Osmar Norberto de Souza

Osmar Norberto de Souza

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Osmar Norberto de Souza

Osmar Norberto de Souza

Publications by authors named "Osmar Norberto de Souza"

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The importance of the quaternary structure to represent conformational ensembles of the major Mycobacterium tuberculosis drug target.

Sci Rep 2019 Sep 23;9(1):13683. Epub 2019 Sep 23.

Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, 90619-900, Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1038/s41598-019-50213-0DOI Listing
September 2019

Missense mutations in DYT-TOR1A dystonia.

Neurol Genet 2019 Aug 6;5(4):e343. Epub 2019 Jun 6.

Department of Neurology (Z.I., L.P., S.P.H., C.C,. I.M.S,. M.T), Oslo University Hospital; Institute of Clinical Medicine (J.K., M.T), University of Oslo; Department of Neurology (J.K), Drammen Hospital, Vestre Viken Hospital Trust; Head and Neck Research Group, Research Center (M.B.R), Akershus University Hospital; Campus Akershus University Hospital (M.B.R), University of Oslo, Norway; and Faculty of Informatics, Laboratory for Bioinformatics, Modelling & Simulation of Biosystems (O.N.D.S), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1212/NXG.0000000000000343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563516PMC
August 2019

A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model.

BMC Bioinformatics 2018 06 22;19(1):235. Epub 2018 Jun 22.

Bioinformatics and Biossystems Modeling and Simulation Lab-LABIO, School of Technology, PUCRS, Av. Ipiranga, 6681, Building 32, Room 602, Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1186/s12859-018-2222-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013854PMC
June 2018

Activity of 2-(quinolin-4-yloxy)acetamides in Mycobacterium tuberculosis clinical isolates and identification of their molecular target by whole-genome sequencing.

Int J Antimicrob Agents 2018 Mar 23;51(3):378-384. Epub 2017 Aug 23.

Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga 6681 - Prédio 92A Tecnopuc, Porto Alegre, RS 90619-900, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil.

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http://dx.doi.org/10.1016/j.ijantimicag.2017.08.023DOI Listing
March 2018

EPSP synthase flexibility is determinant to its function: computational molecular dynamics and metadynamics studies.

J Mol Model 2017 Jul 7;23(7):197. Epub 2017 Jun 7.

Laboratory for Bioinformatics, Modelling and Simulation of Biosystems (LABIO), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681 - LABIO, Prédio 32, Sala 602, Partenon, Porto Alegre, RS, CEP: 90619-900, Brazil.

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http://dx.doi.org/10.1007/s00894-017-3372-2DOI Listing
July 2017

Functional, thermodynamics, structural and biological studies of in silico-identified inhibitors of Mycobacterium tuberculosis enoyl-ACP(CoA) reductase enzyme.

Sci Rep 2017 04 24;7:46696. Epub 2017 Apr 24.

Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1038/srep46696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402281PMC
April 2017

An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features.

PLoS One 2015 28;10(7):e0133172. Epub 2015 Jul 28.

Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas-LABIO, Faculdade de Informática, PUCRS, Av. Ipiranga, 6681- Building 32, Room 602, Porto Alegre, RS, Brasil.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0133172PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517875PMC
May 2016

Clustering molecular dynamics trajectories for optimizing docking experiments.

Comput Intell Neurosci 2015 22;2015:916240. Epub 2015 Mar 22.

Grupo de Pesquisa em Aprendizado de Máquina e Inteligência de Negócio (GPIN), Faculdade de Informática, PUCRS, Prédio 32, Sala 628, 90619-900 Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1155/2015/916240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385651PMC
October 2015

Piperazine derivatives: synthesis, inhibition of the Mycobacterium tuberculosis enoyl-acyl carrier protein reductase and SAR studies.

Eur J Med Chem 2015 Jan 18;90:436-47. Epub 2014 Nov 18.

Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, Rio Grande do Sul, Brazil. Electronic address:

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http://dx.doi.org/10.1016/j.ejmech.2014.11.034DOI Listing
January 2015

Biochemical and cellular analysis of human variants of the DYT1 dystonia protein, TorsinA/TOR1A.

Hum Mutat 2014 Sep 17;35(9):1101-13. Epub 2014 Jul 17.

Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts; Department of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany.

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http://dx.doi.org/10.1002/humu.22602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4134760PMC
September 2014

An interval-based algorithm to represent conformational states of experimentally determined polypeptide templates and fast prediction of approximated 3D protein structures.

Int J Bioinform Res Appl 2013 ;9(5):462-86

LABIO, PPGCC, Faculdade de Informática, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga, 6681, Prédio 32, Sala 602 90619-900 - Porto Alegre - RS - Brasil.

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http://dx.doi.org/10.1504/IJBRA.2013.056075DOI Listing
March 2014

wFReDoW: a cloud-based web environment to handle molecular docking simulations of a fully flexible receptor model.

Biomed Res Int 2013 11;2013:469363. Epub 2013 Apr 11.

Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Faculdade de Informática (FACIN), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1155/2013/469363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652109PMC
December 2013

Biochemical characterization of recombinant nucleoside hydrolase from Mycobacterium tuberculosis H37Rv.

Arch Biochem Biophys 2013 Oct 26;538(2):80-94. Epub 2013 Aug 26.

Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 6681/92-A Av. Ipiranga, 90619-900 Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1016/j.abb.2013.08.011DOI Listing
October 2013

Discovery of new inhibitors of Mycobacterium tuberculosis InhA enzyme using virtual screening and a 3D-pharmacophore-based approach.

J Chem Inf Model 2013 Sep 20;53(9):2390-401. Epub 2013 Aug 20.

Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas - LABIO, Faculdade de Informática, PUCRS , Brazil.

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http://dx.doi.org/10.1021/ci400202tDOI Listing
September 2013

Conformational changes in 2-trans-enoyl-ACP (CoA) reductase (InhA) from M. tuberculosis induced by an inorganic complex: a molecular dynamics simulation study.

J Mol Model 2012 May 12;18(5):1779-90. Epub 2011 Aug 12.

LABIO-Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas, PPGCC, Faculdade de Informática, PUCRS, Porto Alegre, RS, Brasil.

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http://dx.doi.org/10.1007/s00894-011-1200-7DOI Listing
May 2012

FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection.

BMC Genomics 2011 Dec 22;12 Suppl 4:S6. Epub 2011 Dec 22.

LABIO - Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas, PPGCC, Faculdade de Informática, PUCRS, Av, Ipiranga, 6681 - Prédio 32, Sala 602, 90619-900, Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1186/1471-2164-12-S4-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287589PMC
December 2011

Effect of the explicit flexibility of the InhA enzyme from Mycobacterium tuberculosis in molecular docking simulations.

BMC Genomics 2011 Dec 22;12 Suppl 4:S7. Epub 2011 Dec 22.

Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas - LABIO, Programa de Pós-Graduação em Ciência da Computação - PPGCC - Faculdade de Informática - PUCRS - Av, Ipiranga, 6681 Prédio 32 - Sala 608, CEP: 90619-900, Porto Alegre, RS, Brasil.

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http://dx.doi.org/10.1186/1471-2164-12-S4-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287590PMC
December 2011

Mining flexible-receptor docking experiments to select promising protein receptor snapshots.

BMC Genomics 2010 Dec 22;11 Suppl 5:S6. Epub 2010 Dec 22.

LABIO - Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas, PPGCC, Faculdade de Informática, PUCRS, Av. Ipiranga, 6681 - Prédio 32, sala 602, 90619-900, Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1186/1471-2164-11-S5-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045799PMC
December 2010

Mining the protein data bank with CReF to predict approximate 3-D structures of polypeptides.

Int J Data Min Bioinform 2010 ;4(3):281-99

Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas--LABIO, Programa de Pós-Graduação em Ciência da Computação, Faculdade de Informática, Pontificia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil.

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October 2010

Evaluation of the impact of functional diversification on Poaceae, Brassicaceae, Fabaceae, and Pinaceae alcohol dehydrogenase enzymes.

J Mol Model 2010 May 16;16(5):919-28. Epub 2009 Oct 16.

Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970, Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1007/s00894-009-0576-0DOI Listing
May 2010

Sequence and structural aspects of the functional diversification of plant alcohol dehydrogenases.

Gene 2007 Jul 13;396(1):108-15. Epub 2007 Mar 13.

Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970 Porto Alegre, RS, Brazil.

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http://dx.doi.org/10.1016/j.gene.2007.02.016DOI Listing
July 2007

A structural model for chorismate synthase from Mycobacterium tuberculosis in complex with coenzyme and substrate.

Comput Biol Med 2007 Feb 11;37(2):149-58. Epub 2006 Apr 11.

Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas-LABIO, Faculdade de Informática, PUCRS, Brazil.

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http://dx.doi.org/10.1016/j.compbiomed.2006.01.001DOI Listing
February 2007