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SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation

Bioinformatics, 2019-02, Vol.35 (3), p.462-469

2019

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SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

Bioinformatics (Oxford, England), 2012-10, Vol.28 (20), p.2600-2607

2012

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Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

Journal of molecular biology, 2015-09, Vol.427 (19), p.3031-3041

2015

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SwarmDock: a server for flexible protein-protein docking

Bioinformatics, 2013-03, Vol.29 (6), p.807-809

2013

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Scoring functions for protein–protein interactions

Current opinion in structural biology, 2013-12, Vol.23 (6), p.862-867

2013

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

BMC bioinformatics, 2013-10, Vol.14 (1), p.286-286, Article 286

2013

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SwarmDock and the use of normal modes in protein-protein docking

International journal of molecular sciences, 2010-09, Vol.11 (10), p.3623-3648

2010

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Protein-protein binding affinity prediction on a diverse set of structures

Bioinformatics, 2011-11, Vol.27 (21), p.3002-3009

2011

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KA-Search, a method for rapid and exhaustive sequence identity search of known antibodies

Scientific reports, 2023-07, Vol.13 (1), p.11612-11612, Article 11612

2023

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A structure‐based benchmark for protein–protein binding affinity

Protein science, 2011-03, Vol.20 (3), p.482-491

2011

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CCharPPI web server: computational characterization of protein-protein interactions from structure

Bioinformatics (Oxford, England), 2015-01, Vol.31 (1), p.123-125

2015

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Kinetic rate constant prediction supports the conformational selection mechanism of protein binding

PLoS computational biology, 2012-01, Vol.8 (1), p.e1002351-e1002351

2012

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Detection and refinement of encounter complexes for protein-protein docking: Taking account of macromolecular crowding

Proteins, structure, function, and bioinformatics, 2010-11, Vol.78 (15), p.3189-3196

2010

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Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization

PLoS computational biology, 2013-09, Vol.9 (9), p.e1003216

2013

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A Markov-chain model description of binding funnels to enhance the ranking of docked solutions

Proteins, structure, function, and bioinformatics, 2013-12, Vol.81 (12), p.2143-2149

2013

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AbLang: an antibody language model for completing antibody sequences

Bioinformatics advances, 2022-01, Vol.2 (1), p.vbac046-vbac046

2022

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Intermolecular Contact Potentials for Protein–Protein Interactions Extracted from Binding Free Energy Changes upon Mutation

Journal of chemical theory and computation, 2013-08, Vol.9 (8), p.3715-3727

2013

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Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States

Molecular biology and evolution, 2019-09, Vol.36 (9), p.2086-2103

2019

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IRaPPA: information retrieval based integration of biophysical models for protein assembly selection

Bioinformatics (Oxford, England), 2017-06, Vol.33 (12), p.1806-1813

2017

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A systematic analysis of scoring functions in rigid‐body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining

Proteins, structure, function, and bioinformatics, 2017-07, Vol.85 (7), p.1287-1297

2017

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Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method

Journal of chemical theory and computation, 2017-03, Vol.13 (3), p.1401-1410

2017

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A Guide for Protein-Protein Docking Using SwarmDock

Methods in molecular biology (Clifton, N.J.), 2020-01, Vol.2165, p.199

2020

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Comment on 'protein-protein binding affinity prediction from amino acid sequence'

Bioinformatics (Oxford, England), 2015-02, Vol.31 (4), p.614-615

2015

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pyDock scoring for the new modeling challenges in docking: Protein–peptide, homo‐multimers, and domain–domain interactions

Proteins, structure, function, and bioinformatics, 2017-03, Vol.85 (3), p.487-496

2017

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Flexible Protein-Protein Docking with SwarmDock

Methods in molecular biology (Clifton, N.J.), 2018, Vol.1764, p.413

2018

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SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

SwarmDock: a server for flexible protein-protein docking

Scoring functions for protein–protein interactions

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

SwarmDock and the use of normal modes in protein-protein docking

Protein-protein binding affinity prediction on a diverse set of structures

KA-Search, a method for rapid and exhaustive sequence identity search of known antibodies

A structure‐based benchmark for protein–protein binding affinity

CCharPPI web server: computational characterization of protein-protein interactions from structure

Kinetic rate constant prediction supports the conformational selection mechanism of protein binding

Detection and refinement of encounter complexes for protein-protein docking: Taking account of macromolecular crowding

Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization

A Markov-chain model description of binding funnels to enhance the ranking of docked solutions

AbLang: an antibody language model for completing antibody sequences

Intermolecular Contact Potentials for Protein–Protein Interactions Extracted from Binding Free Energy Changes upon Mutation

Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection

A systematic analysis of scoring functions in rigid‐body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining

Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method

A Guide for Protein-Protein Docking Using SwarmDock

Comment on 'protein-protein binding affinity prediction from amino acid sequence'

pyDock scoring for the new modeling challenges in docking: Protein–peptide, homo‐multimers, and domain–domain interactions

Flexible Protein-Protein Docking with SwarmDock

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