Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem
Honorato, Rodrigo V., Koukos, Panagiotis I., Jiménez-García, Brian, Tsaregorodtsev, Andrei, Verlato, Marco, Giachetti, Andrea, Rosato, Antonio, Bonvin, Alexandre M. J. J.
Published in Frontiers in molecular biosciences (28.07.2021)
Published in Frontiers in molecular biosciences (28.07.2021)
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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
An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45
Koukos, Panagiotis I., Roel‐Touris, Jorge, Ambrosetti, Francesco, Geng, Cunliang, Schaarschmidt, Jörg, Trellet, Mikael E., Melquiond, Adrien S. J., Xue, Li C., Honorato, Rodrigo V., Moreira, Irina, Kurkcuoglu, Zeynep, Vangone, Anna, Bonvin, Alexandre M. J. J.
Published in Proteins, structure, function, and bioinformatics (01.08.2020)
Published in Proteins, structure, function, and bioinformatics (01.08.2020)
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Journal Article
MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing
Honorato, Rodrigo V., Roel-Touris, Jorge, Bonvin, Alexandre M. J. J.
Published in Frontiers in molecular biosciences (01.10.2019)
Published in Frontiers in molecular biosciences (01.10.2019)
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Journal Article
Information-driven modeling of biomolecular complexes
van Noort, Charlotte W., Honorato, Rodrigo V., Bonvin, Alexandre M.J.J.
Published in Current opinion in structural biology (01.10.2021)
Published in Current opinion in structural biology (01.10.2021)
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Journal Article
Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
Lensink, Marc F., Brysbaert, Guillaume, Nadzirin, Nurul, Velankar, Sameer, Chaleil, Raphaël A. G., Gerguri, Tereza, Bates, Paul A., Laine, Elodie, Carbone, Alessandra, Grudinin, Sergei, Kong, Ren, Liu, Ran‐Ran, Xu, Xi‐Ming, Shi, Hang, Chang, Shan, Eisenstein, Miriam, Karczynska, Agnieszka, Czaplewski, Cezary, Lubecka, Emilia, Lipska, Agnieszka, Krupa, Paweł, Mozolewska, Magdalena, Golon, Łukasz, Samsonov, Sergey, Liwo, Adam, Crivelli, Silvia, Pagès, Guillaume, Karasikov, Mikhail, Kadukova, Maria, Yan, Yumeng, Huang, Sheng‐You, Rosell, Mireia, Rodríguez‐Lumbreras, Luis A., Romero‐Durana, Miguel, Díaz‐Bueno, Lucía, Christoffer, Charles, Shin, Woong‐Hee, Aderinwale, Tunde, Maddhuri Venkata Subraman, Sai Raghavendra, Kihara, Daisuke, Kozakov, Dima, Vajda, Sandor, Porter, Kathryn, Padhorny, Dzmitry, Desta, Israel, Beglov, Dmitri, Ignatov, Mikhail, Kotelnikov, Sergey, Moal, Iain H., Ritchie, David W., Chauvot de Beauchêne, Isaure, Maigret, Bernard, Devignes, Marie‐Dominique, Ruiz Echartea, Maria E., Barradas‐Bautista, Didier, Cao, Zhen, Cavallo, Luigi, Oliva, Romina, Cao, Yue, Shen, Yang, Park, Taeyong, Woo, Hyeonuk, Seok, Chaok, Braitbard, Merav, Bitton, Lirane, Scheidman‐Duhovny, Dina, Dapkūnas, Justas, Olechnovič, Kliment, Venclovas, Česlovas, Kundrotas, Petras J., Belkin, Saveliy, Chakravarty, Devlina, Badal, Varsha D., Vakser, Ilya A., Vreven, Thom, Vangaveti, Sweta, Borrman, Tyler, Weng, Zhiping, Guest, Johnathan D., Gowthaman, Ragul, Pierce, Brian G., Xu, Xianjin, Qiu, Liming, Hou, Jie, Ryan Merideth, Benjamin, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Koukos, Panagiotis I., Roel‐Touris, Jorge, Ambrosetti, Francesco, Geng, Cunliang, Trellet, Mikael E., Melquiond, Adrien S. J., Xue, Li, Jiménez‐García, Brian, Noort, Charlotte W., Honorato, Rodrigo V., Bonvin, Alexandre M. J. J., Wodak, Shoshana J.
Published in Proteins, structure, function, and bioinformatics (01.12.2019)
Published in Proteins, structure, function, and bioinformatics (01.12.2019)
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Journal Article
An antibiotic from an uncultured bacterium binds to an immutable target
Shukla, Rhythm, Peoples, Aaron J., Ludwig, Kevin C., Maity, Sourav, Derks, Maik G.N., De Benedetti, Stefania, Krueger, Annika M., Vermeulen, Bram J.A., Harbig, Theresa, Lavore, Francesca, Kumar, Raj, Honorato, Rodrigo V., Grein, Fabian, Nieselt, Kay, Liu, Yangping, Bonvin, Alexandre M.J.J., Baldus, Marc, Kubitscheck, Ulrich, Breukink, Eefjan, Achorn, Catherine, Nitti, Anthony, Schwalen, Christopher J., Spoering, Amy L., Ling, Losee Lucy, Hughes, Dallas, Lelli, Moreno, Roos, Wouter H., Lewis, Kim, Schneider, Tanja, Weingarth, Markus
Published in Cell (14.09.2023)
Published in Cell (14.09.2023)
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Journal Article
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes
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
Published in Nature protocols (17.06.2024)
Published in Nature protocols (17.06.2024)
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Journal Article
KVFinder: steered identification of protein cavities as a PyMOL plugin
Oliveira, Saulo H P, Ferraz, Felipe A N, Honorato, Rodrigo V, Xavier-Neto, José, Sobreira, Tiago J P, de Oliveira, Paulo S L
Published in BMC bioinformatics (17.06.2014)
Published in BMC bioinformatics (17.06.2014)
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Journal Article
Thioredoxin-1 Negatively Modulates ADAM17 Activity Through Direct Binding and Indirect Reductive Activity
Granato, Daniela C, E Costa, Rute A P, Kawahara, Rebeca, Yokoo, Sami, Aragão, Annelize Z, Domingues, Romênia R, Pauletti, Bianca A, Honorato, Rodrigo V, Fattori, Juliana, Figueira, Ana Carolina M, Oliveira, Paulo S L, Consonni, Silvio R, Fernandes, Denise, Laurindo, Francisco, Hansen, Hinrich P, Paes Leme, Adriana F
Published in Antioxidants & redox signaling (10.09.2018)
Published in Antioxidants & redox signaling (10.09.2018)
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Calcium and magnesium ions modulate the oligomeric state and function of mitochondrial 2-Cys peroxiredoxins in Leishmania parasites
Morais, Mariana A.B., Giuseppe, Priscila O., Souza, Tatiana A. C.B., Castro, Helena, Honorato, Rodrigo V., Oliveira, Paulo S.L., Netto, Luis E.S., Tomas, Ana M., Murakami, Mario T.
Published in The Journal of biological chemistry (28.04.2017)
Published in The Journal of biological chemistry (28.04.2017)
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Journal Article
Structural Insights into Functional Overlapping and Differentiation among Myosin V Motors
Nascimento, Andrey F.Z., Trindade, Daniel M., Tonoli, Celisa C.C., de Giuseppe, Priscila O., Assis, Leandro H.P., Honorato, Rodrigo V., de Oliveira, Paulo S.L., Mahajan, Pravin, Burgess-Brown, Nicola A., von Delft, Frank, Larson, Roy E., Murakami, Mario T.
Published in The Journal of biological chemistry (22.11.2013)
Published in The Journal of biological chemistry (22.11.2013)
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Journal Article
Identification of Novel Interaction between ADAM17 (a Disintegrin and Metalloprotease 17) and Thioredoxin-1
Aragão, Annelize Z.B., Nogueira, Maria Luiza C., Granato, Daniela C., Simabuco, Fernando M., Honorato, Rodrigo V., Hoffman, Zaira, Yokoo, Sami, Laurindo, Francisco R.M., Squina, Fabio M., Zeri, Ana Carolina M., Oliveira, Paulo S.L., Sherman, Nicholas E., Paes Leme, Adriana F.
Published in The Journal of biological chemistry (14.12.2012)
Published in The Journal of biological chemistry (14.12.2012)
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Journal Article
Mechanistic Strategies for Catalysis Adopted by Evolutionary Distinct Family 43 Arabinanases
Santos, Camila R., Polo, Carla C., Costa, Maria C.M.F., Nascimento, Andrey F.Z., Meza, Andreia N., Cota, Junio, Hoffmam, Zaira B., Honorato, Rodrigo V., Oliveira, Paulo S.L., Goldman, Gustavo H., Gilbert, Harry J., Prade, Rolf A., Ruller, Roberto, Squina, Fabio M., Wong, Dominic W.S., Murakami, Mário T.
Published in The Journal of biological chemistry (14.03.2014)
Published in The Journal of biological chemistry (14.03.2014)
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Journal Article
A specific interdomain interaction preserves the structural and binding properties of the ModA protein from the phytopathogen Xanthomonas citri domain interaction and transport in ModA
Santacruz-Perez, Carolina, Pegos, Vanessa Rodrigues, Honorato, Rodrigo V., Verli, Hugo, Lindahl, Erik, Barbosa, João Alexandre Ribeiro Gonçalves, Balan, Andrea
Published in Archives of biochemistry and biophysics (01.11.2013)
Published in Archives of biochemistry and biophysics (01.11.2013)
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Journal Article
P-I class metalloproteinase from Bothrops moojeni venom is a post-proline cleaving peptidase with kininogenase activity: Insights into substrate selectivity and kinetic behavior
Okamoto, Débora N., Kondo, Marcia Y., Oliveira, Lilian C.G., Honorato, Rodrigo V., Zanphorlin, Leticia M., Coronado, Monika A., Araújo, Mariana S., da Motta, Guacyara, Veronez, Camila L., Andrade, Sheila S., Oliveira, Paulo S.L., Arni, Raghuvir K., Cintra, Adelia C.O., Sampaio, Suely V., Juliano, Maria A., Juliano, Luiz, Murakami, Mário T., Gouvea, Iuri E.
Published in Biochimica et biophysica acta (01.03.2014)
Published in Biochimica et biophysica acta (01.03.2014)
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Journal Article
Structural studies of the Trypanosoma cruzi Old Yellow Enzyme: Insights into enzyme dynamics and specificity
Murakami, Mário T., Rodrigues, Nathalia C., Gava, Lisandra M., Honorato, Rodrigo V., Canduri, Fernanda, Barbosa, Leandro R.S., Oliva, Glaucius, Borges, Júlio C.
Published in Biophysical chemistry (31.12.2013)
Published in Biophysical chemistry (31.12.2013)
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Journal Article
Bactericidal Activity Identified in 2S Albumin from Sesame Seeds and In silico Studies of Structure–Function Relations
Maria-Neto, Simone, Honorato, Rodrigo V., Costa, Fábio T., Almeida, Renato G., Amaro, Daniel S., Oliveira, José T. A., Vasconcelos, Ilka M., Franco, Octávio L.
Published in Protein Journal (01.06.2011)
Published in Protein Journal (01.06.2011)
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