Search Results - "Ribeiro, André A"

Mixed monte carlo/molecular dynamics simulations in explicit solvent by Ribeiro, André A. S. T., de Alencastro, Ricardo B.

“…A mixed Monte Carlo/Molecular Dynamics method using the trial moves for peptide backbone sampling known as Concerted Rotations with Angles was implemented. The…”
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A Chemical Perspective on Allostery by Ribeiro, Andre A. S. T, Ortiz, Vanessa

“…Much work has been done in the past decade to quantify the phenomenon of allosteric communication in proteins. Every new study unveils an extra piece of the…”
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Determination of Signaling Pathways in Proteins through Network Theory: Importance of the Topology by Ribeiro, Andre A. S. T, Ortiz, Vanessa

“…Network theory methods are being increasingly applied to proteins to investigate complex biological phenomena. Residues that are important for signaling…”
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Energy Propagation and Network Energetic Coupling in Proteins by Ribeiro, Andre A. S. T, Ortiz, Vanessa

“…Understanding how allosteric proteins respond to changes in their environment is a major goal of current biological research. We show that these responses can…”
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The Diamond STING server by Neshich, Goran, Borro, Luiz C., Higa, Roberto H., Kuser, Paula R., Yamagishi, Michel E. B., Franco, Eduardo H., Krauchenco, Joao N., Fileto, Renato, Ribeiro, André A., Bezerra, George B. P., Velludo, Thiago M., Jimenez, Tomás S., Furukawa, Noboru, Teshima, Hirofumi, Kitajima, Koji, Bava, Abdulla, Sarai, Akinori, Togawa, Roberto C., Mancini, Adauto L.

“…Diamond STING is a new version of the STING suite of programs for a comprehensive analysis of a relationship between protein sequence, structure, function and…”
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MKTOP: a program for automatic construction of molecular topologies by Ribeiro, André A. S. T., Horta, Bruno A. C., Alencastro, Ricardo B. de

“…Molecular mechanics methods are widely-used for simulations of biomolecules. A molecular topology file containing all atom types, which depend on the chemical…”
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Solvent effects in Spectroscopy and Reactivity of Molecular Liquids: Contributions from Sylvio Canuto by Ribeiro, André A. S. T., de Alencastro, Ricardo B.

“…Sylvio Canuto obtained his PhD in 1979 at the University of Uppsala (Sweden). His scientific contributions include about 180 well‐cited articles. He is…”
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Theoretical study of the gas-phase reaction between formyl cation and aromatics by Ribeiro, André A. S. T., Mota, Claudio J. A.

“…Theoretical calculations of the reaction of formyl cation (CHO+) with toluene, cumene and p-cresol showed that proton transfer is thermodynamically preferred…”
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MDN: A Web Portal for Network Analysis of Molecular Dynamics Simulations by Ribeiro, Andre A.S.T., Ortiz, Vanessa

“…We introduce a web portal that employs network theory for the analysis of trajectories from molecular dynamics simulations. Users can create protein energy…”
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Local elastic constants of LacI and implications for allostery by Ribeiro, Andre A.S.T., Ortiz, Vanessa

“…[Display omitted] •We calculate elastic constants of a protein system (lac repressor).•We determine a stiffness map of the protein and show regions prone to…”
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Mixed Monte Carlo/Molecular Dynamics simulations of the prion protein by Ribeiro, Andre A.S.T., de Alencastro, Ricardo B.

“…[Display omitted] ► We applied the recently proposed MC(CRA)/MD scheme to the prion protein. ► The MC/MD simulations revealed structural changes that were not…”
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PDB-Metrics: a web tool for exploring the PDB contents by Fileto, Renato, Kuser, Paula R, Yamagishi, Michel E B, Ribeiro, André A, Quinalia, Thiago G, Franco, Eduardo H, Mancini, Adauto L, Higa, Roberto H, Oliveira, Stanley R M, Santos, Edgard H, Vieira, Fabio D, Mazoni, Ivan, Cruz, Sergio A B, Neshich, Goran

“…PDB-Metrics (http://sms.cbi.cnptia.embrapa.br/SMS/pdb_metrics/index.html) is a component of the Diamond STING suite of programs for the analysis of protein…”
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Resection of a rapid-growing 40-cm giant liver hemangioma by Koszka, Andreas Jm, Ferreira, Fabio G, de Aquino, Caio Gg, Ribeiro, Maurício A, Gallo, André S, Aranzana, Elisa Mc, Szutan, Luiz A

“…Hemangiomas are the most frequent benign tumors of the liver. Most hemangiomas are asymptomatic and therefore largely diagnosed only in routine screening…”
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Analysis of 12 variants in the development of gastric and colorectal cancers by Cavalcante, Giovanna C, Amador, Marcos At, Ribeiro Dos Santos, André M, Carvalho, Darlen C, Andrade, Roberta B, Pereira, Esdras Eb, Fernandes, Marianne R, Costa, Danielle F, Santos, Ney Pc, Assumpção, Paulo P, Ribeiro Dos Santos, Ândrea, Santos, Sidney

“…AIM To evaluate the relation between 12 polymorphisms and the development of gastric cancer(GC) and colorectal cancer(CRC).METHODS In this study,we included…”
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