TY - JOUR AU - Yıldırım, M. A. AU - Goh, K. -. I. AU - Cusick, M. E. AU - Barabási, A. -. L. AU - Vidal, M. PY - 2007 DA - 2007// TI - Drug-target network JO - Nat Biotechnol VL - 25 UR - https://doi.org/10.1038/nbt1338 DO - 10.1038/nbt1338 ID - Yıldırım2007 ER - TY - JOUR AU - Chou, K. -. C. AU - Shen, H. -. B. PY - 2007 DA - 2007// TI - MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM JO - Biochem Biophys Res Commun VL - 360 UR - https://doi.org/10.1016/j.bbrc.2007.06.027 DO - 10.1016/j.bbrc.2007.06.027 ID - Chou2007 ER - TY - JOUR AU - Arif, M. AU - Hayat, M. AU - Jan, Z. PY - 2018 DA - 2018// TI - iMem-2LSAAC: a two-level model for discrimination of membrane proteins and their types by extending the notion of SAAC into Chou’s pseudo amino acid composition JO - J Theor Biol VL - 442 UR - https://doi.org/10.1016/j.jtbi.2018.01.008 DO - 10.1016/j.jtbi.2018.01.008 ID - Arif2018 ER - TY - JOUR AU - Kyte, J. AU - Doolittle, R. F. PY - 1982 DA - 1982// TI - A simple method for displaying the hydropathic character of a protein JO - J Mol Biol VL - 157 UR - https://doi.org/10.1016/0022-2836(82)90515-0 DO - 10.1016/0022-2836(82)90515-0 ID - Kyte1982 ER - TY - JOUR AU - Heijne, G. PY - 1992 DA - 1992// TI - Membrane hydrophobicity protein structure prediction analysis and the positive-inside JO - J Mol Biol VL - 225 UR - https://doi.org/10.1016/0022-2836(92)90934-C DO - 10.1016/0022-2836(92)90934-C ID - Heijne1992 ER - TY - JOUR AU - Nugent, T. AU - Jones, D. T. PY - 2009 DA - 2009// TI - Transmembrane protein topology prediction using support vector machines JO - BMC Bioinform VL - 10 UR - https://doi.org/10.1186/1471-2105-10-159 DO - 10.1186/1471-2105-10-159 ID - Nugent2009 ER - TY - JOUR AU - Tsirigos, K. D. AU - Hennerdal, A. AU - Käll, L. AU - Elofsson, A. PY - 2012 DA - 2012// TI - A guideline to proteome-wide $$\alpha $$α-helical membrane protein topology predictions JO - Proteomics VL - 12 UR - https://doi.org/10.1002/pmic.201100495 DO - 10.1002/pmic.201100495 ID - Tsirigos2012 ER - TY - JOUR AU - Tsirigos, K. D. AU - Peters, C. AU - Shu, N. AU - Käll, L. AU - Elofsson, A. PY - 2015 DA - 2015// TI - The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides JO - Nucl Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gkv485 DO - 10.1093/nar/gkv485 ID - Tsirigos2015 ER - TY - JOUR AU - Tsirigos, K. D. AU - Govindarajan, S. AU - Bassot, C. AU - Västermark, Å. AU - Lamb, J. AU - Shu, N. AU - Elofsson, A. PY - 2018 DA - 2018// TI - Topology of membrane proteins-predictions, limitations and variations JO - Curr Opin Struct Biol VL - 50 UR - https://doi.org/10.1016/j.sbi.2017.10.003 DO - 10.1016/j.sbi.2017.10.003 ID - Tsirigos2018 ER - TY - JOUR AU - Reynolds, S. M. AU - Käll, L. AU - Riffle, M. E. AU - Bilmes, J. A. AU - Noble, W. S. PY - 2008 DA - 2008// TI - Transmembrane topology and signal peptide prediction using dynamic Bayesian networks JO - PLoS Comput Biol VL - 4 UR - https://doi.org/10.1371/journal.pcbi.1000213 DO - 10.1371/journal.pcbi.1000213 ID - Reynolds2008 ER - TY - JOUR AU - Käll, L. AU - Krogh, A. AU - Sonnhammer, E. L. PY - 2005 DA - 2005// TI - An HMM posterior decoder for sequence feature prediction that includes homology information JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1014 DO - 10.1093/bioinformatics/bti1014 ID - Käll2005 ER - TY - JOUR AU - Viklund, H. AU - Elofsson, A. PY - 2008 DA - 2008// TI - OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn221 DO - 10.1093/bioinformatics/btn221 ID - Viklund2008 ER - TY - JOUR AU - Viklund, H. AU - Bernsel, A. AU - Skwark, M. AU - Elofsson, A. PY - 2008 DA - 2008// TI - SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn550 DO - 10.1093/bioinformatics/btn550 ID - Viklund2008 ER - TY - JOUR AU - Bernsel, A. AU - Viklund, H. AU - Falk, J. AU - Lindahl, E. AU - Heijne, G. AU - Elofsson, A. PY - 2008 DA - 2008// TI - Prediction of membrane-protein topology from first principles JO - Proc Natl Acad Sci VL - 105 UR - https://doi.org/10.1073/pnas.0711151105 DO - 10.1073/pnas.0711151105 ID - Bernsel2008 ER - TY - JOUR AU - Berven, F. S. AU - Flikka, K. AU - Jensen, H. B. AU - Eidhammer, I. PY - 2004 DA - 2004// TI - BOMP: a program to predict integral $$\beta $$β-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria JO - Nucl Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh351 DO - 10.1093/nar/gkh351 ID - Berven2004 ER - TY - JOUR AU - Hu, J. AU - Yan, C. PY - 2008 DA - 2008// TI - A method for discovering transmembrane $$\beta $$β-barrel proteins in gram-negative bacterial proteomes JO - Comput Biol Chem VL - 32 UR - https://doi.org/10.1016/j.compbiolchem.2008.03.010 DO - 10.1016/j.compbiolchem.2008.03.010 ID - Hu2008 ER - TY - JOUR AU - Jacoboni, I. AU - Martelli, P. L. AU - Fariselli, P. AU - Pinto, V. AU - Casadio, R. PY - 2001 DA - 2001// TI - Prediction of the transmembrane regions of $$\beta $$β-barrel membrane proteins with a neural network-based predictor JO - Protein Sci VL - 10 UR - https://doi.org/10.1110/ps.37201 DO - 10.1110/ps.37201 ID - Jacoboni2001 ER - TY - JOUR AU - Ou, Y. AU - Gromiha, M. M. AU - Chen, S. AU - Suwa, M. PY - 2008 DA - 2008// TI - TMBETADISC-RBF: discrimination of $$\beta $$β-barrel membrane proteins using RBF networks and PSSM profiles JO - Comput Biol Chem VL - 32 UR - https://doi.org/10.1016/j.compbiolchem.2008.03.002 DO - 10.1016/j.compbiolchem.2008.03.002 ID - Ou2008 ER - TY - JOUR AU - Bagos, P. G. AU - Liakopoulos, T. D. AU - Spyropoulos, I. C. AU - Hamodrakas, S. J. PY - 2004 DA - 2004// TI - PRED-TMBB: a web server for predicting the topology of $$\beta $$β-barrel outer membrane proteins JO - Nucl Acids Research VL - 32 UR - https://doi.org/10.1093/nar/gkh417 DO - 10.1093/nar/gkh417 ID - Bagos2004 ER - TY - JOUR AU - Singh, N. K. AU - Goodman, A. AU - Walter, P. AU - Helms, V. AU - Hayat, S. PY - 2011 DA - 2011// TI - TMBHMM: a frequency profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane residues JO - Biochim Biophys Acta (BBA) Proteins Proteomics VL - 1814 UR - https://doi.org/10.1016/j.bbapap.2011.03.004 DO - 10.1016/j.bbapap.2011.03.004 ID - Singh2011 ER - TY - JOUR AU - Hayat, S. AU - Elofsson, A. PY - 2012 DA - 2012// TI - BOCTOPUS: improved topology prediction of transmembrane $$\beta $$β barrel proteins JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/btr710 DO - 10.1093/bioinformatics/btr710 ID - Hayat2012 ER - TY - JOUR AU - Tsirigos, K. D. AU - Elofsson, A. AU - Bagos, P. G. PY - 2016 DA - 2016// TI - PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins JO - Bioinformatics VL - 32 UR - https://doi.org/10.1093/bioinformatics/btw444 DO - 10.1093/bioinformatics/btw444 ID - Tsirigos2016 ER - TY - JOUR AU - Ou, Y. -. Y. AU - Chen, S. -. A. AU - Gromiha, M. M. PY - 2010 DA - 2010// TI - Prediction of membrane spanning segments and topology in $$\beta $$β-barrel membrane proteins at better accuracy JO - J Comput Chem VL - 31 UR - https://doi.org/10.1002/jcc.21281 DO - 10.1002/jcc.21281 ID - Ou2010 ER - TY - JOUR AU - Garrow, A. G. AU - Agnew, A. AU - Westhead, D. R. PY - 2005 DA - 2005// TI - TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins JO - BMC Bioinform VL - 6 UR - https://doi.org/10.1186/1471-2105-6-56 DO - 10.1186/1471-2105-6-56 ID - Garrow2005 ER - TY - JOUR AU - Lin, H. PY - 2008 DA - 2008// TI - The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou’s pseudo amino acid composition JO - J Theor Biol VL - 252 UR - https://doi.org/10.1016/j.jtbi.2008.02.004 DO - 10.1016/j.jtbi.2008.02.004 ID - Lin2008 ER - TY - JOUR AU - Bagos, P. G. AU - Liakopoulos, T. D. AU - Hamodrakas, S. J. PY - 2005 DA - 2005// TI - Evaluation of methods for predicting the topology of $$\beta $$β-barrel outer membrane proteins and a consensus prediction method JO - BMC Bioinform VL - 6 UR - https://doi.org/10.1186/1471-2105-6-7 DO - 10.1186/1471-2105-6-7 ID - Bagos2005 ER - TY - JOUR AU - Remmert, M. AU - Linke, D. AU - Lupas, A. N. AU - Söding, J. PY - 2009 DA - 2009// TI - HHomp–prediction and classification of outer membrane proteins JO - Nucl Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp325 DO - 10.1093/nar/gkp325 ID - Remmert2009 ER - TY - JOUR AU - Butt, A. H. AU - Rasool, N. AU - Khan, Y. D. PY - 2017 DA - 2017// TI - A treatise to computational approaches towards prediction of membrane protein and its subtypes JO - J Membr Biol VL - 250 UR - https://doi.org/10.1007/s00232-016-9937-7 DO - 10.1007/s00232-016-9937-7 ID - Butt2017 ER - TY - JOUR AU - Butt, A. H. AU - Khan, S. A. AU - Jamil, H. AU - Rasool, N. AU - Khan, Y. D. PY - 2016 DA - 2016// TI - A prediction model for membrane proteins using moments based features JO - BioMed Res Int VL - 2016 UR - https://doi.org/10.1155/2016/8370132 DO - 10.1155/2016/8370132 ID - Butt2016 ER - TY - JOUR AU - Li, W. AU - Godzik, A. PY - 2006 DA - 2006// TI - CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl158 DO - 10.1093/bioinformatics/btl158 ID - Li2006 ER - TY - JOUR AU - Tusnady, G. E. AU - Simon, I. PY - 2001 DA - 2001// TI - The HMMTOP transmembrane topology prediction server JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.9.849 DO - 10.1093/bioinformatics/17.9.849 ID - Tusnady2001 ER - TY - JOUR AU - Krogh, A. AU - Larsson, B. AU - Heijne, G. AU - Sonnhammer, E. L. PY - 2001 DA - 2001// TI - Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes JO - J Mol Biol VL - 305 UR - https://doi.org/10.1006/jmbi.2000.4315 DO - 10.1006/jmbi.2000.4315 ID - Krogh2001 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schäffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucl Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Chou, K. -. C. PY - 2001 DA - 2001// TI - Prediction of protein cellular attributes using pseudo-amino acid composition JO - Proteins Struct Funct Bioinf VL - 43 UR - https://doi.org/10.1002/prot.1035 DO - 10.1002/prot.1035 ID - Chou2001 ER - TY - JOUR AU - Tanford, C. PY - 1962 DA - 1962// TI - Contribution of hydrophobic interactions to the stability of the globular conformation of proteins JO - J Am Chem Soc VL - 84 UR - https://doi.org/10.1021/ja00881a009 DO - 10.1021/ja00881a009 ID - Tanford1962 ER - TY - JOUR AU - Hopp, T. P. AU - Woods, K. R. PY - 1981 DA - 1981// TI - Prediction of protein antigenic determinants from amino acid sequences JO - Proc Natl Acad Sci VL - 78 UR - https://doi.org/10.1073/pnas.78.6.3824 DO - 10.1073/pnas.78.6.3824 ID - Hopp1981 ER - TY - JOUR AU - Hayat, M. a. q. s. o. o. d. AU - Khan, A. s. i. f. u. l. l. a. h. PY - 2012 DA - 2012// TI - MemHyb: predicting membrane protein types by hybridizing SAAC and PSSM JO - J Theor Biol VL - 292 UR - https://doi.org/10.1016/j.jtbi.2011.09.026 DO - 10.1016/j.jtbi.2011.09.026 ID - Hayat2012 ER - TY - JOUR AU - Denoeux, T. PY - 1995 DA - 1995// TI - A K-nearest neighbor classification rule based on Dempster–Shafer theory JO - IEEE Trans Syst Man Cybern VL - 25 UR - https://doi.org/10.1109/21.376493 DO - 10.1109/21.376493 ID - Denoeux1995 ER - TY - JOUR AU - Kuhn, M. PY - 2008 DA - 2008// TI - Building predictive models in R using the caret package JO - J Stat Softw VL - 28 UR - https://doi.org/10.18637/jss.v028.i05 DO - 10.18637/jss.v028.i05 ID - Kuhn2008 ER - TY - JOUR AU - Peng, H. AU - Long, F. AU - Ding, C. PY - 2005 DA - 2005// TI - Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy JO - IEEE Trans Pattern Anal Mach Intell VL - 27 UR - https://doi.org/10.1109/TPAMI.2005.159 DO - 10.1109/TPAMI.2005.159 ID - Peng2005 ER - TY - STD TI - Huang T, Shi X-H, Wang P, He Z, Feng K-Y, Hu L, Kong X, Li Y-X, Cai Y-D, Chou K-C. Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PloS One. 2010;5(6): ID - ref41 ER - TY - STD TI - Opitz DW, Shavlik JW. Generating accurate and diverse members of a neural-network ensemble. In: Advances in Neural Information Processing Systems, 1996;535–541. ID - ref42 ER - TY - STD TI - Krogh A, Vedelsby J. Neural network ensembles, cross validation, and active learning. In: Advances in Neural Information Processing Systems, 1995;231–238. ID - ref43 ER -