Search Results - "Rodrigues, L. G."

Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient by 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.

“…The bacterial flagellum is an amazing nanomachine. Understanding how such complex structures arose is crucial to our understanding of cellular evolution. We…”
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pdb-tools: a swiss army knife for molecular structures [version 1; peer review: 2 approved] by Rodrigues, João P. G. L. M, Teixeira, João M.C, Trellet, Mikaël, Bonvin, Alexandre M. J. J

“…The pdb-tools are a collection of Python scripts for working with molecular structure data in the Protein Data Bank (PDB) format. They allow users to edit,…”
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Defining distance restraints in HADDOCK by Bonvin, Alexandre M. J. J., Karaca, Ezgi, Kastritis, Panagiotis L., Rodrigues, João P. G. L. M.

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

“…Salmeterol is a partial agonist for the β 2 adrenergic receptor (β 2 AR) and the first long-acting β 2 AR agonist to be widely used clinically for the…”
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Sequence co-evolution gives 3D contacts and structures of protein complexes by 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

“…Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and…”
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Insights on cross-species transmission of SARS-CoV-2 from structural modeling by Rodrigues, João P G L M, Barrera-Vilarmau, Susana, M C Teixeira, João, Sorokina, Marija, Seckel, Elizabeth, Kastritis, Panagiotis L, Levitt, Michael

“…Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing global pandemic that has infected more than 31 million people in…”
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Integrative computational modeling of protein interactions by Rodrigues, João P. G. L. M., Bonvin, Alexandre M. J. J.

“…Protein interactions define the homeostatic state of the cell. Our ability to understand these interactions and their role in both health and disease is tied…”
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The solution structure of monomeric CCL5 in complex with a doubly sulfated N‐terminal segment of CCR5 by Abayev, Meital, Rodrigues, João P. G. L. M., Srivastava, Gautam, Arshava, Boris, Jaremko, Łukasz, Jaremko, Mariusz, Naider, Fred, Levitt, Michael, Anglister, Jacob

“…The inflammatory chemokine CCL5, which binds the chemokine receptor CCR5 in a two‐step mechanism so as to activate signaling pathways in hematopoetic cells,…”
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Binding Hotspots of BAZ2B Bromodomain: Histone Interaction Revealed by Solution NMR Driven Docking by 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

“…Bromodomains are epigenetic reader domains, which have come under increasing scrutiny both from academic and pharmaceutical research groups. Effective…”
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KoBaMIN: a knowledge-based minimization web server for protein structure refinement by Rodrigues, João P G L M, Levitt, Michael, Chopra, Gaurav

“…The KoBaMIN web server provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on…”
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PDB‐tools web: A user‐friendly interface for the manipulation of PDB files by Jiménez‐García, Brian, Teixeira, João M. C., Trellet, Mikael, Rodrigues, João P. G. L. M., Bonvin, Alexandre M. J. J.

“…The Protein Data Bank (PDB) file format remains a popular format used and supported by many software to represent coordinates of macromolecular structures. It…”
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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 by Coskun, Dilek, Lihan, Muyun, Rodrigues, João P. G. L. M., Vass, Márton, Robinson, Daniel, Friesner, Richard A., Miller, Edward B.

“…Free energy perturbation (FEP) remains an indispensable method for computationally assaying prospective compounds in advance of synthesis. However, before FEP…”
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Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK by Roel-Touris, Jorge, Don, Charleen G, V. Honorato, Rodrigo, Rodrigues, João P. G. L. M, Bonvin, Alexandre M. J. J

“…Predicting the 3D structure of protein interactions remains a challenge in the field of computational structural biology. This is in part due to difficulties…”
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The HADDOCK2.4 web server for integrative modeling of biomolecular complexes by 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.

“…Interactions between macromolecules, such as proteins and nucleic acids, are essential for cellular functions. Experimental methods can fail to provide all the…”
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Chemistry and Atomic Distortion at the Surface of an Epitaxial BaTiO3 Thin Film after Dissociative Adsorption of Water by Wang, J. L, Gaillard, F, Pancotti, A, Gautier, B, Niu, G, Vilquin, B, Pillard, V, Rodrigues, G. L. M. P, Barrett, N

“…We present a study of the atomic and chemical structure of the surface of a fully strained, TiO2-terminated, ferroelectric BaTiO3 (BTO) (001) epitaxial film on…”
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Clustering biomolecular complexes by residue contacts similarity by Rodrigues, João P. G. L. M., Trellet, Mikaël, Schmitz, Christophe, Kastritis, Panagiotis, Karaca, Ezgi, Melquiond, Adrien S. J., Bonvin, Alexandre M. J. J.

“…Inaccuracies in computational molecular modeling methods are often counterweighed by brute‐force generation of a plethora of putative solutions. These are then…”
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Environmental Co-Exposure to Lead and Manganese and Intellectual Deficit in School-Aged Children by Menezes-Filho, José A, Carvalho, Chrissie F, Rodrigues, Juliana L G, Araújo, Cecília F S, Dos Santos, Nathália R, Lima, Cássio S, Bandeira, Matheus J, Marques, Breno L de S, Anjos, Ana Laura S, Bah, Homegnon A F, Abreu, Neander, Philibert, Alline, Mergler, Donna

“…Studies have demonstrated that, for urban children, dust represents the main exposure to sources of metals like lead (Pb) and manganese (Mn). We aimed to…”
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The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail by 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

“…Nanovesicles self-assembled from amphiphilic peptides are promising candidates for applications in drug delivery. However, complete high-resolution data on the…”
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Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design by Sorokina, Marija, M. C. Teixeira, João, Barrera-Vilarmau, Susana, Paschke, Reinhard, Papasotiriou, Ioannis, Rodrigues, João P. G. L. M., Kastritis, Panagiotis L.

“…Emergence of coronaviruses poses a threat to global health and economy. The current outbreak of SARS-CoV-2 has infected more than 28,000,000 people and killed…”
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Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl by Karakulak, Tülay, Rifaioglu, Ahmet Sureyya, Rodrigues, João P. G. L. M., Karaca, Ezgi

“…Owing to its clinical significance, modulation of functionally relevant amino acids in protein-protein complexes has attracted a great deal of attention. To…”
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