Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2

Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, +10

Journal of Computer-Aided Molecular Design

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Marc F. Lensink, Guillaume Brysbaert, Nurul Nadzirin, +102

Proteins Structure Function and Bioinformatics

Structural BioinformaticsBiomolecular Structure PredictionMolecular BiologyCapri Round 46Protein Folding +14

LightDock: a new multi-scale approach to protein–protein docking

Brian Jiménez‐García, Jorge Roel‐Touris, Miguel Romero‐Durana, +3

Bioinformatics

Protein AssemblyMolecular BiologyAnalytical UltracentrifugationBioinformatics OnlineNew Multi-scale Approach +14

Prediction of protein assemblies, the next frontier: The <scp>CASP14‐CAPRI</scp> experiment

Marc F. Lensink, Guillaume Brysbaert, Théo Mauri, +106

Proteins Structure Function and Bioinformatics

Finding the ΔΔ<i>G</i> spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?

Cunliang Geng, Li C. Xue, Jorge Roel‐Touris, +1

Wiley Interdisciplinary Reviews Computational Molecular Science

Protein–protein InteractionsEngineeringMachine LearningMolecular BiologyAre Predictors +21

Modeling Antibody-Antigen Complexes by Information-Driven Docking

Francesco Ambrosetti, Brian Jiménez‐García, Jorge Roel‐Touris, +1

Structure

Molecular DockingEngineeringMedicineComputational BiologyImmunology +5

Impact of <scp>AlphaFold</scp> on structure prediction of protein complexes: The <scp>CASP15‐CAPRI</scp> experiment

Marc F. Lensink, Guillaume Brysbaert, Nessim Raouraoua, +109

Proteins Structure Function and Bioinformatics

The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota

Victòria Andreu, Jorge Roel‐Touris, Dylan Dodd, +2

Nucleic Acids Research

De novo design of immunoglobulin-like domains

Tamuka M. Chidyausiku, Soraia R. Mendes, Jason C. Klima, +11

Nature Communications

Protein AssemblyImmunologyMolecular BiologyPeptide ScienceImmunoglobulin-like Domains +20

Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK

Jorge Roel‐Touris, Charleen G. Don, Rodrigo V. Honorato, +2

Journal of Chemical Theory and Computation

EngineeringMolecular BiologyMolecular DynamicsMolecular DesignProtein Folding +20