R
Rodrigo V. Honorato
Researcher at Utrecht University
Publications - 37
Citations - 1053
Rodrigo V. Honorato is an academic researcher from Utrecht University. The author has contributed to research in topics: Glutaminase & Macromolecular docking. The author has an hindex of 13, co-authored 35 publications receiving 589 citations. Previous affiliations of Rodrigo V. Honorato include University of São Paulo & Universidade Católica de Brasília.
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Journal ArticleDOI
Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem
Rodrigo V. Honorato,Panagiotis I. Koukos,Brian Jiménez-García,Andrei Tsaregorodtsev,M. Verlato,Andrea Giachetti,Antonio Rosato,Alexandre M. J. J. Bonvin +7 more
TL;DR: The European Open Science Cloud (EOSC) portal has been used for the WeNMR project as mentioned in this paper since 2010 and has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field.
Journal ArticleDOI
KVFinder: steered identification of protein cavities as a PyMOL plugin
Saulo H. P. de Oliveira,Saulo H. P. de Oliveira,Felipe Augusto Nunes Ferraz,Rodrigo V. Honorato,José Xavier-Neto,Tiago J. P. Sobreira,Paulo S. L. Oliveira +6 more
TL;DR: KVFinder presents novel usability features, granting full customizable and highly detailed cavity prospection on proteins, alongside with a friendly graphical interface, which outperform all other compared methods.
Journal ArticleDOI
Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
Outi M. H. Salo-Ahen,Ida Alanko,Rajendra Bhadane,Alexandre M. J. J. Bonvin,Rodrigo V. Honorato,Shakhawath Hossain,André H. Juffer,Aleksei Kabedev,Maija Lahtela-Kakkonen,Anders S. Larsen,Eveline Lescrinier,Parthiban Marimuthu,Muhammad Usman Mirza,Ghulam Mustafa,Ariane Nunes-Alves,Ariane Nunes-Alves,Tatu Pantsar,Tatu Pantsar,Atefeh Saadabadi,Kalaimathy Singaravelu,Michiel Vanmeert +20 more
TL;DR: A broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development is given, including how MD can be used in studying the crystalline and amorphous solids, the stability ofAmorphous drug or drug-polymer formulations, and drug solubility.
Journal ArticleDOI
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.
Marc F. Lensink,Guillaume Brysbaert,Nurul Nadzirin,Sameer Velankar,Raphael A. G. Chaleil,Tereza Gerguri,Paul A. Bates,Elodie Laine,Alessandra Carbone,Alessandra Carbone,Sergei Grudinin,Ren Kong,Ranran Liu,Xu Ximing,Hang Shi,Shan Chang,Miriam Eisenstein,Agnieszka S. Karczyńska,Cezary Czaplewski,Emilia A. Lubecka,Agnieszka G. Lipska,Paweł Krupa,Magdalena A. Mozolewska,Łukasz Golon,Sergey A. Samsonov,Adam Liwo,Adam Liwo,Silvia Crivelli,Guillaume Pagès,Mikhail Karasikov,Maria Kadukova,Maria Kadukova,Yumeng Yan,Sheng-You Huang,Mireia Rosell,Mireia Rosell,Luis A. Rodríguez-Lumbreras,Luis A. Rodríguez-Lumbreras,Miguel Romero-Durana,Lucía Díaz-Bueno,Juan Fernández-Recio,Juan Fernández-Recio,Charles Christoffer,Genki Terashi,Woong-Hee Shin,Tunde Aderinwale,Sai Raghavendra Maddhuri Venkata Subraman,Daisuke Kihara,Dima Kozakov,Sandor Vajda,Kathyn Porter,Dzmitry Padhorny,Israel Desta,Dmitri Beglov,Mikhail Ignatov,Sergey Kotelnikov,Sergey Kotelnikov,Iain H. Moal,David W. Ritchie,Isaure Chauvot de Beauchêne,Bernard Maigret,Marie-Dominique Devignes,Maria Elisa Ruiz Echartea,Didier Barradas-Bautista,Zhen Cao,Luigi Cavallo,Romina Oliva,Yue Cao,Yang Shen,Minkyung Baek,Taeyong Park,Hyeonuk Woo,Chaok Seok,M. Braitbard,Lirane Bitton,Dina Scheidman-Duhovny,Justas Dapkūnas,Kliment Olechnovič,Česlovas Venclovas,Petras J. Kundrotas,Saveliy Belkin,Devlina Chakravarty,Varsha D. Badal,Ilya A. Vakser,Thom Vreven,Sweta Vangaveti,Tyler M. Borrman,Zhiping Weng,Johnathan D. Guest,Ragul Gowthaman,Brian G. Pierce,Xianjin Xu,Rui Duan,Liming Qiu,Jie Hou,Benjamin Ryan Merideth,Zhiwei Ma,Jianlin Cheng,Xiaoqin Zou,Panos Koukos,Jorge Roel-Touris,Francesco Ambrosetti,Cunliang Geng,Jörg Schaarschmidt,Mikael Trellet,Adrien S. J. Melquiond,Li C. Xue,Brian Jiménez-García,Charlotte W. van Noort,Rodrigo V. Honorato,Alexandre M. J. J. Bonvin,Shoshana J. Wodak +111 more
TL;DR: CAPRI Round 46 indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.
Journal ArticleDOI
Active Glutaminase C Self-assembles into a Supratetrameric Oligomer That Can Be Disrupted by an Allosteric Inhibitor
Amanda Petrina Scotá Ferreira,Alexandre Cassago,Kaliandra de Almeida Gonçalves,Marília M. Dias,Douglas Adamoski,Carolline Fernanda Rodrigues Ascenção,Rodrigo V. Honorato,Juliana Ferreira de Oliveira,Igor M. Ferreira,Camila Fornezari,Jefferson Bettini,Paulo S. L. Oliveira,Adriana Franco Paes Leme,Rodrigo Villares Portugal,Andre Luis Berteli Ambrosio,Sandra Martha Gomes Dias +15 more
TL;DR: It is demonstrated that activated glutaminase C (GAC) self-assembles into a helical, fiber-like double-stranded oligomer and proposed a molecular model consisting of seven tetramer copies per turn per strand interacting via the N-terminal domains, which yield unique implications for the development of GAC-oriented therapeutics targeting tumor metabolism.