A.C. Wanderley-Nogueira, N.M. Soares-Cavalcanti, D.A.L. Morais,L.C. Belarmino, A. Barbosa-Silva, A.M. Benko-IsepponPublished October 05, 2007Genet. Mol. Res. 6 (4): 866-889 (2007) About the authorsA.C. Wanderley-Nogueira, N.M. Soares-Cavalcanti, D.A.L. Morais,L.C. Belarmino, A. Barbosa-Silva, A.M. Benko-Iseppon Corresponding authorA.M. Benko-IsepponE-mail: ana.benko.iseppon@pesquisador.cnpq.br ABSTRACT Resistance genes (R-genes) are responsible for the first interaction of the plant with pathogens being responsible for […]
Application of MUTIC to the explorationof gene expression data in prostate cancer
B. Goertzel, C. Pennachin, L.S. Coelho, M.A. MudadoPublished October 05, 2007Genet. Mol. Res. 6 (4): 890-900 (2007) About the authorsB. Goertzel, C. Pennachin, L.S. Coelho, M.A. Mudado Corresponding authorL.S. CoelhoE-mail: lucio@biomind.com ABSTRACT We show here an example of the application of a novel method, MUTIC (model utilization-based clustering), used for identifying complex interactions between genes […]
Ab initio 3-D structure predictionof an artificially designed three-α-helix bundlevia all-atom molecular dynamics simulations
A. Breda, D.S. Santos, L.A. Basso2,3, O. Norberto de SouzaPublished October 05, 2007Genet. Mol. Res. 6 (4): 901-910 (2007) About the authorsA. Breda, D.S. Santos, L.A. Basso2,3, O. Norberto de Souza Corresponding authorO. Norberto de SouzaE-mail: osmar.norberto@pucrs.br ABSTRACT The rate at which knowledge about genomic sequences and their protein products is produced is increasing much […]
Sting_rdb: a relational database of structuralparameters for protein analysis with supportfor data warehousing and data mining
S.R.M. Oliveira, G.V. Almeida, K.R.R. Souza, D.N. Rodrigues, P.R. Kuser-Falcão, M.E.B. Yamagishi, E.H. Santos, F.D. Vieira, J.G. Jardine, G. NeshichPublished October 05, 2007Genet. Mol. Res. 6 (4): 911-922 (2007) About the authorsS.R.M. Oliveira, G.V. Almeida, K.R.R. Souza, D.N. Rodrigues, P.R. Kuser-Falcão, M.E.B. Yamagishi, E.H. Santos, F.D. Vieira, J.G. Jardine, G. Neshich Corresponding authorG. NeshichE-mail: neshich@cbi.cnptia.embrapa.br […]
Electrostatic potential calculationfor biomolecules – creating a databaseof pre-calculated values reported on a perresidue basis for all PDB protein structures
W. Rocchia, G. NeshichPublished October 05, 2007Genet. Mol. Res. 6 (4): 923-936 (2007) About the authorsW. Rocchia, G. Neshich Corresponding authorG. NeshichE-mail: neshich@cbi.cnptia.embrapa.br ABSTRACT STING and JavaProtein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. […]
Finding protein-protein interaction patterns by contact map matching
R.C. Melo, C. Ribeiro, C.S. Murray, C.J.M. Veloso, C.H. da Silveira, G. Neshich, W. Meira Jr., R.L. Carceroni, M.M. SantoroPublished October 05, 2007Genet. Mol. Res. 6 (4): 946-963 (2007) About the authorsR.C. Melo, C. Ribeiro, C.S. Murray, C.J.M. Veloso, C.H. da Silveira, G. Neshich, W. Meira Jr., R.L. Carceroni, M.M. Santoro Corresponding authorR.C. MeloE-mail: raquelcm@gmail.com/neshich@cbi.cnptia.embrapa.br […]
BNDb – Biomolecules Nucleus Database:an integrated proteomics and transcriptomicsdatabase
A.C. Faria-Campos, R.R. Gomes, F.S. Moratelli, H. Rausch-Fernandes, G.R. Franco, S.V.A. CamposPublished October 05, 2007Genet. Mol. Res. 6 (4): 937-945 (2007) About the authorsA.C. Faria-Campos, R.R. Gomes, F.S. Moratelli, H. Rausch-Fernandes, G.R. Franco, S.V.A. Campos Corresponding authorA.C. Faria-CamposE-mail: alessa@icb.ufmg.br ABSTRACT Proteomics correspond to the identification and quantitative analysis of proteins expressed in different conditions or […]
Application of latent semantic indexing to evaluate the similarity of sets of sequences without multiple alignments character-by-character
B.R.G.M. Couto, A.P. Ladeira, M.A. SantosPublished October 05, 2007Genet. Mol. Res. 6 (4): 983-999 (2007) About the authorsB.R.G.M. Couto, A.P. Ladeira, M.A. Santos Corresponding authorB.R.G.M. CoutoE-mail: bcouto@acad.unibh.br ABSTRACT Most molecular analyses, including phylogenetic inference, are based on sequence alignments. We present an algorithm that estimates relatedness between biomolecules without the requirement of sequence alignment by […]
A simple genetic algorithm for multiple sequence alignment
C. Gondro, B.P. KinghornPublished October 05, 2007Genet. Mol. Res. 6 (4): 964-982 (2007) About the authorsC. Gondro, B.P. Kinghorn Corresponding authorC. GondroE-mail: cgondro2@une.edu.au ABSTRACT Multiple sequence alignment plays an important role in molecular sequence analysis. An alignment is the arrangement of two (pairwise alignment) or more (multiple alignment) sequences of ‘residues’ (nucleotides or amino acids) […]
Prediction and biochemical characterization ofintrinsic disorder in the structure of proteolysis inducing factor/dermcidin
G. Majczak, S. Lilla*,M. Garay-Malpartida, J. Markovic,F.J. Medrano, G. de Nucci, J.E. BelizárioPublished October 5, 2007Genet. Mol. Res. 6 (4): 1000-1011 (2007) About the authorsG. Majczak, S. Lilla*,M. Garay-Malpartida, J. Markovic,F.J. Medrano, G. de Nucci, J.E. Belizário Corresponding authorJ.E. BelizárioE-mail: jebeliza@usp.br ABSTRACT Proteolysis-inducing factor/dermcidin (PIF/DCD) is a novel human gene, located on chromosome 12, locus […]