João P. G. L. M. Rodrigues

Molecular Biology · 2012–2024

A researcher in the Science corpus: 10 papers; trusts 14 researchers and is trusted by 1 researcher here, as inferred from the citation graph.

Subfields

• Molecular Biology — 145 citations into it; #14,346 of 17,773 by trust here, #3,835 by citations
• Materials Chemistry — 71 citations into it
• Computational Biology & Bioinformatics — 49 citations into it
• Computational Theory and Mathematics — 42 citations into it
• Spectroscopy — 19 citations into it
• Computational Chemistry & Drug Discovery — 13 citations into it

Whom João P. G. L. M. Rodrigues trusts overall

Their strongest outbound trust, strongest first, inferred from their citations.

1. Joël Janin
2. Alexandre M. J. J. Bonvin
3. A. W. Sousa da Silva
4. A. Brunger
5. Marc F. Lensink
6. S. D. de Vries
7. Rolf Boelens
8. Wim F. Vranken
9. Alpeshkumar K. Malde
10. Anna Vangone

Who trusts João P. G. L. M. Rodrigues overall

1. Zeynep Kurkcuoglu
2. Alexandre M. J. J. Bonvin
3. Rodrigo Vargas Honorato
4. Rui Yin
5. G. V. Zundert
6. Cunliang Geng
7. Jorge Roel‐Touris
8. Tatu Pantsar

Papers from João P. G. L. M. Rodrigues's perspective

Ordered by how strongly the researchers João P. G. L. M. Rodrigues trusts endorse each paper. Same corpus, a different order for every researcher.

1. Protein data bank
2. TM-align: a protein structure alignment algorithm based on the TM-score
3. Docking and scoring protein complexes: CAPRI 3rd Edition
4. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.
5. CAPRI: A Critical Assessment of PRedicted Interactions (Proteins: Structure, Function, and Bioinformatics)
6. Identification of direct residue contacts in protein–protein interaction by message passing
7. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing
8. Biological Crystallography Experimental Phasing with Shelxc/d/e: Combining Chain Tracing with Density Modification
9. ARIA: automated NOE assignment and NMR structure calculation
10. Assessing predictions of protein–protein interaction: The CAPRI experiment

Their papers

• Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment (2016) — 130 citations
• Sequence co-evolution gives 3D contacts and structures of protein complexes (2014) — 496 citations
• Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK. (2017) — 39 citations
• Clustering biomolecular complexes by residue contacts similarity (2012) — 123 citations
• The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. (2016) — 2,479 citations
• PRODIGY: a web server for predicting the binding affinity of protein-protein complexes (2016) — 1,281 citations
• Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 (2017) — 130 citations
• The HADDOCK2.4 web server for integrative modeling of biomolecular complexes (2024) — 478 citations
• Information-driven structural modelling of protein-protein interactions. (2015) — 13 citations
• Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions (2013) — 102 citations