2026
51.
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, 2026
50.
Accurate physics-based flexible docking of macrocyclic ligands
J Robson-Tull, JP Rodrigues
Journal of Medicinal Chemistry 69 (4), 4745-4754, 2026
49.
Generalization and Usability of Co-Folded GPCR–Ligand Complexes: A Physics-Guided Assessment
L Zhang, RA Friesner, EB Miller, JP Rodrigues
ChemRxiv 2026 (0107), 2026
2024
48.
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
47.
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
2023
46.
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, 2023
45.
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, 2023
2022
44.
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
2021
43.
Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2
IR Fischhoff, AA Castellanos, JP Rodrigues, A Varsani, BA Han
Biorxiv, 2021
42.
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
41.
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
40.
Predicting the Specificity-Determining Positions of Paralogous Complexes
T Karakulak, AS Rifaioglu, JP Rodrigues, E Karaca
bioRxiv, 2021.01. 26.428202, 2021
2020
39.
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
38.
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
37.
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
36.
Interfacea: Open-Source Library for Protein Interface Analysis
JPGLM Rodrigues, M Levitt
Biophysical Journal 118 (3), 516a, 2020
2019
35.
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
34.
JoaoRodrigues/interfacea: First beta version of the API
J Rodrigues, C Valentine, B Jimenez
Zenodo https://doi. org/10.5281/zenodo 3516439, 2019
2018
33.
pdb-tools: A swiss army knife for molecular structures
JP Rodrigues, JMC Teixeira, M Trellet, AMJJ Bonvin
F1000Research 7, 1961, 2018
32.
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
31.
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
30.
Defining distance restraints in HADDOCK
AMJJ Bonvin, E Karaca, PL Kastritis, JP Rodrigues
Nature protocols 13 (7), 1503-1503, 2018
29.
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
28.
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
27.
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
26.
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
2017
25.
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
24.
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
23.
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
22.
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
21.
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
20.
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
2016
19.
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
18.
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
17.
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
16.
15.
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
2015
14.
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
2014
13.
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
12.
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
11.
Information-driven structural modelling of protein–protein interactions
JP Rodrigues, E Karaca, AMJJ Bonvin
Molecular modeling of proteins, 399-424, 2014
10.
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
9.
Integrative computational modeling of protein interactions
JP Rodrigues, AMJJ Bonvin
The FEBS journal 281 (8), 1988-2003, 2014
8.
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), 826-836, 2014
2013
7.
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
6.
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
5.
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
2012
4.
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
3.
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
2010
2.
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
1.
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