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Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors. Repositório Alice
RIBEIRO, C.; TOGAWA, R. C.; NESHICH, I. A. P.; MAZONI, I.; MANCINI, A. L.; MINARDI, R. C. de M.; SILVEIRA, C. H. da; JARDINE, J. G.; SANTORO, M. M.; NESHICH, G..
Background: Enzymes belonging to the same super family of proteins in general operate on variety of substrates and are inhibited by wide selection of inhibitors. In this work our main objective was to expand the scope of studies that consider only the catalytic and binding pocket amino acids while analyzing enzyme specificity and instead, include a wider category which we have named the Interface Forming Residues (IFR). We were motivated to identify those amino acids with decreased accessibility to solvent after docking of different types of inhibitors to sub classes of serine proteases and then create a table (matrix) of all amino acid positions at the interface as well as their respective occupancies. Our goal is to establish a platform for analysis of...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Enzimas; Propriedades ligantes; Proteases; Binding properties; Enzymes; Interface Forming Residues.
Ano: 2010 URL: http://www.alice.cnptia.embrapa.br/handle/doc/867859
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Biologia computacional molecular e suas aplicações na agricultura. Repositório Alice
JARDINE, J. G.; NESHICH, I. A. P.; MAZONI, I.; YANO, I. H.; MORAES, F. R. de; SALIM, J. A.; BORRO, L.; NISHIMURA, L. S.; NESHICH, G..
Biologia computacional, uma nova ciência aplicada. Desenho racional de drogas, fármacos e agroquímicos. Biologia computacional na Embrapa.
Tipo: Capítulo em livro científico (ALICE) Palavras-chave: Bioinformática; Biologia computacional; Agricultura; Bioinformatics; Agriculture.
Ano: 2014 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1010715
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Identification of new Sphingomyelinases D in pathogenic fungi and other pathogenic organisms. Repositório Alice
DIAS-LOPES, C.; NESHICH, I. A. P.; NESHICH, G.; ORTEGA, J. M.; GRANIER, C.; CHÁVEZ-OLORTEGUI, C.; MOLINA, F.; FELICORI, L..
Sphingomyelinases D (SMases D) or dermonecrotic toxins are well characterized in Loxosceles spider venoms and have been described in some strains of pathogenic microorganisms, such as Corynebacterium sp. After spider bites, the SMase D molecules cause skin necrosis and occasional severe systemic manifestations, such as acute renal failure. In this paper, we identified new SMase D amino acid sequences from various organisms belonging to 24 distinct genera, of which, 19 are new. These SMases D share a conserved active site and a C-terminal motif. We suggest that the C-terminal tail is responsible for stabilizing the entire internal structure of the SMase D Tim barrel and that it can be considered an SMase D hallmark in combination with the amino acid...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Bioinformática; Esfingomielinas; Enzimas; Bioinformatics; Sphingomyelins; Enzymes.
Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/handle/doc/974829
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Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages. Repositório Alice
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 still not fully understood. Structural and computational biology contributed greatly to the elucidation of the mechanism of protein interactions. In this paper, we present a collection of the physicochemical and structural characteristics that distinguish interface-forming residues (IFR) from free surface residues (FSR). We formulated a linear discriminative analysis (LDA) classifier to assess whether chosen descriptors from the BlueStar STING database (http://www.cbi.cnptia.embrapa.br/SMS/) are suitable for such a task. Receiver operating characteristic (ROC)...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Interações proteína-proteína; Biologia; Proteins; Biological sciences.
Ano: 2014 URL: http://www.alice.cnptia.embrapa.br/handle/doc/981215
Registros recuperados: 4
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