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

Volltext

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.

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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.

Volltext

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

Volltext

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.

Volltext

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

Volltext

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

Volltext

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.

Volltext

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

Volltext

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

Volltext

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.

Volltext

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.

Volltext

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

Volltext

Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2 von Fischhoff, Ilya R, Castellanos, Adrian A, Rodrigues, João P G L M, Varsani, Arvind, Han, Barbara A

Volltext

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.

Volltext