Search Results - "MACHADO, Karina S"

Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data by Barros, Rodrigo C, Winck, Ana T, Machado, Karina S, Basgalupp, Márcio P, de Carvalho, André C P L F, Ruiz, Duncan D, de Souza, Osmar Norberto

“…This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem…”
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FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection by Machado, Karina S, Schroeder, Evelyn K, Ruiz, Duncan D, Cohen, Elisângela M L, de Souza, Osmar Norberto

“…In silico molecular docking is an essential step in modern drug discovery when driven by a well defined macromolecular target. Hence, the process is called…”
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Inference of regulatory networks with a convergence improved MCMC sampler by Agostinho, Nilzair B, Machado, Karina S, Werhli, Adriano V

“…One of the goals of the Systems Biology community is to have a detailed map of all biological interactions in an organism. One small yet important step in this…”
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In vitro and in silico analysis of the efficiency of tetrahydropyridines as drug efflux inhibitors in Escherichia coli by Silva, Lande, Carrion, Lillian Lucas, von Groll, Andrea, Costa, Sofia Santos, Junqueira, Elisabete, Ramos, Daniela Fernandes, Cantos, Jéssica, Seus, Vinicius Rosa, Couto, Isabel, Fernandes, Liana da Silva, Bonacorso, Hélio Gauze, Martins, Marcos Antônio Pinto, Zanatta, Nilo, Viveiros, Miguel, Machado, Karina S, Almeida da Silva, Pedro Eduardo

“…Highlights • Tetrahydropyridine derivatives are capable of inhibiting efflux by AcrB. • Tetrahydropyridine derivative NUNL02 was found to be an AcrB efflux…”
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Decrypting Strong and Weak Single-Walled Carbon Nanotubes Interactions with Mitochondrial Voltage-Dependent Anion Channels Using Molecular Docking and Perturbation Theory by González-Durruthy, Michael, Werhli, Adriano V., Seus, Vinicius, Machado, Karina S., Pazos, Alejandro, Munteanu, Cristian R., González-Díaz, Humberto, Monserrat, José M.

“…The current molecular docking study provided the Free Energy of Binding (FEB) for the interaction (nanotoxicity) between VDAC mitochondrial channels of three…”
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Sedimentary record of PAHs in the Barigui River and its relation to the socioeconomic development of Curitiba, Brazil by Machado, Karina S., Figueira, Rubens C.L., Côcco, Lilian C., Froehner, Sandro, Fernandes, Cristovão V.S., Ferreira, Paulo A.L.

“…Concentrations of polycyclic aromatic hydrocarbons (PAHs) were determined in a sediment core collected from the Barigui River, in Curitiba, South Brazil. The…”
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A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers by Rocha, Rafael E. O., Chaves, Elton J. F., Fischer, Pedro H. C., Costa, Leon S. C., Grillo, Igor Barden, da Cruz, Luiz E. G., Guedes, Fabiana C., da Silveira, Carlos H., Scotti, Marcus T., Camargo, Alex D., Machado, Karina S., Werhli, Adriano V., Ferreira, Rafaela S., Rocha, Gerd B., de Lima, Leonardo H. F.

“…The main-protease (M pro ) catalyzes a crucial step for the SARS-CoV-2 life cycle. The recent SARS-CoV-2 presents the main protease (M CoV2 pro ) with 12…”
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Assessment of historical fecal contamination in Curitiba, Brazil, in the last 400years using fecal sterols by Machado, Karina S., Froehner, Sandro, Sánez, Juan, Figueira, Rubens C.L., Ferreira, Paulo A.L.

“…A 400-year sedimentary record of the Barigui River was investigated using fecal biomarkers and nutrient distribution. The temporal variability in cholesterol,…”
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Assessment of historical fecal contamination in Curitiba, Brazil, in the last 400 years using fecal sterols by MACHADO, Karina S, FROEHNER, Sandro, SANEZ, Juan, FIGUEIRA, Rubens C. L, FERREIRA, Paulo A. L

“…A 400-year sedimentary record of the Barigui River was investigated using fecal biomarkers and nutrient distribution. The temporal variability in cholesterol,…”
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Effect of the explicit flexibility of the InhA enzyme from Mycobacterium tuberculosis in molecular docking simulations by Cohen, Elisangela M L, Machado, Karina S, Cohen, Marcelo, de Souza, Osmar Norberto

“…Protein/receptor explicit flexibility has recently become an important feature of molecular docking simulations. Taking the flexibility into account brings the…”
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Context-based preprocessing of molecular docking data by Winck, Ana T, Machado, Karina S, de Souza, Osmar Norberto, Ruiz, Duncan D

“…Data preprocessing is a major step in data mining. In data preprocessing, several known techniques can be applied, or new ones developed, to improve data…”
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An Infrastructure to Mine Molecular Descriptors for Ligand Selection on Virtual Screening by Seus, Vinicius Rosa, Perazzo, Giovanni Xavier, Winck, Ana T., Werhli, Adriano V., Machado, Karina S.

“…The receptor-ligand interaction evaluation is one important step in rational drug design. The databases that provide the structures of the ligands are growing…”
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Mining flexible-receptor docking experiments to select promising protein receptor snapshots by Machado, Karina S, Winck, Ana T, Ruiz, Duncan D A, de Souza, Osmar Norberto

“…Molecular docking simulation is the Rational Drug Design (RDD) step that investigates the affinity between protein receptors and ligands. Typically, molecular…”
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Mining flexible-receptor molecular docking data by Machado, Karina S., Winck, Ana T., Ruiz, Duncan D., Norberto de Souza, Osmar

“…Knowledge discovery in databases has become an integral part of practically every aspect of bioinformatics research, which usually produces, and has to…”
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Whole-genome sequencing as a tool for studying the microevolution of drug-resistant serial Mycobacterium tuberculosis isolates by de Lourdes do Carmo Guimarães Diniz, Jaciara, von Groll, Andrea, Unis, Gisela, Dalla-Costa, Elis Regina, Rosa Rossetti, Maria Lúcia, Vianna, Júlia Silveira, Ramos, Daniela Fernandes, Reis, Ana Júlia, Bartolomeu Halicki, Priscila Cristina, Rheingantz Scaini, João Luis, Castillos de Ibrahim das Neves, Yasmin, Phelan, Jody, Gomes, Ana Rita, Campino, Susana, Machado, Karina dos Santos, Werhli, Adriano Velasque, Pain, Arnab, Clark, Taane Gregory, Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Almeida Silva, Pedro Eduardo

“…Treatment of drug-resistant tuberculosis requires extended use of more toxic and less effective drugs and may result in retreatment cases due to failure,…”
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Parallel Algorithm for the HP Protein Folding Problem by Dos Santos, Matheus M., Goulart, Mauricio G., Gelatti, Giovana J., Machado, Karina S., Werhli, Adriano V., Mendizabal, Odorico M.

“…Proteins play a key role in cells' function and metabolism. Their functions are directly related with the three-dimensional (3D) native structure. Different…”
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