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Master's Dissertation
DOI
10.11606/D.60.2010.tde-17112010-093652
Document
Author
Full name
Tulio Marcus Ribeiro Calixto
E-mail
Institute/School/College
Knowledge Area
Date of Defense
Published
Ribeirão Preto, 2010
Supervisor
Committee
Silva, Fernando Luis Barroso da (President)
Delbem, Alexandre Cláudio Botazzo
Vencio, Ricardo Zorzetto Nicoliello
Title in Portuguese
Análises de propriedades eletrostáticas e estruturais de complexos de proteínas para o desenvolvimento de preditores de complexação em larga escala
Keywords in Portuguese
Banco de dados de proteínas
Biocomputação
Coeficiente de virial
Potenciais estatísticos
Preditores de complexos protéicos
Propriedades eletrostáticas
Regulação de cargas
Abstract in Portuguese
Estudos teóricos dos mecanismos moleculares responsáveis pela formação e estabilidade de complexos moleculares vêm ganhando relevância pelas possibilidades práticas que oferecem, por exemplo, na compreensão de diversas doenças e no desenho racional de fármacos. Neste projeto, nossa ênfase está no estudo de complexos de proteínas, extraídos do banco de dados de proteínas (PDB), onde desenvolvemos ferramentas computacionais as quais permitem efetuar análises em duas direções: 1) efetuar previsões básicas, através do emprego de propriedades eletrostáticas de proteínas, em diferentes condições e níveis preditivos e 2) realização de um conjunto de análises estatísticas, como freqüência de contato, em busca de preditores de complexos de proteínas e identificar padrões de interação entre seus aminoácidos em função da distância de separação. Com base nos resultados obtidos por ambos os estudos, objetivamos quantificar as forças físicas envolvidas na formação dos complexos protéicos. O foco do projeto, a longo prazo, é prever o fenômeno da complexação através da fusão dessas duas linhas de estudos: preditor básico de complexos protéicos e análise do potencial estatístico entre os aminoácidos que formam o complexo. O presente projeto é concluído com a construção de portais web que disponibilizarão os resultados obtidos por nossos trabalhos bem como a possibilidade de qualquer usuário, efetuar consultas por propriedades de proteínas e/ou grupo de proteínas.
Title in English
Analysis of electrostatic and structural properties of protein complexes to the development of complexation predictors in high-throughput computing
Keywords in English
Biocomputing
Charge regulation
Electrostatic Interactions
Predictor of protein complexes
Protein data bank
Statistical potential
Virial coefficient
Abstract in English
Theoretical studies of the molecular mechanisms responsible for the formation and stability of molecular complexes are gaining relevance for the practical possibilities that they offer, for example, in the understanding of diverse diseases and rational drug design. In this project, our emphasis is on the study of protein complexes, extracted from protein data bank (PDB). We have developed computational tools which allow to perform analyses in two directions: 1) to make basic complexation forecasts, through the use of electrostatics properties of proteins, in different conditions and predictive levels, and 2) to carry out a set of statistical analyses, as contacts frequency, in order to build up predictor of protein complexes and to identify patters of interactions between the amino acids as a function of their separation distance. Based on the results obtained on both studies, we aim quantify the physical forces involved in the formation of protein complexes. The focus of the project, in the long run, is to foresee the phenomenon of the protein complexes through the fusing of these two study lines: a coarse-grained predictor of protein complexes and analysis of the statistical potentials between the amino acids that form the complex. The present project is concluded with the construction of web services where we make available the results obtained on our works. This server also has the possibility to be used by any computer user, that wishes to perform search on protein and/or protein group properties
 
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Publishing Date
2011-07-11
 
WARNING: The material described below relates to works resulting from this thesis or dissertation. The contents of these works are the author's responsibility.
  • Bojczuk, Daniel, et al. OMX Prometheus Tools: Large-scale study of proteins interaction/complexation. In X-meeting - 5th International Conference of the Brazilian Association for Bioinformatics and Computational Biology, Angra dos Reis, 2009. X-meeting., 2009. Abstract. Available from: http://www.x-meeting.com/.
  • Calixto, Tulio Marcus Ribeiro, and Da SILVA, F. L. B. Molesa - a web service for MOLEcular Structural Analyses. In X-meeting - 5th International Conference of the Brazilian Association for Bioinformatics and Computational Biology, Angra dos Reis, 2009. X-meeting., 2009. Abstract. Available from: http://www.x-meeting.com/.
  • Calixto, Tulio Marcus Ribeiro, Faccioli, Rodrigo, and Da SILVA, F. L. B. PROMETHEUS: A WEBSERVER FOR ESTIMATING ELECTROSTATIC AND COMPLEXATION PROPERTIES OF BIOMOLECULES. In X-meeting - 5th International Conference of the Brazilian Association for Bioinformatics and Computational Biology, Angra dos Reis, 2009. X-meeting., 2009. Abstract. Available from: http://www.x-meeting.com/.
All rights of the thesis/dissertation are from the authors
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