TMBETADISC-RBF: Discrimination of -barrel membrane proteins using RBF networks and PSSM profiles
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Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389
Bagos, 2004, A hidden markov model method, capable of predicting and discriminating beta-barrel outer membrane proteins, BMC Bioinformatics, 5, 29, 10.1186/1471-2105-5-29
Berven, 2004, BOMP: a program to predict integral b-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria, Nucleic Acids Res., 32, W394, 10.1093/nar/gkh351
Bigelow, 2006, PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins, Nucleic Acids Res., 34, W186, 10.1093/nar/gkl262
Garrow, 2005, TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins, Nucleic Acids Res., 33, W188, 10.1093/nar/gki384
Garrow, 2007, A consensus algorithm to screen genomes for novel families of transmembrane beta barrel proteins, Proteins, 69, 8, 10.1002/prot.21439
Gnanasekaran, 2000, Profiles from structure based sequence alignment of porins can identify β stranded integral membrane proteins, Bioinformatics, 16, 839, 10.1093/bioinformatics/16.9.839
Gromiha, 2005, Motifs in outer membrane protein sequences, Biophys. Chem., 117, 65, 10.1016/j.bpc.2005.04.005
Gromiha, 2005, Application of residue distribution along the sequence for discriminating outer membrane proteins, Comput. Biol. Chem., 29, 135, 10.1016/j.compbiolchem.2005.02.006
Gromiha, 2005, A simple statistical method for discriminating outer membrane proteins with better accuracy, Bioinformatics, 21, 961, 10.1093/bioinformatics/bti126
Gromiha, 2006, Discrimination of outer membrane proteins using machine learning algorithms, Proteins: Structure, Function, and Bioinformatics, 63, 1031, 10.1002/prot.20929
Gromiha, 2007, Current developments on-barrel membrane proteins: sequence and structure analysis, discrimination and prediction, Curr. Protein Pept. Sci., 8, 580, 10.2174/138920307783018712
Jones, 1999, Protein secondary structure prediction based on position-specific scoring matrices, J. Mol. Biol., 292, 195, 10.1006/jmbi.1999.3091
Li, 2001, Clustering of highly homologous sequences to reduce the size of large protein databases, Bioinformatics, 17, 282, 10.1093/bioinformatics/17.3.282
Liu, 2003, Identification of b-barrel membrane proteins based on amino acid composition properties and predicted secondary structure, Comput. Biol. Chem., 27, 355, 10.1016/S1476-9271(02)00085-3
Martelli, 2002, A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins, Bioinformatics, 18, 46, 10.1093/bioinformatics/18.suppl_1.S46
Murzin, 1995, SCOP: a structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol., 247, 536, 10.1016/S0022-2836(05)80134-2
Natt, 2004, Prediction of transmembrane regions of beta-barrel proteins using ann and svm-based methods, Proteins, 56, 11, 10.1002/prot.20092
Ou, 2005, A novel radial basis function network classifier with centers set by hierarchical clustering, 1383
Park, 2005, Discrimination of outer membrane proteins using support vector machines, Bioinformatics, 21, 4223, 10.1093/bioinformatics/bti697
Press, 1992
Saier, 2006, TCDB: the transporter classification database for membrane transport protein analyses and information, Nucleic Acids Res., 34, D181, 10.1093/nar/gkj001
Su, 2006, Protein disorder prediction by condensed PSSM considering propensity for order or disorder, BMC Bioinformatics, 7, 319, 10.1186/1471-2105-7-319
Takasaki, 2006, Selecting effective siRNA sequences by using radial basis function network and decision tree learning, BMC Bioinformatics, 7, S22, 10.1186/1471-2105-7-S5-S22
Tusnády, 2005, PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank, Nucleic Acids Res., 33, D275, 10.1093/nar/gki002
Witten, 2005
Xie, 2005, LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST, Nucleic Acids Res., 33, W105, 10.1093/nar/gki359
Yang, 2005, Bio-basis function neural network for prediction of protease cleavage sites in proteins, Neural Netw. IEEE Trans., 16, 263, 10.1109/TNN.2004.836196