J. Rodrigues

发表

pdb-tools: a swiss army knife for molecular structures

J. Rodrigues, João M. C. Teixeira, M. Trellet, 2018, bioRxiv.

Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface.

G. Folkers, R. Boelens, P. Kastritis, 2014, Journal of molecular biology.

Integrative computational modeling of protein interactions

J. Rodrigues, A. Bonvin, 2014, The FEBS journal.

Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions

Julie C. Mitchell, Jeffrey J. Gray, Z. Weng, 2013, Proteins.

Sequence co-evolution gives 3D contacts and structures of protein complexes

Thomas A. Hopf, Anna G. Green, Charlotta P I Schärfe, 2014, eLife.

Sequence co-evolution gives 3D contacts and structures of protein complexes

Debora S. Marks, Chris Sander, Thomas A. Hopf, 2014, bioRxiv.

Computational Structural Biology of Macromolecular Interactions

J. Rodrigues, J. Garcia Lopes Maia Rodrigues, 2014 .

Clustering biomolecular complexes by residue contacts similarity

Alexandre M J J Bonvin, João P G L M Rodrigues, Ezgi Karaca, 2012, Proteins.

Defining the limits of homology modeling in information‐driven protein docking

A. Bordogna, E. Karaca, P. Kastritis, 2013, Proteins.

Unveiling the Interaction of Vanadium Compounds with Human Serum Albumin by Using 1H STD NMR and Computational Docking Studies

J. Rodrigues, A. Bonvin, M. Castro, 2013 .

Theoretical analysis of the effects of counterions on the supramolecular arrangement of sulfamethoxazole

J. Rodrigues, H. Napolitano, A. Camargo, 2022, Journal of Molecular Modeling.

EVcomplex Supplementary Data

Debora S. Marks, Thomas A. Hopf, Charlotta P. I. Schärfe, 2014 .

New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies*

A. Bonvin, J. Rodrigues, E. Breukink, 2016, The Journal of Biological Chemistry.

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

G C P van Zundert, J P G L M Rodrigues, M Trellet, 2016, Journal of molecular biology.

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes

Alexandre M. J. J. Bonvin, Anna Vangone, João P. G. L. M. Rodrigues, 2016, Bioinform..

Template-based protein–protein docking exploiting pairwise interfacial residue restraints

Vasant Honavar, Drena Dobbs, Alexandre M. J. J. Bonvin, 2016, Briefings Bioinform..

Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment

Daisuke Kihara, Keehyoung Joo, Daisuke Kuroda, 2016, Proteins.

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

João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin, C. G. Don, 2019, bioRxiv.

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

Irina S. Moreira, Anna Vangone, Cunliang Geng, 2017, Journal of Computer-Aided Molecular Design.

HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein–Protein Interaction Inhibitors

Alexandre M. J. J. Bonvin, João P. G. L. M. Rodrigues, Panagiotis L. Kastritis, 2014, J. Chem. Inf. Model..

Supramolecular Organization and Functional Implications of K+ Channel Clusters in Membranes

J. Rodrigues, A. Bonvin, M. Baldus, 2017, Angewandte Chemie.

Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking.

Chris Abell, João P G L M Rodrigues, Rolf Boelens, 2014, Biochemistry.

M3: an integrative framework for structure determination of molecular machines

Alexandre M J J Bonvin, João P G L M Rodrigues, Ezgi Karaca, 2017, Nature Methods.

The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail.

Alexandre M J J Bonvin, Wim E Hennink, João P G L M Rodrigues, 2015, Journal of the American Chemical Society.

Information-driven structural modelling of protein-protein interactions.

Alexandre M J J Bonvin, João P G L M Rodrigues, Ezgi Karaca, 2015, Methods in molecular biology.

Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1

G C P van Zundert, M Trellet, Z Kurkcuoglu, 2016, Proteins.

Strengths and weaknesses of data‐driven docking in critical assessment of prediction of interactions

Alexandre M J J Bonvin, Annalisa Bordogna, João P G L M Rodrigues, 2010, Proteins.

Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK.

Alexandre M J J Bonvin, Cunliang Geng, João P G L M Rodrigues, 2017, Methods in molecular biology.

Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl

J. Rodrigues, E. Karaca, A. Rifaioglu, 2021, Frontiers in Molecular Biosciences.

Integrative computational modeling of protein interactions

J. Rodrigues, A. Bonvin, 2014, The FEBS journal.

Sense and Simplicity in HADDOCK Scoring: Lessons from CASP‐CAPRI (page 418)

M. Nellen, E. Karaca, P. Kastritis, 2017, Proteins.