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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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Finding protein-protein interaction patterns by contact map matching. Repositório Alice
MELO, R. C.; RIBEIRO, C.; MURRAY, C. S.; VELOSO, C. J. M.; SILVEIRA, C. H. da; NESHICH, G.; MEIRA JUNIOR, W.; CARCERONI, R. L.; SANTORO, M. M..
We propose a novel method for defining patterns of contacts present in protein-protein complexes. A new use of the traditional contact maps (more frequently used for representation of the intra-chain contacts) is presented for analysis of inter-chain contacts. Using an algorithm based on image processing techniques, we can compare protein-protein interaction maps and also obtain a dissimilarity score between them. The same algorithm used to compare the maps can align the contacts of all the complexes and be helpful in the determination of a pattern of conserved interactions at the interfaces. We present an example for the application of this method by analyzing the pattern of interaction of bovine pancreatic trypsin inhibitors and trypsins, chymotrypsins,...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Bioinformática; Interação proteína-proteína; Mapas de contato; Protein-protein interactions; Contact maps; Serine proteases; Bioinformatics; Serine proteinases.
Ano: 2007 URL: http://www.alice.cnptia.embrapa.br/handle/doc/969
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Protein cutoff scanning: a comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. Repositório Alice
SILVEIRA, C. H. da; PIRES, D. E. V.; MINARDI, R.; RIBEIRO, C.; VELOSO, C. J. M.; LOPES, J. C. D.; MEIRA JÚNIOR, W.; NESHICH, G.; RAMOS, C. H. I.; HABESCH, R.; SANTORO, M. M..
In this study, we carried out a comparative analysis between two classical methodologies to prospect residue contacts in proteins: the traditional cutoff dependent (CD) approach and cutoff free Delaunay tessellation (DT). In addition, two alternative coarse-grained forms to represent residues were tested: using alpha carbon (CA) and side chain geometric center (GC). A database was built, comprising three top classes: all alpha, all beta, and alpha/beta. We found that the cutoff value? at about 7.0 A emerges as an important distance parameter.? Up to 7.0 A, CD and DT properties are unified, which implies that at this distance all contacts are complete and legitimate (not occluded). We also have shown that DT has an intrinsic missing edges problem when...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Proteina.
Ano: 2009 URL: http://www.alice.cnptia.embrapa.br/handle/doc/664411
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