pdb-tools: a swiss army knife for molecular structures [version 1; peer review: 2 approved] von Rodrigues, João P. G. L. M, Teixeira, João M.C, Trellet, Mikaël, Bonvin, Alexandre M. J. J

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Defining distance restraints in HADDOCK von Bonvin, Alexandre M. J. J., Karaca, Ezgi, Kastritis, Panagiotis L., Rodrigues, João P. G. L. M.

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Insights on cross-species transmission of SARS-CoV-2 from structural modeling von Rodrigues, João P G L M, Barrera-Vilarmau, Susana, M C Teixeira, João, Sorokina, Marija, Seckel, Elizabeth, Kastritis, Panagiotis L, Levitt, Michael

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Sequence co-evolution gives 3D contacts and structures of protein complexes von 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

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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 von Coskun, Dilek, Lihan, Muyun, Rodrigues, João P. G. L. M., Vass, Márton, Robinson, Daniel, Friesner, Richard A., Miller, Edward B.

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Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK von Roel-Touris, Jorge, Don, Charleen G, V. Honorato, Rodrigo, Rodrigues, João P. G. L. M, Bonvin, Alexandre M. J. J

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The solution structure of monomeric CCL5 in complex with a doubly sulfated N‐terminal segment of CCR5 von Abayev, Meital, Rodrigues, João P. G. L. M., Srivastava, Gautam, Arshava, Boris, Jaremko, Łukasz, Jaremko, Mariusz, Naider, Fred, Levitt, Michael, Anglister, Jacob

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PDB‐tools web: A user‐friendly interface for the manipulation of PDB files von Jiménez‐García, Brian, Teixeira, João M. C., Trellet, Mikael, Rodrigues, João P. G. L. M., Bonvin, Alexandre M. J. J.

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Integrative computational modeling of protein interactions von Rodrigues, João P. G. L. M., Bonvin, Alexandre M. J. J.

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Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design von Sorokina, Marija, M. C. Teixeira, João, Barrera-Vilarmau, Susana, Paschke, Reinhard, Papasotiriou, Ioannis, Rodrigues, João P. G. L. M., Kastritis, Panagiotis L.

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Spatiotemporal model for estimating electric vehicles adopters von Rodrigues, João L., Bolognesi, Hugo M., Melo, Joel D., Heymann, Fabian, Soares, F.J.

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KoBaMIN: a knowledge-based minimization web server for protein structure refinement von Rodrigues, João P G L M, Levitt, Michael, Chopra, Gaurav

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Supramolecular Organization and Functional Implications of K+ Channel Clusters in Membranes von 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

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Structural insights into binding specificity, efficacy and bias of a β2AR partial agonist von 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.

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Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl von Karakulak, Tülay, Rifaioglu, Ahmet Sureyya, Rodrigues, João P. G. L. M., Karaca, Ezgi

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Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK von Geng, Cunliang, Narasimhan, Siddarth, Rodrigues, João P. G. L. M., Bonvin, Alexandre M. J. J.

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The HADDOCK2.4 web server for integrative modeling of biomolecular complexes von Honorato, Rodrigo V., Trellet, Mikael E., Jiménez-García, Brian, Schaarschmidt, Jörg J., Giulini, Marco, Reys, Victor, Koukos, Panagiotis I., Rodrigues, João P. G. L. M., Karaca, Ezgi, van Zundert, Gydo C. P., Roel-Touris, Jorge, van Noort, Charlotte W., Jandová, Zuzana, Melquiond, Adrien S. J., Bonvin, Alexandre M. J. J.

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New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies von 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.

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Binding Hotspots of BAZ2B Bromodomain: Histone Interaction Revealed by Solution NMR Driven Docking von 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

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Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient von Kaplan, Mohammed, Sweredoski, Michael J., Rodrigues, Joa˜o P. G. L. M., Tocheva, Elitza I., Chang, Yi-Wei, Ortega, Davi R., Beeby, Morgan, Jensen, Grant J.

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