Search Results - "Polêto, Marcelo D."

Making it Rain: Cloud-Based Molecular Simulations for Everyone by Arantes, Pablo R, Polêto, Marcelo D, Pedebos, Conrado, Ligabue-Braun, Rodrigo

“…We present a user-friendly front-end for running molecular dynamics (MD) simulations using the OpenMM toolkit on the Google Colab framework. Our goals are (1)…”
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Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G‑Quadruplexes by Polêto, Marcelo D., Lemkul, Justin A.

“…The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA, producing highly stable and structurally diverse noncanonical nucleic…”
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TUPÃ: Electric field analyses for molecular simulations by Polêto, Marcelo D., Lemkul, Justin A.

“…We introduce TUPÃ, a Python‐based algorithm to calculate and analyze electric fields in molecular simulations. To demonstrate the features in TUPÃ, we present…”
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Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F430 Modifications by Polêto, Marcelo D., Allen, Kylie D., Lemkul, Justin A.

“…Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in…”
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Role of structural ions on the dynamics of the Pseudomonas fluorescens 07A metalloprotease by Polêto, Marcelo D., Alves, Maura P., Ligabue-Braun, Rodrigo, Eller, Monique R., De carvalho, Antonio Fernandes

“…•The metalloprotease is composed by three conserved domains.•The Mn+2 and Ca+2 ions partially protect the enzyme from thermal denaturation.•A dynamical model…”
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The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains by Arantes, Pablo R, Pedebos, Conrado, Polêto, Marcelo D, Pol-Fachin, Laércio, Verli, Hugo

“…Lipid-linked oligosaccharides (LLOs) play an important role in the N-glycosylation pathway as the donor substrate of oligosaccharyl­transferases (OSTs), which…”
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Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities by Polêto, Marcelo D, Rusu, Victor H, Grisci, Bruno I, Dorn, Marcio, Lins, Roberto D, Verli, Hugo

“…The identification of lead compounds usually includes a step of chemical diversity generation. Its rationale may be supported by both qualitative (SAR) and…”
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Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids by Arantes, Pablo R, Polêto, Marcelo D, John, Elisa B. O, Pedebos, Conrado, Grisci, Bruno I, Dorn, Marcio, Verli, Hugo

“…Chalcones and flavonoids constitute a large family of plant secondary metabolites that have been explored as a potential source of novel pharmaceutical…”
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ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories by Polêto, Marcelo D, Grisci, Bruno I, Dorn, Marcio, Verli, Hugo

“…Abstract Motivation The conformational space of small molecules can be vast and difficult to assess. Molecular dynamics (MD) simulations of free ligands in…”
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Integration of experimental data and use of automated fitting methods in developing protein force fields by Polêto, Marcelo D., Lemkul, Justin A.

“…The development of accurate protein force fields has been the cornerstone of molecular simulations for the past 50 years. During this period, many lessons have…”
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An Unusual Intramolecular Halogen Bond Guides Conformational Selection by Tesch, Roberta, Becker, Christian, Müller, Matthias Philipp, Beck, Michael Edmund, Quambusch, Lena, Getlik, Matthäus, Lategahn, Jonas, Uhlenbrock, Niklas, Costa, Fanny Nascimento, Polêto, Marcelo D., Pinheiro, Pedro de Sena Murteira, Rodrigues, Daniel Alencar, Sant'Anna, Carlos Mauricio R., Ferreira, Fabio Furlan, Verli, Hugo, Fraga, Carlos Alberto Manssour, Rauh, Daniel

“…PIK‐75 is a phosphoinositide‐3‐kinase (PI3K) α‐isoform‐selective inhibitor with high potency. Although published structure–activity relationship data show the…”
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Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein by Giacon, Noah, Lo Cascio, Ettore, Davidson, Darcy S., Polêto, Marcelo D., Lemkul, Justin A., Pennacchietti, Valeria, Pagano, Livia, Zamparelli, Carlotta, Toto, Angelo, Arcovito, Alessandro

“…The Envelope (E) protein of SARS-CoV-2 plays a key role in virus maturation, assembly, and virulence mechanisms. The E protein is characterized by the presence…”
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Discovery of novel West Nile Virus protease inhibitor based on isobenzonafuranone and triazolic derivatives of eugenol and indan-1,3-dione scaffolds by de Oliveira, André S, Gazolla, Poliana A R, Oliveira, Ana Flávia C da S, Pereira, Wagner L, de S Viol, Lívia C, Maia, Angélica F da S, Santos, Edjon G, da Silva, Ítalo E P, Mendes, Tiago A de Oliveira, da Silva, Adalberto M, Dias, Roberto S, da Silva, Cynthia C, Polêto, Marcelo D, Teixeira, Róbson R, de Paula, Sergio O

“…The West Nile Virus (WNV) NS2B-NS3 protease is an attractive target for the development of therapeutics against this arboviral pathogen. In the present…”
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ESI-MS/MS of expanded porphyrins: a look into their structure and aromaticity by Ramos, Catarina IV, Figueira, Flávio, Polêto, Marcelo D, Amado, Francisco ML, Verli, Hugo, Tomé, João PC, Neves, M Graça PMS

“…Electrospray mass spectrometry/mass spectrometry was used to investigate the gas‐phase properties of protonated expanded porphyrins, in order to correlate…”
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Structural and Electronic Properties of Poly(ethylene terephthalate) (PET) from Polarizable Molecular Dynamics Simulations by Polêto, Marcelo D., Lemkul, Justin A.

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porcine circovirus-2 mutant isolated in Brazil contains low-frequency substitutions in regions of immunoprotective epitopes in the capsid protein by Salgado, Rafael Locatelli, Vidigal, Pedro Marcus Pereira, Gonzaga, Natalia F, de Souza, Luiz F. L, Polêto, Marcelo D, Onofre, Thiago Souza, Eller, Monique R, Pereira, Carlos Eduardo Real, Fietto, Juliana L. R, Bressan, Gustavo C, Guedes, Roberto M. C, Almeida, Márcia R, Silva Júnior, Abelardo

“…Porcine circovirus-2 (PCV2) is the etiologic agent of several diseases in pigs, including multi-systemic wasting syndrome (PMWS). In this work, a new mutant…”
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Active-site electronic properties and conformational dynamics of pet-degrading enzymes by Polêto, Marcelo D., Lemkul, Justin A.

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Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F 430 Modifications by Polêto, Marcelo D, Allen, Kylie D, Lemkul, Justin A

“…Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in…”
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Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations by Fischer, Nina M, Polêto, Marcelo D, Steuer, Jakob, van der Spoel, David

“…Abstract The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg2+ cations to stabilize structural…”
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Integration of experimental data and use of automated fitting methods in developing protein force fields by Polêto, Marcelo D, Lemkul, Justin A

“…The development of accurate protein force fields has been the cornerstone of molecular simulations for the past 50 years. During this period, many lessons have…”
Get full text