| Year |
Citation |
Score |
| 2020 |
Rodrigues JP, Barrera-Vilarmau S, Teixeira JM, Seckel E, Kastritis P, Levitt M. Insights on cross-species transmission of SARS-CoV-2 from structural modeling. Biorxiv : the Preprint Server For Biology. PMID 32577636 DOI: 10.1101/2020.06.05.136861 |
0.769 |
|
| 2019 |
Rodrigues J, Levitt M. interfacea: open-source library for protein interface analysis F1000research. 8. DOI: 10.7490/F1000Research.1117105.1 |
0.495 |
|
| 2018 |
Pataki CI, Rodrigues J, Zhang L, Qian J, Efron B, Hastie T, Elias JE, Levitt M, Kopito RR. Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors. Proceedings of the National Academy of Sciences of the United States of America. PMID 30104359 DOI: 10.1073/Pnas.1807981115 |
0.516 |
|
| 2018 |
Abayev M, Rodrigues JP, Srivastava G, Arshava B, Jaremko Ł, Jaremko M, Naider F, Levitt M, Anglister J. The solution structure of monomeric CCL5 in complex with a doubly-sulfated N-terminal segment of CCR5. The Febs Journal. PMID 29619777 DOI: 10.1111/Febs.14460 |
0.442 |
|
| 2017 |
Geng C, Narasimhan S, Rodrigues JP, Bonvin AM. Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK. Methods in Molecular Biology (Clifton, N.J.). 1561: 109-138. PMID 28236236 DOI: 10.1007/978-1-4939-6798-8_8 |
0.782 |
|
| 2016 |
Vangone A, Rodrigues JP, Xue LC, van Zundert GC, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond AS, Visscher KM, Trellet M, Kastritis PL, Bonvin AM. Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI Round1. Proteins. PMID 27802573 DOI: 10.1002/Prot.25198 |
0.731 |
|
| 2016 |
Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A. PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics (Oxford, England). PMID 27503228 DOI: 10.1093/Bioinformatics/Btw514 |
0.818 |
|
| 2016 |
Liu Y, Rodrigues JP, Bonvin AM, Zaal EA, Berkers CR, Heger M, Gawarecka K, Swiezewska E, Breukink E, Egmond MR. New insight in the catalytic mechanism of bacterial MraY from enzyme kinetics and docking studies. The Journal of Biological Chemistry. PMID 27226570 DOI: 10.1074/jbc.M116.717884 |
0.499 |
|
| 2016 |
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Rodrigues JP, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007 |
0.782 |
|
| 2016 |
Xue LC, Rodrigues JP, Dobbs D, Honavar V, Bonvin AM. Template-based protein-protein docking exploiting pairwise interfacial residue restraints. Briefings in Bioinformatics. PMID 27013645 DOI: 10.1093/bib/bbw027 |
0.578 |
|
| 2016 |
Rodrigues JP, Melquiond AS, Bonvin AM. Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students. Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology. PMID 26751257 DOI: 10.1002/bmb.20941 |
0.766 |
|
| 2015 |
van Zundert GC, Rodrigues JP, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond AS, van Dijk M, de Vries SJ, Bonvin AM. The HADDOCK2.2 web server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology. PMID 26410586 DOI: 10.1016/J.Jmb.2015.09.014 |
0.734 |
|
| 2015 |
Rad-Malekshahi M, Visscher KM, Rodrigues JP, de Vries R, Hennink WE, Baldus M, Bonvin AM, Mastrobattista E, Weingarth M. The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail. Journal of the American Chemical Society. 137: 7775-84. PMID 26022089 DOI: 10.1021/Jacs.5B02919 |
0.482 |
|
| 2015 |
Rodrigues JP, Karaca E, Bonvin AM. Information-driven structural modelling of protein-protein interactions. Methods in Molecular Biology (Clifton, N.J.). 1215: 399-424. PMID 25330973 DOI: 10.1007/978-1-4939-1465-4_18 |
0.803 |
|
| 2014 |
Ferguson FM, Dias DM, Rodrigues JP, Wienk H, Boelens R, Bonvin AM, Abell C, Ciulli A. Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking. Biochemistry. 53: 6706-16. PMID 25266743 DOI: 10.1021/Bi500909D |
0.658 |
|
| 2014 |
Hopf TA, Schärfe CP, Rodrigues JP, Green AG, Kohlbacher O, Sander C, Bonvin AM, Marks DS. Sequence co-evolution gives 3D contacts and structures of protein complexes. Elife. 3. PMID 25255213 DOI: 10.7554/Elife.03430 |
0.627 |
|
| 2014 |
Kastritis PL, Rodrigues JP, Folkers GE, Boelens R, Bonvin AM. Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface. Journal of Molecular Biology. 426: 2632-52. PMID 24768922 DOI: 10.1016/J.Jmb.2014.04.017 |
0.798 |
|
| 2014 |
Rodrigues JP, Bonvin AM. Integrative computational modeling of protein interactions. The Febs Journal. 281: 1988-2003. PMID 24588898 DOI: 10.1111/febs.12771 |
0.609 |
|
| 2014 |
Kastritis PL, Rodrigues JP, Bonvin AM. HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors. Journal of Chemical Information and Modeling. 54: 826-36. PMID 24521147 DOI: 10.1021/Ci4005332 |
0.801 |
|
| 2014 |
van der Cruijsen E, Visscher K, Rodrigues J, Bonvin A, Baldus M, Weingarth M. Ion Channel - Ion Channel Interaction at Atomic Resolution Biophysical Journal. 106: 628a. DOI: 10.1016/J.Bpj.2013.11.3474 |
0.535 |
|
| 2013 |
Rodrigues JP, Melquiond AS, Karaca E, Trellet M, van Dijk M, van Zundert GC, Schmitz C, de Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AM. Defining the limits of homology modeling in information-driven protein docking. Proteins. 81: 2119-28. PMID 23913867 DOI: 10.1002/Prot.24382 |
0.756 |
|
| 2013 |
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356 |
0.799 |
|
| 2012 |
Rodrigues JP, Levitt M, Chopra G. KoBaMIN: a knowledge-based minimization web server for protein structure refinement. Nucleic Acids Research. 40: W323-8. PMID 22564897 DOI: 10.1093/Nar/Gks376 |
0.567 |
|
| 2012 |
Rodrigues JP, Trellet M, Schmitz C, Kastritis P, Karaca E, Melquiond AS, Bonvin AM. Clustering biomolecular complexes by residue contacts similarity. Proteins. 80: 1810-7. PMID 22489062 DOI: 10.1002/Prot.24078 |
0.731 |
|
| 2012 |
Rodrigues J, Schmitz C, Trellet M, Melquiond A, Bonvin A. Clustering biomolecular structures by residue contact similarity F1000research. 3. DOI: 10.7490/F1000Research.1090095.1 |
0.733 |
|
| 2011 |
Rodrigues J, Nogueira A, Salvador P, Rodrigues JJ. IPTV service based on a content-zapping paradigm Multimedia Systems. 17: 351-364. DOI: 10.1007/S00530-010-0215-8 |
0.305 |
|
| 2010 |
de Vries SJ, Melquiond AS, Kastritis PL, Karaca E, Bordogna A, van Dijk M, Rodrigues JP, Bonvin AM. Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions. Proteins. 78: 3242-9. PMID 20718048 DOI: 10.1002/Prot.22814 |
0.784 |
|
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