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Role of hydrophobicity in protein evolution. Author(s): LEITE, V.; SILVA, R.; YAMAGISHI, M.; CHAHINE, J. Effect of mutations on the stability of proteins is a crucial issue in protein evolution. Such effects depend strongly on the overall hydrophobic protein character. In a recent work we suggested two s... ... Repository: BDPA Publication year: 2010
Analysing protein-protein interface using JPIV. Author(s): YAMAGISHI, M. E. B.; FALCAO, P. R. K.; BORRO, L. C.; OLIVEIRA, S. R. de M.; SANTOS, E. H. dos; JARDINE, J. G.; VIEIRA, F. D.; MAZONI, I.; NARCISO, M. G.; NESHICH, G. Short Abstract: In this work we present Java Protein Interface Viewer (JPIV). It is a web-based software designed to visualize and analyse protein-protein interfaces. It uses Delaunay triangulation in... ... Repository: BDPA Publication year: 2006
2D maps of protein surface. Author(s): NARCISO, M. G.; YAMAGISHI, M. E. B.; KUSER-FALCÃO, P. R.; NESHICH, G. Short Abstract: In this work, we present 2DIM (Two Dimensional Interface Maps). It is a graphical interface that permits to visualize the protein-protein interfaces in 2D maps. Repository: BDPA Publication year: 2006
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
Classifiers of the protein interactions with their substrate/inhibitors. Author(s): GARCIA, V. S.; FALCÃO, P. K. Short Abstract: Basically all biological processes require protein-ligand identifications. One major challenge to biophysics-chemistry is try to predict these interactions. One step towards solving th... ... Repository: BDPA Publication year: 2006
The nucleoprotein of Tomato spotted wilt virus as protein tag for easy purification and enhanced production of recombinant proteins in plants. Author(s): LACORTE, C.; RIBEIRO, S. G.; LOHUIS, D.; GOLDBACH, R.; PRINS, M. Repository: BDPA Publication year: 2007
Finding protein-protein interaction patterns by contact map matching. Author(s): 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... ... Repository: BDPA Publication year: 2007
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
Protein structure topology comparison based on contact maps. Author(s): MELO, R. C.; MAZONI, I.; NESHICH, G.; SANTORO, M. M.; MEIRA JUNIOR, W. Short Abstract: Topologs (Topology Homologous) is a tool which is part of the Star Sting Suite (http://sms.cbi.cnptia.embrapa.br/SMS). It is a structural classification of proteins totally based on th... ... Repository: BDPA Publication year: 2006
Protein cutoff scanning: a comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. Author(s): 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 Delaun... ... Repository: BDPA Publication year: 2009

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