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Contacts as the key elements for comparing two protein structures. Author(s): MELO, R. C.; MAZONI, I.; NESHICH, G.; SANTORO, M. M.; MEIRA JÚNIOR, W. Short Abstract: TopSiMap (Topological Similarity Map) is and interactive tool which is part of the Star Sting Suite (http://sms.cbi.cnptia.embrapa.br/SMS).As contacts pattern is very conserved in each... ... Repository: BDPA Publication year: 2006
Using linear algebra for protein structural comparison and classification. Author(s): GOMIDE, J.; MELO-MINARDI, R.; SANTOS, M. A. dos; NESHICH, G.; MEIRA JUNIOR, W.; LOPES, J. C.; SANTORO, M. In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used eff... ... Repository: BDPA Publication year: 2009
BlueStar STING platform for analysis of protein structure / function relationship: designing agrochemicals to fit new protein targets for bacterial, fungal and insect control. Author(s): NESHICH, G. Blue Star STING suite of programs for comprehensive analysis of structure, function and stability of proteins and their complexes, has matured over a decade of development. We will present the in sili... ... Repository: BDPA Publication year: 2012
Structural analysis of the protein twitching motility. Author(s): JARDINE, J. G.; NESHICH, G.; FALCAO, P. R. K.; YAMAGISHI, M. E. B.; OLIVEIRA, S. R. de M.; MAZONI, I.; SANTOS, E. H. dos; VIEIRA, F. D.; MARANGONI, S.; MARTINS, D.; WINCK, F. V.; NOVELLO, J. C.; PAPINE, J. M.; VIEIRA, M. S. Short Abstract: We have concentrated our effort in understanding some crucial features of protein Twitching Motility of Xylella fastidiosa. Our study is based on the model of this protein, constructed... ... Repository: BDPA Publication year: 2006
Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures. Author(s): ROCCHIA, W.; NESHICH, G. Abstract. STING and JavaProtein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensi... ... Repository: BDPA Publication year: 2007
Predicting enzyme class from protein structure using Bayesian classification. Author(s): BORRO, L. C.; OLIVEIRA, S. R. M.; YAMAGISHI, M. E. B.; MANCINI, A. L.; JARDINE, J. G.; MAZONI, I.; SANTOS, E. H. dos; HIGA, R. H.; KUSER, P. R.; NESHICH, G. ABSTRACT. Predicting enzyme class from protein structure parameters is a challenging problem in protein analysis. We developed a method to predict enzyme class that combines the strengths of statistic... ... Repository: BDPA Publication year: 2006
The Star STING server: a multiplatform environment for protein structure analysis. Author(s): NESHICH, G.; MAZONI, I.; OLIVEIRA, S. R. M.; YAMAGISHI, M. E. B.; KUSER-FALCÃO, P. R.; BORRO, L. C.; MORITA, D. U.; SOUZA, K. R. R.; ALMEIDA, G. V.; RODRIGUES, D. N.; JARDINE, J. G.; TOGAWA, R. C.; MANCINI, A. L.; HIGA, R. H.; CRUZ, S. A. B.; VIEIRA, F. D.; SANTOS, E. H.; MELO, R. C.; SANTORO, M. M. ABSTRACT. Star STING is the latest version of the STING suite of programs and corresponding database. We report on five important aspects of this package that have acquired some new characteristics, d... ... Repository: BDPA Publication year: 2006
Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages. Author(s): MORAES, F. R. de; NESHICH, I. A. P.; MAZONI, I.; YANO, I. H.; PEREIRA, J. G. C.; SALIM, J. A.; JARDINE, J. G.; NESHICH, G. Protein-protein interactions are involved in nearly all regulatory processes in the cell and are considered one of the most important issues in molecular biology and pharmaceutical sciences but are st... ... Repository: BDPA Publication year: 2014
Binding affinity prediction using a nonparametric regression model based on physicochemical and structural descriptors of the nano-environment for protein-ligand interactions. Author(s): BORRO, L.; YANO, I. H.; MAZONI, I.; NESHICH, G. We propose a new empirical scoring function for binding affinity prediction modeled based on physicochemical and structural descriptors that characterize the nano-environment that encompass both ligan... ... Repository: BDPA Publication year: 2016
Structural analyses of CRY 1Ac protein from Bacillus thuringiensis. Author(s): JESUS, K. R. E. de; FALCAO, P. R. K.; NESHICH, G. Cry protein is a delta endotoxin of the Bacillus family that provides an entomopatogenic activity to Bacilius thuringiensis. These proteins have a specific toxic activity against three types of insect... ... Repository: BDPA Publication year: 2005

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