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Native fold and docking pose discrimination by the same residue‐based scoring function

https://doi.org/10.1002/prot.24764
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What this work says

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

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Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
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Effective energy function for proteins in solution
inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot
CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
inferredcites →https://doi.org/10.1002/pmic.200700739openalex-snapshot
Monitoring the interference of protein‐protein interactions in vivo by bimolecular fluorescence complementation: the DnaK case
inferredcites →https://doi.org/10.1002/pro.687openalex-snapshot
Integrating atom‐based and residue‐based scoring functions for protein–protein docking
inferredcites →https://doi.org/10.1002/prot.10286openalex-snapshot
Structure validation by Cα geometry: ϕ,ψ and Cβ deviation
inferredcites →https://doi.org/10.1002/prot.10381openalex-snapshot
CAPRI: A Critical Assessment of PRedicted Interactions
inferredcites →https://doi.org/10.1002/prot.10454openalex-snapshot
An improved protein decoy set for testing energy functions for protein structure prediction
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.21373openalex-snapshot
ZRANK: Reranking protein docking predictions with an optimized energy function
inferredcites →https://doi.org/10.1002/prot.21419openalex-snapshot
pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking
inferredcites →https://doi.org/10.1002/prot.21495openalex-snapshot
FireDock: Fast interaction refinement in molecular docking
inferredcites →https://doi.org/10.1002/prot.21715openalex-snapshot
QMEAN: A comprehensive scoring function for model quality assessment
inferredcites →https://doi.org/10.1002/prot.22534openalex-snapshot
Evaluation of CASP8 model quality predictions
inferredcites →https://doi.org/10.1002/prot.22550openalex-snapshot
PIE—Efficient filters and coarse grained potentials for unbound protein–protein docking
inferredcites →https://doi.org/10.1002/prot.22830openalex-snapshot
Protein–protein docking benchmark version 4.0
inferredcites →https://doi.org/10.1002/prot.22831openalex-snapshot
Protein–protein docking with binding site patch prediction and network‐based terms enhanced combinatorial scoring
inferredcites →https://doi.org/10.1002/prot.24214openalex-snapshot
Improving ranking of models for protein complexes with side chain modeling and atomic potentials
inferredcites →https://doi.org/10.1016/j.cpc.2013.07.019openalex-snapshot
BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures
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/10.1021/ja00214a001openalex-snapshot
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1021/jp2120143openalex-snapshot
Combining Statistical Potentials with Dynamics-Based Entropies Improves Selection from Protein Decoys and Docking Poses
inferredcites →https://doi.org/10.1038/340245a0openalex-snapshot
A novel genetic system to detect protein–protein interactions
inferredcites →https://doi.org/10.1038/srep00351openalex-snapshot
A simple and efficient statistical potential for scoring ensembles of protein structures
inferredcites →https://doi.org/10.1093/bioinformatics/btq662openalex-snapshot
Toward the estimation of the absolute quality of individual protein structure models
inferredcites →https://doi.org/10.1093/bioinformatics/bts628openalex-snapshot
A method for integrative structure determination of protein-protein complexes
inferredcites →https://doi.org/10.1093/nar/gku399openalex-snapshot
PASTA 2.0: an improved server for protein aggregation prediction
inferredcites →https://doi.org/10.1186/1471-2105-11-128openalex-snapshot
New statistical potential for quality assessment of protein models and a survey of energy functions
inferredcites →https://doi.org/10.1186/1471-2105-9-40openalex-snapshot
I-TASSER server for protein 3D structure prediction
inferredcites →https://doi.org/10.1186/1472-6807-9-35openalex-snapshot
QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information
inferredcites →https://doi.org/10.1371/journal.pcbi.0020170openalex-snapshot
Insight into the Structure of Amyloid Fibrils from the Analysis of Globular Proteins
inferredcites →https://doi.org/10.1371/journal.pcbi.1000191openalex-snapshot
Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes
inferredcites →https://doi.org/10.1371/journal.pone.0024657openalex-snapshot
Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

What points at this work

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

inferred← citeshttps://doi.org/10.1002/prot.25079openalex-snapshot
Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses
inferred← citeshttps://doi.org/10.1002/prot.25454openalex-snapshot
Vibrational entropy estimation can improve binding affinity prediction for non‐obligatory protein complexes
inferred← citeshttps://doi.org/10.1007/10_2016_41openalex-snapshot
Rigid-Docking Approaches to Explore Protein–Protein Interaction Space
inferred← citeshttps://doi.org/10.1007/978-1-0716-2609-2_19openalex-snapshot
Antibody Affinity Maturation Using Computational Methods: From an Initial Hit to Small-Scale Expression of Optimized Binders
inferred← citeshttps://doi.org/10.1007/978-1-0716-2974-1_2openalex-snapshot
Illuminating the “Twilight Zone”: Advances in Difficult Protein Modeling
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2023.107819openalex-snapshot
Replica-exchange optimization of antibody fragments
inferred← citeshttps://doi.org/10.1016/j.cpc.2020.107716openalex-snapshot
PARCE: Protocol for Amino acid Refinement through Computational Evolution
inferred← citeshttps://doi.org/10.1016/j.csbj.2023.02.031openalex-snapshot
Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 of Paracoccidioides brasiliensis as a benchmark study
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00403openalex-snapshot
Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c01225openalex-snapshot
Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔG Predictions
inferred← citeshttps://doi.org/10.1039/c7cp08116bopenalex-snapshot
Binding affinity prediction of nanobody–protein complexes by scoring of molecular dynamics trajectories
inferred← citeshttps://doi.org/10.1039/c7cp08170gopenalex-snapshot
Toward a unified scoring function for native state discrimination and drug-binding pocket recognition
inferred← citeshttps://doi.org/10.1039/c9cc06182gopenalex-snapshot
A consensus protocol for the in silico optimisation of antibody fragments
inferred← citeshttps://doi.org/10.1101/2021.12.13.472521openalex-snapshot
Sequence based prediction of protein phase separation into disordered condensates using machine learning
inferred← citeshttps://doi.org/10.1371/journal.pone.0254969openalex-snapshot
Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules
inferred← citeshttps://doi.org/10.21203/rs.3.rs-267481/v1openalex-snapshot
Statistical Potentials from the Gaussian Scaling Behaviour of Chain Fragments Buried within Protein Globules
inferred← citeshttps://doi.org/10.26226/morressier.616e5c2462ba8657678b1405openalex-snapshot
PARCE: Protocol for Amino acid Refinement through Computational Evolution
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