João Rodrigues

Structural Plasticity and Ligand Promiscuity of CYP3A4 Revealed by Cryo-EM.
AK Orta, JH Schäfer, GJ Correy, JO Norman, J Pampel, KK Huddleston, ...
Biorxiv: the Preprint Server for Biology, 2026

On the generalization and usability of cofolding models for GPCR drug discovery
L Zhang, RA Friesner, EB Miller, JP GLM Rodrigues
npj Drug Discovery 3 (1), 30, 2026

Towards better structural models from cryo‐electron microscopy data with physics‐based methods
H Boyaci Selcuk, G Reggiano, J Robson‐Tull, L Zhang, ...
FEBS letters 600 (10), 1549-1557, 2026

Accurate physics-based flexible docking of macrocyclic ligands
J Robson-Tull, JP Rodrigues
Journal of Medicinal Chemistry 69 (4), 4745-4754, 2026

The HADDOCK2. 4 web server for integrative modeling of biomolecular complexes
RV Honorato, ME Trellet, B Jiménez-García, JJ Schaarschmidt, M Giulini, ...
Nature protocols 19 (11), 3219-3241, 2024

Enabling structure-based drug discovery utilizing predicted models
EB Miller, H Hwang, M Shelley, A Placzek, JP Rodrigues, RK Suto, ...
Cell 187 (3), 521-525, 2024

OpenMM 8: molecular dynamics simulation with machine learning potentials
P Eastman, R Galvelis, RP Peláez, CRA Abreu, SE Farr, E Gallicchio, ...
The Journal of Physical Chemistry B 128 (1), 109-116, 2024

Using AlphaFold and experimental structures for the prediction of the structure and binding affinities of GPCR complexes via induced fit docking and free energy perturbation
D Coskun, M Lihan, JP Rodrigues, M Vass, D Robinson, RA Friesner, ...
Journal of Chemical Theory and Computation 20 (1), 477-489, 2024

An electrostatically-steered conformational selection mechanism promotes sars-cov-2 spike protein variation
M Sorokina, J Belapure, C Tüting, R Paschke, I Papasotiriou, ...
Journal of molecular biology 434 (13), 167637, 2022

Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2
IR Fischhoff, AA Castellanos, JP Rodrigues, A Varsani, BA Han
Biorxiv, 2021

Predicting the specificity-determining positions of receptor tyrosine kinase Axl
T Karakulak, AS Rifaioglu, JP Rodrigues, E Karaca
Frontiers in molecular biosciences 8, 658906, 2021

PDB‐tools Web: A User‐friendly Interface for the Manipulation of PDB Files
B Jiménez‐García, JMC Teixeira, M Trellet, JP Rodrigues, AMJJ Bonvin
Proteins: Structure, Function, and Bioinformatics 89 (3), 330-335, 2021

Insights on cross-species transmission of SARS-CoV-2 from structural modeling
JP Rodrigues, S Barrera-Vilarmau, J Mc Teixeira, M Sorokina, E Seckel, ...
PLoS computational biology 16 (12), e1008449, 2020

Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design
M Sorokina, J MC Teixeira, S Barrera-Vilarmau, R Paschke, I Papasotiriou, ...
Scientific data 7 (1), 309, 2020

Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient
M Kaplan, MJ Sweredoski, JP Rodrigues, EI Tocheva, YW Chang, ...
Proceedings of the National Academy of Sciences 117 (16), 8941-8947, 2020

Interfacea: Open-Source Library for Protein Interface Analysis
JPGLM Rodrigues, M Levitt
Biophysical Journal 118 (3), 516a, 2020

Less is more: coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK
J Roel-Touris, CG Don, R V. Honorato, JP Rodrigues, AMJJ Bonvin
Journal of chemical theory and computation 15 (11), 6358-6367, 2019

JoaoRodrigues/interfacea: First beta version of the API.
J Rodrigues, C Valentine, B Jimenez
Zenodo, 2019

pdb-tools: A swiss army knife for molecular structures
JP Rodrigues, JMC Teixeira, M Trellet, AMJJ Bonvin
F1000Research 7, 1961, 2018

Structural insights into binding specificity, efficacy and bias of a β2AR partial agonist
M Masureel, Y Zou, LP Picard, E van der Westhuizen, JP Mahoney, ...
Nature chemical biology 14 (11), 1059-1066, 2018

Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors
CI Pataki, J Rodrigues, L Zhang, J Qian, B Efron, T Hastie, JE Elias, ...
Proceedings of the National Academy of Sciences 115 (35), E8172-E8180, 2018

Defining distance restraints in HADDOCK.
AMJJ Bonvin, E Karaca, PL Kastritis, JP Rodrigues
Nature protocols 13 (7), 1503-1504, 2018

The solution structure of monomeric CCL 5 in complex with a doubly sulfated N‐terminal segment of CCR 5
M Abayev, JP Rodrigues, G Srivastava, B Arshava, Ł Jaremko, M Jaremko, ...
The FEBS journal 285 (11), 1988-2003, 2018

SILAC-based phosphoproteomics reveals new PP2A-Cdc55-regulated processes in budding yeast
B Baro, S Jativa, I Calabria, J Vinaixa, JJ Bech-Serra, C de LaTorre, ...
Gigascience 7 (5), giy047, 2018

Augmenting research, education, and outreach with client-side web programming
LA Abriata, JP Rodrigues, M Salathé, L Patiny
Trends in biotechnology 36 (5), 473-476, 2018

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
Z Kurkcuoglu, PI Koukos, N Citro, ME Trellet, J Rodrigues, IS Moreira, ...
Journal of computer-aided molecular design 32 (1), 175-185, 2018

Supramolecular Organization and Functional Implications of K+ Channel Clusters in Membranes
KM Visscher, J Medeiros‐Silva, D Mance, JP Rodrigues, M Daniëls, ...
Angewandte Chemie International Edition 56 (43), 13222-13227, 2017

M3: an integrative framework for structure determination of molecular machines
E Karaca, JP Rodrigues, A Graziadei, AMJJ Bonvin, T Carlomagno
Nature methods 14 (9), 897-902, 2017

Template-based protein–protein docking exploiting pairwise interfacial residue restraints
LC Xue, JP Rodrigues, D Dobbs, V Honavar, AMJJ Bonvin
Briefings in Bioinformatics 18 (3), 458-466, 2017

Structural and functional analysis of a β2-adrenergic receptor complex with GRK5
KE Komolov, Y Du, NM Duc, RM Betz, JP Rodrigues, RD Leib, D Patra, ...
Cell 169 (3), 407-421. e16, 2017

Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1
A Vangone, J Rodrigues, LC Xue, GCP Van Zundert, C Geng, ...
Proteins: Structure, Function, and Bioinformatics 85 (3), 417-423, 2017

Information-driven, ensemble flexible peptide docking using HADDOCK
C Geng, S Narasimhan, JP Rodrigues, AMJJ Bonvin
Modeling Peptide-Protein Interactions: Methods and Protocols, 109-138, 2017

PRODIGY: a web server for predicting the binding affinity of protein–protein complexes
LC Xue, JP Rodrigues, PL Kastritis, AM Bonvin, A Vangone
Bioinformatics 32 (23), 3676-3678, 2016

Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment
MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ...
Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016

New insight into the catalytic mechanism of bacterial MraY from enzyme kinetics and docking studies
Y Liu, JP Rodrigues, AMJJ Bonvin, EA Zaal, CR Berkers, M Heger, ...
Journal of Biological Chemistry 291 (29), 15057-15068, 2016

Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands‐on collaborative practical sessions for undergraduate students
JP Rodrigues, ASJ Melquiond, AMJJ Bonvin
Biochemistry and Molecular Biology Education 44 (2), 160-167, 2016

The HADDOCK2. 2 web server: user-friendly integrative modeling of biomolecular complexes
GCP Van Zundert, J Rodrigues, M Trellet, C Schmitz, PL Kastritis, ...
Journal of molecular biology 428 (4), 720-725, 2016

The supramolecular organization of a peptide-based nanocarrier at high molecular detail
M Rad-Malekshahi, KM Visscher, JP Rodrigues, R De Vries, WE Hennink, ...
Journal of the American Chemical Society 137 (24), 7775-7784, 2015

Binding hotspots of BAZ2B bromodomain: histone interaction revealed by solution NMR driven docking
FM Ferguson, DM Dias, JP Rodrigues, H Wienk, R Boelens, AMJJ Bonvin, ...
Biochemistry 53 (42), 6706-6716, 2014

Sequence co-evolution gives 3D contacts and structures of protein complexes
TA Hopf, CPI Schärfe, JP Rodrigues, AG Green, O Kohlbacher, C Sander, ...
elife 3, e03430, 2014

Information-driven structural modelling of protein–protein interactions
JP Rodrigues, E Karaca, AMJJ Bonvin
Molecular modeling of proteins, 399-424, 2014

Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface
PL Kastritis, JP Rodrigues, GE Folkers, R Boelens, AMJJ Bonvin
Journal of molecular biology 426 (14), 2632-2652, 2014

Integrative computational modeling of protein interactions
JP Rodrigues, AMJJ Bonvin
The FEBS journal 281 (8), 1988-2003, 2014

HADDOCK2P2I: a biophysical model for predicting the binding affinity of protein–protein interaction inhibitors
PL Kastritis, JP Rodrigues, AMJJ Bonvin
Journal of Chemical Information and Modeling 54 (3), 826, 2014

Defining the limits of homology modeling in information‐driven protein docking
J Rodrigues, ASJ Melquiond, E Karaca, M Trellet, M Van Dijk, ...
Proteins: Structure, Function, and Bioinformatics 81 (12), 2119-2128, 2013

Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions
R Moretti, SJ Fleishman, R Agius, M Torchala, PA Bates, PL Kastritis, ...
Proteins: Structure, Function, and Bioinformatics 81 (11), 1980-1987, 2013

Unveiling the Interaction of Vanadium Compounds with Human Serum Albumin by Using 1H STD NMR and Computational Docking Studies
DM Dias, JP Rodrigues, NS Domingues, AMJJ Bonvin, MMCA Castro
European Journal of Inorganic Chemistry 2013 (26), 4619-4627, 2013

Clustering biomolecular complexes by residue contacts similarity
JP Rodrigues, M Trellet, C Schmitz, P Kastritis, E Karaca, ASJ Melquiond, ...
Proteins: Structure, Function, and Bioinformatics 80 (7), 1810-1817, 2012

KoBaMIN: a knowledge-based minimization web server for protein structure refinement
JP Rodrigues, M Levitt, G Chopra
Nucleic acids research 40 (W1), W323-W328, 2012

Strengths and weaknesses of data‐driven docking in critical assessment of prediction of interactions
SJ de Vries, ASJ Melquiond, PL Kastritis, E Karaca, A Bordogna, ...
Proteins: Structure, Function, and Bioinformatics 78 (15), 3242-3249, 2010

Concept-based query expansion for retrieving gene related publications from MEDLINE
S Matos, JP Arrais, J Maia-Rodrigues, JL Oliveira
BMC bioinformatics 11 (1), 212, 2010