A Cyclisation and Docking Protocol for Cyclic Peptide-Protein Modelling using HADDOCK2.4

A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance

ARCTIC-3D: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

AbTune: layer-wise selective Fine-Tuning of protein language models for Antibodies

Accelerating Protein-Protein Interaction screens with reduced AlphaFold-Multimer sampling

An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45

Combining AI structure prediction and integrative modelling for nanobody-antigen complexes

DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model

DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Interfaces

DeepRank: A deep learning framework for data mining 3D protein-protein interfaces

Faculty Opinions recommendation of Evolving new protein-protein interaction specificity through promiscuous intermediates.

Faculty Opinions recommendation of High-Confidence Protein-Ligand Complex Modeling by NMR-Guided Docking Enables Early Hit Optimization.

Faculty Opinions recommendation of InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information.

Faculty Opinions recommendation of Local Interaction Signal Analysis Predicts Protein-Protein Binding Affinity.

Faculty Opinions recommendation of MFIB: a repository of protein complexes with mutual folding induced by binding.

Faculty Opinions recommendation of Mapping local conformational landscapes of proteins in solution.

Faculty Opinions recommendation of MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution.

Faculty Opinions recommendation of Modeling disordered protein interactions from biophysical principles.

Faculty Opinions recommendation of Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies.

Faculty Opinions recommendation of Non-interacting proteins may resemble interacting proteins: prevalence and implications.

Faculty Opinions recommendation of PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets.

Faculty Opinions recommendation of Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field.

Faculty Opinions recommendation of Statistical database analysis of the role of loop dynamics for protein-protein complex formation and allostery.

Faculty Opinions recommendation of iPPI-DB: an online database of modulators of protein-protein interactions.

HADDOCK3: A modular and versatile platform for integrative modelling of biomolecular complexes

Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Improved structural modelling of antibodies and their complexes with clustered diffusion ensembles

Improving the Quality of Co-evolution Intermolecular Contact Prediction with DisVis

Integrative Modeling of Membrane-associated Protein Assemblies

Integrative modeling in the age of machine learning: a summary of HADDOCK strategies in CAPRI rounds 47-55

Integrative modeling in the age of machine learning: a summary of HADDOCK strategies in CAPRI rounds 47-55

Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4

Less is more: Coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK

LightDock goes information-driven

Modelling Protein-Glycan Interactions with HADDOCK

Native or non-native protein-protein docking models? Molecular dynamics to the rescue

Navigating the Pre- and Post-AlphaFold Divide: CAPRI 8th evaluation meeting, February 12-14, Grenoble, FR

Predicting binding events in very flexible, allosteric, multi-domain proteins

Protein-protein interaction prediction in the pre- and post-AlphaFold era: the 8th CAPRI evaluation

The SH Protein of Mumps Virus is a Druggable Pentameric Viroporin

Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking

Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe

iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines

pdb-tools: a swiss army knife for molecular structures