Defining distance restraints in HADDOCK
Bonvin, Alexandre M. J. J., Karaca, Ezgi, Kastritis, Panagiotis L., Rodrigues, João P. G. L. M.
Published in Nature protocols (01.07.2018)
Published in Nature protocols (01.07.2018)
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Sequence co-evolution gives 3D contacts and structures of protein complexes
Hopf, Thomas A, Schärfe, Charlotta P I, Rodrigues, João P G L M, Green, Anna G, Kohlbacher, Oliver, Sander, Chris, Bonvin, Alexandre M J J, Marks, Debora S
Published in eLife (25.09.2014)
Published in eLife (25.09.2014)
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Insights on cross-species transmission of SARS-CoV-2 from structural modeling
Rodrigues, João P G L M, Barrera-Vilarmau, Susana, M C Teixeira, João, Sorokina, Marija, Seckel, Elizabeth, Kastritis, Panagiotis L, Levitt, Michael
Published in PLoS computational biology (01.12.2020)
Published in PLoS computational biology (01.12.2020)
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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
Coskun, Dilek, Lihan, Muyun, Rodrigues, João P. G. L. M., Vass, Márton, Robinson, Daniel, Friesner, Richard A., Miller, Edward B.
Published in Journal of chemical theory and computation (09.01.2024)
Published in Journal of chemical theory and computation (09.01.2024)
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Journal Article
Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK
Roel-Touris, Jorge, Don, Charleen G, V. Honorato, Rodrigo, Rodrigues, João P. G. L. M, Bonvin, Alexandre M. J. J
Published in Journal of chemical theory and computation (12.11.2019)
Published in Journal of chemical theory and computation (12.11.2019)
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Journal Article
The solution structure of monomeric CCL5 in complex with a doubly sulfated N‐terminal segment of CCR5
Abayev, Meital, Rodrigues, João P. G. L. M., Srivastava, Gautam, Arshava, Boris, Jaremko, Łukasz, Jaremko, Mariusz, Naider, Fred, Levitt, Michael, Anglister, Jacob
Published in The FEBS journal (01.06.2018)
Published in The FEBS journal (01.06.2018)
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Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design
Sorokina, Marija, M. C. Teixeira, João, Barrera-Vilarmau, Susana, Paschke, Reinhard, Papasotiriou, Ioannis, Rodrigues, João P. G. L. M., Kastritis, Panagiotis L.
Published in Scientific data (16.09.2020)
Published in Scientific data (16.09.2020)
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Theoretical analysis of the effects of counterions on the supramolecular arrangement of sulfamethoxazole
Morais, Álice C. B., Borges, Igor D., Rodrigues, João P. M., Aguiar, Antônio S. N., Dias, Lucas D., Camargo, Ademir J., Martins, José L. R., Oliveira, Solemar S., Napolitano, Hamilton B.
Published in Journal of molecular modeling (01.10.2022)
Published in Journal of molecular modeling (01.10.2022)
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KoBaMIN: a knowledge-based minimization web server for protein structure refinement
Rodrigues, João P G L M, Levitt, Michael, Chopra, Gaurav
Published in Nucleic acids research (01.07.2012)
Published in Nucleic acids research (01.07.2012)
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Supramolecular Organization and Functional Implications of K+ Channel Clusters in Membranes
Visscher, Koen M., Medeiros‐Silva, João, Mance, Deni, Rodrigues, João P. G. L. M., Daniëls, Mark, Bonvin, Alexandre M. J. J., Baldus, Marc, Weingarth, Markus
Published in Angewandte Chemie International Edition (16.10.2017)
Published in Angewandte Chemie International Edition (16.10.2017)
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Methoxylated Quinoline-Chalcones with Potential Pesticidal Activity: From Synthesis to Supramolecular Framework
Aguiar, Antônio, Rodrigues, João, Borges, Leonardo, Vaz, Wesley, D'Oliveira, Giulio, Perez, Caridad, Napolitano, Hamilton
Published in Journal of the Brazilian Chemical Society (2024)
Published in Journal of the Brazilian Chemical Society (2024)
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Journal Article
Structural insights into binding specificity, efficacy and bias of a β2AR partial agonist
Masureel, Matthieu, Zou, Yaozhong, Picard, Louis-Philippe, van der Westhuizen, Emma, Mahoney, Jacob P., Rodrigues, João P. G. L. M., Mildorf, Thomas J., Dror, Ron O., Shaw, David E., Bouvier, Michel, Pardon, Els, Steyaert, Jan, Sunahara, Roger K., Weis, William I., Zhang, Cheng, Kobilka, Brian K.
Published in Nature chemical biology (01.11.2018)
Published in Nature chemical biology (01.11.2018)
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Journal Article
Binding Hotspots of BAZ2B Bromodomain: Histone Interaction Revealed by Solution NMR Driven Docking
Ferguson, Fleur M, Dias, David M, Rodrigues, João P. G. L. M, Wienk, Hans, Boelens, Rolf, Bonvin, Alexandre M. J. J, Abell, Chris, Ciulli, Alessio
Published in Biochemistry (Easton) (28.10.2014)
Published in Biochemistry (Easton) (28.10.2014)
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Journal Article
New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies
Liu, Yao, 刘, 垚, Rodrigues, João P.G.L.M., Bonvin, Alexandre M.J.J., Zaal, Esther A., Berkers, Celia R., Heger, Michal, Gawarecka, Katarzyna, Swiezewska, Ewa, Breukink, Eefjan, Egmond, Maarten R.
Published in The Journal of biological chemistry (15.07.2016)
Published in The Journal of biological chemistry (15.07.2016)
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Journal Article
Publisher Correction: Structural insights into binding specificity, efficacy and bias of a β2AR partial agonist
Masureel, Matthieu, Zou, Yaozhong, Picard, Louis-Philippe, van der Westhuizen, Emma, Mahoney, Jacob P., Rodrigues, João P. G. L. M., Mildorf, Thomas J., Dror, Ron O., Shaw, David E., Bouvier, Michel, Pardon, Els, Steyaert, Jan, Sunahara, Roger K., Weis, William I., Zhang, Cheng, Kobilka, Brian K.
Published in Nature chemical biology (01.02.2019)
Published in Nature chemical biology (01.02.2019)
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