10.1093/proeng/gzg021openalex-snapshot
Effect of local shape modifications of molecular surfaces on rigid-body protein–protein docking
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.041222905openalex-snapshot
Improved side‐chain modeling for protein–protein docking
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.19202openalex-snapshot
Soft protein–protein docking in internal coordinates
inferredcites →https://doi.org/10.1110/ps.24902openalex-snapshot
Side‐chain modeling with an optimized scoring function
inferredcites →https://doi.org/10.1110/ps.2830102openalex-snapshot
Protein–protein docking with multiple residue conformations and residue substitutions
inferredcites →https://doi.org/10.1145/224170.224218openalex-snapshot
Surveying molecular interactions with DOT
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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Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase
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Current progress of immunoinformatics approach harnessed for cellular- and antibody-dependent vaccine design
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Additional file 1 of Identification and genetic characterization of a minor norovirus genotype, GIX.1[GII.P15], from China
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Additional file 2 of Identification and genetic characterization of a minor norovirus genotype, GIX.1[GII.P15], from China
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