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Sampling and scoring: A marriage made in heaven

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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)1097-0282(199609)39:3<455::aid-bip16>3.0.co;2-aopenalex-snapshot

Low-resolution docking: Prediction of complexes for underdetermined structures

inferredcites →https://doi.org/10.1002/1097-0134(20000815)40:3<525::aid-prot190>3.0.co;2-fopenalex-snapshot

Scoring docked conformations generated by rigid-body protein-protein docking

inferredcites →https://doi.org/10.1002/jcc.10124openalex-snapshot

MOPED: Method for optimizing physical energy parameters using decoys

inferredcites →https://doi.org/10.1002/jcc.21545openalex-snapshot

SKATE: A docking program that decouples systematic sampling from scoring

inferredcites →https://doi.org/10.1002/jcc.21604openalex-snapshot

A large decoy set of protein–protein complexes produced by flexible docking

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/prot.10171openalex-snapshot

Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all‐atom force field and the surface generalized born solvent model

inferredcites →https://doi.org/10.1002/prot.10381openalex-snapshot

CAPRI: A Critical Assessment of PRedicted Interactions

inferredcites →https://doi.org/10.1002/prot.10383openalex-snapshot

ICM‐DISCO docking by global energy optimization with fully flexible side‐chains

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.10454openalex-snapshot

An improved protein decoy set for testing energy functions for protein structure prediction

inferredcites →https://doi.org/10.1002/prot.10460openalex-snapshot

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

inferredcites →https://doi.org/10.1002/prot.10613openalex-snapshot

A hierarchical approach to all‐atom protein loop 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.20560openalex-snapshot

Protein–protein docking benchmark 2.0: An update

inferredcites →https://doi.org/10.1002/prot.20562openalex-snapshot

Geometry‐based flexible and symmetric 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

inferredcites →https://doi.org/10.1002/prot.20859openalex-snapshot

Optimal design of protein docking potentials: Efficiency and limitations

inferredcites →https://doi.org/10.1002/prot.21117openalex-snapshot

PIPER: An FFT‐based protein docking program with pairwise potentials

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.21495openalex-snapshot

FireDock: Fast interaction refinement in molecular docking

inferredcites →https://doi.org/10.1002/prot.21502openalex-snapshot

Integrating statistical pair potentials into protein complex prediction

inferredcites →https://doi.org/10.1002/prot.21795openalex-snapshot

ClusPro: Performance in CAPRI rounds 6–11 and the new server

inferredcites →https://doi.org/10.1002/prot.21804openalex-snapshot

Docking and scoring protein complexes: CAPRI 3rd Edition

inferredcites →https://doi.org/10.1002/prot.21949openalex-snapshot

An iterative knowledge‐based scoring function for protein–protein recognition

inferredcites →https://doi.org/10.1002/prot.21997openalex-snapshot

Discrimination of near‐native structures in protein–protein docking by testing the stability of local minima

inferredcites →https://doi.org/10.1002/prot.22106openalex-snapshot

Protein–protein docking benchmark version 3.0

inferredcites →https://doi.org/10.1002/prot.22170openalex-snapshot

Principles of flexible protein–protein docking

inferredcites →https://doi.org/10.1002/prot.22252openalex-snapshot

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

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.22818openalex-snapshot

Docking and scoring protein interactions: CAPRI 2009

inferredcites →https://doi.org/10.1002/prot.22830openalex-snapshot

Protein–protein docking benchmark version 4.0

inferredcites →https://doi.org/10.1006/jmbi.1996.0256openalex-snapshot

Energy Functions that Discriminate X-ray and Near-native Folds from Well-constructed Decoys

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.1998.2439openalex-snapshot

The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht

inferredcites →https://doi.org/10.1007/s00894-010-0758-9openalex-snapshot

dockYard–a repository to assist modeling of protein-protein docking

inferredcites →https://doi.org/10.1016/0022-2836(91)80222-gopenalex-snapshot

Protein docking and complementarity

inferredcites →https://doi.org/10.1016/j.sbi.2009.02.008openalex-snapshot

Convergence and combination of methods in protein–protein docking

inferredcites →https://doi.org/10.1016/j.str.2006.11.010openalex-snapshot

All-Atom Ab Initio Folding of a Diverse Set of Proteins

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/s0076-6879(04)83004-0openalex-snapshot

Protein Structure Prediction Using Rosetta

inferredcites →https://doi.org/10.1016/s0959-440x(02)00285-3openalex-snapshot

Prediction of protein–protein interactions by docking methods

inferredcites →https://doi.org/10.1063/1.3615722openalex-snapshot

Energy design for protein-protein interactions

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/10.1093/bioinformatics/btg371openalex-snapshot

ClusPro: an automated docking and discrimination method for the prediction of protein complexes

inferredcites →https://doi.org/10.1093/bioinformatics/btn497openalex-snapshot

D ockground protein–protein docking decoy set

inferredcites →https://doi.org/10.1093/bioinformatics/bts493openalex-snapshot

Application of asymmetric statistical potentials to antibody–protein docking

inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot

The Protein Data Bank

inferredcites →https://doi.org/10.1093/nar/gkg460openalex-snapshot

Comparative protein structure modeling by iterative alignment, model building and model assessment

inferredcites →https://doi.org/10.1093/nar/gki481openalex-snapshot

PatchDock and SymmDock: servers for rigid and symmetric docking

inferredcites →https://doi.org/10.1093/nar/gkl206openalex-snapshot

GRAMM-X public web server for protein-protein docking

inferredcites →https://doi.org/10.1110/ps.9.7.1399openalex-snapshot

Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction

inferredcites →https://doi.org/10.1371/journal.pone.0015386openalex-snapshot

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

inferredcites →https://doi.org/10.1385/1-59259-368-2:399openalex-snapshot

Protein-Protein Docking: Generation and Filtering of Complexes

inferredcites →https://doi.org/10.1529/biophysj.104.058768openalex-snapshot

Optimal Clustering for Detecting Near-Native Conformations in Protein Docking

inferredcites →https://doi.org/10.1529/biophysj.108.135814openalex-snapshot

DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking

inferredcites →https://doi.org/10.2174/138920308783565741openalex-snapshot

Recent Progress and Future Directions in Protein-Protein Docking

What points at this work

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

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Computational Methods for Protein–Protein Interactions

inferred← citeshttps://doi.org/10.1002/jcc.23513openalex-snapshot

Efficient computation of root mean square deviations under rigid transformations

inferred← citeshttps://doi.org/10.1002/jcc.24273openalex-snapshot

Focused grid‐based resampling for protein docking and mapping

inferred← citeshttps://doi.org/10.1002/jcc.24795openalex-snapshot

Fast and accurate grid representations for atom‐based docking with partner flexibility

inferred← citeshttps://doi.org/10.1002/jcc.25797openalex-snapshot

Modeling large protein–glycosaminoglycan complexes using a fragment‐based approach

inferred← citeshttps://doi.org/10.1002/jmr.2471openalex-snapshot

Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

inferred← citeshttps://doi.org/10.1002/prot.24403openalex-snapshot

How good is automated protein docking?

inferred← citeshttps://doi.org/10.1002/prot.24678openalex-snapshot

Score_set: A CAPRI benchmark for scoring protein complexes

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A machine learning approach for ranking clusters of docked protein‐protein complexes by pairwise cluster comparison

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New additions to the C lus P ro server motivated by CAPRI

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Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking

inferred← citeshttps://doi.org/10.1002/prot.25874openalex-snapshot

Challenges and opportunities of automated protein‐protein docking: HDOCK server vs human predictions in CAPRI Rounds 38‐46

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Application of docking methodologies to modeled proteins

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Refinement of pairwise potentials via logistic regression to score protein‐protein interactions

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Rigid-Docking Approaches to Explore Protein–Protein Interaction Space

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A Guide for Protein–Protein Docking Using SwarmDock

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Flexible Protein-Protein Docking with SwarmDock

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Approaching Pharmacological Space: Events and Components

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Antibody Affinity Maturation by Computational Design

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Docking and Pharmacophore Modelling for Virtual Screening

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Protein-Protein Docking: From Interaction to Interactome

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EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks

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Search strategies and evaluation in protein–protein docking: principles, advances and challenges

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Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking

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Challenges in structural approaches to cell modeling

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Computational Modeling of Designed Ankyrin Repeat Protein Complexes with Their Targets

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Computational modeling of RNA 3D structures and interactions

inferred← citeshttps://doi.org/10.1016/j.sbi.2018.12.010openalex-snapshot

What method to use for protein–protein docking?

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Advances to tackle backbone flexibility in protein docking

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SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes

inferred← citeshttps://doi.org/10.1016/j.ymeth.2013.09.014openalex-snapshot

Computational modeling of protein–RNA complex structures

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00078openalex-snapshot

FlexAID: Revisiting Docking on Non-Native-Complex Structures

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00082openalex-snapshot

ProPairs: A Data Set for Protein–Protein Docking

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AF3Score: A Score-Only Adaptation of AlphaFold3 for Biomolecular Structure Evaluation

inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01765openalex-snapshot

Sampling and Ranking of Protein Conformations Using Machine Learning Techniques Do Not Improve the Quality of Rigid Protein–Protein Docking

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00445openalex-snapshot

CoDockPP: A Multistage Approach for Global and Site-Specific Protein–Protein Docking

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GroScore: Accurate Scoring of Protein–Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations

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Baseline Comparisons of Complementary Sampling Methods for Assembly Driven by Short-Ranged Pair Potentials toward Fast and Flexible Hybridization

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Evaluation of protein–RNA Docking Web Servers for Template-Free Docking and Comparison with the AlphaFold Server

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Evaluation of Predicted Protein–Protein Complexes by Binding Free Energy Simulations

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Insights into the Architecture of the eIF2Bα/β/δ Regulatory Subcomplex

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The HDOCK server for integrated protein–protein docking

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Integrated structure prediction of protein–protein docking with experimental restraints using ColabDock

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Properties that rank protein:protein docking poses with high accuracy

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Protein–protein interactions of human glyoxalase II: findings of a reliable docking protocol

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Evaluation of DNA–protein complex structures using the deep learning method

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Protein–protein docking with interface residue restraints*

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Differentiation of RNA–protein docking structures through molecular dynamics simulation and machine learning methods

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PIQLE: protein–protein interface quality estimation by deep graph learning of multimeric interaction geometries

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DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes

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3DRobot: automated generation of diverse and well-packed protein structure decoys

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HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

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ColabDock: inverting AlphaFold structure prediction model for protein-protein docking with experimental restraints

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Bayesian Occam’s Razor to Optimize Metamodeling for Complex Biological Systems

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Progress and Research Trends of Artificial Intelligence Incorporation in Protein Structure Prediction

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Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors

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The scoring of poses in protein-protein docking: current capabilities and future directions

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Simulated unbound structures for benchmarking of protein docking in the Dockground resource

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Pushing the accuracy limit of shape complementarity for protein-protein docking

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In silico formulation of a next-generation multiepitope vaccine for use as a prophylactic candidate against Crimean-Congo hemorrhagic fever

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Computing the Dynamic Supramolecular Structural Proteome

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Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking

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Development of a potential vaccine against Capripox virus implementing reverse vaccinology and pan-genomic immunoinformatics

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Machine Learning and Artificial Intelligence: A Paradigm Shift in Big Data-Driven Drug Design and Discovery

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De novo Molecular Design using Deep Learning

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Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes

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Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design

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Molecular Simulations of Disulfide-Rich Venom Peptides with Ion Channels and Membranes

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Molecular Docking at a Glance

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Molecular Docking at a Glance

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Additional file 1 of In silico formulation of a next-generation multiepitope vaccine for use as a prophylactic candidate against Crimean-Congo hemorrhagic fever

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Développement de méthodologies innovantes pour la caractérisation d’interfaces protéine-protéine et la conception d’inhibiteurs spécifiques : exploration de l’interface protéique de RhoA /ArhGEF1

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Nouvelles méthodes de calcul pour la prédiction des interactions protéine-protéine au niveau structural

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Caractérisation structurale de la liaison de l'ARN aux domaines à Motif de Reconnaissance de l'ARN (RRM) à l'aide de l'intégration de données, la modélisation 3D et la simulation dynamique moléculaire

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Fragment-based modelling of protein-RNA complexes for protein design

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