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

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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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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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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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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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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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Clustering biomolecular complexes by residue contacts similarity von Rodrigues, João P. G. L. M., Trellet, Mikaël, Schmitz, Christophe, Kastritis, Panagiotis, Karaca, Ezgi, Melquiond, Adrien S. J., 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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The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail von Rad-Malekshahi, Mazda, Visscher, Koen M, Rodrigues, João P. G. L. M, de Vries, Renko, Hennink, Wim E, Baldus, Marc, Bonvin, Alexandre M. J. J, Mastrobattista, Enrico, Weingarth, Markus

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Chemistry and Atomic Distortion at the Surface of an Epitaxial BaTiO3 Thin Film after Dissociative Adsorption of Water von Wang, J. L, Gaillard, F, Pancotti, A, Gautier, B, Niu, G, Vilquin, B, Pillard, V, Rodrigues, G. L. M. P, Barrett, N

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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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Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 von Kurkcuoglu, Zeynep, Koukos, Panagiotis I., Citro, Nevia, Trellet, Mikael E., Rodrigues, J. P. G. L. M., Moreira, Irina S., Roel-Touris, Jorge, Melquiond, Adrien S. J., Geng, Cunliang, Schaarschmidt, Jörg, Xue, Li C., Vangone, Anna, Bonvin, A. M. J. J.

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Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 von Vangone, A., Rodrigues, J. P. G. L. M., Xue, L. C., van Zundert, G. C. P., Geng, C., Kurkcuoglu, Z., Nellen, M., Narasimhan, S., Karaca, E., van Dijk, M., Melquiond, A. S. J., Visscher, K. M., Trellet, M., Kastritis, P. L., Bonvin, A. M. J. J.

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