TY - JOUR AU - Whisstock, J. C. AU - Lesk, A. M. PY - 2003 DA - 2003// TI - Prediction of protein function from protein sequence and structure JO - Quarterly Reviews of Biophysics VL - 36 UR - https://doi.org/10.1017/S0033583503003901 DO - 10.1017/S0033583503003901 ID - Whisstock2003 ER - TY - JOUR AU - Murzin, A. G. PY - 1998 DA - 1998// TI - How far divergent evolution goes in proteins JO - Current Opinion in Structural Biology VL - 8 UR - https://doi.org/10.1016/S0959-440X(98)80073-0 DO - 10.1016/S0959-440X(98)80073-0 ID - Murzin1998 ER - TY - JOUR AU - Grishin, N. PY - 2001 DA - 2001// TI - Fold change in evolution of protein structures JO - Journal of Structural Biology VL - 134 UR - https://doi.org/10.1006/jsbi.2001.4335 DO - 10.1006/jsbi.2001.4335 ID - Grishin2001 ER - TY - JOUR AU - Copley, R. R. AU - Bork, P. PY - 2000 DA - 2000// TI - Homology among (beta-alpha)(8) barrels: implications for the evolution of metabolic pathways JO - Journal of Molecular Biology VL - 303 UR - https://doi.org/10.1006/jmbi.2000.4152 DO - 10.1006/jmbi.2000.4152 ID - Copley2000 ER - TY - CHAP AU - Pandey, G. AU - Kumar, V. AU - Steinbach, M. PY - 2006 DA - 2006// TI - Computational approaches for protein function prediction BT - Tech Rep TR 06-028 PB - Department of Computer Science and Engineering, University of Minnesota CY - Twin Cities ID - Pandey2006 ER - TY - JOUR AU - Rost, B. PY - 2002 DA - 2002// TI - Enzyme function less conserved than anticipated JO - J Mol Biol VL - 318 UR - https://doi.org/10.1016/S0022-2836(02)00016-5 DO - 10.1016/S0022-2836(02)00016-5 ID - Rost2002 ER - TY - JOUR AU - Ofran, Y. AU - Punta, M. AU - Schneider, R. AU - Rost, B. PY - 2005 DA - 2005// TI - Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery JO - Drug Discovery Today VL - 10 UR - https://doi.org/10.1016/S1359-6446(05)03621-4 DO - 10.1016/S1359-6446(05)03621-4 ID - Ofran2005 ER - TY - JOUR AU - Wilson, C. A. AU - Kreychman, J. AU - Gerstein, M. PY - 2000 DA - 2000// TI - Assesing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores JO - Journal of Molecular Biology VL - 297 UR - https://doi.org/10.1006/jmbi.2000.3550 DO - 10.1006/jmbi.2000.3550 ID - Wilson2000 ER - TY - JOUR AU - Todd, A. E. AU - Orengo, C. A. AU - Thornton, J. M. PY - 2001 DA - 2001// TI - Evolution of protein function, from a structural perspective JO - Journal of Molecular Biology VL - 307 UR - https://doi.org/10.1006/jmbi.2001.4513 DO - 10.1006/jmbi.2001.4513 ID - Todd2001 ER - TY - JOUR AU - Devos, D. AU - Valencia, A. PY - 2000 DA - 2000// TI - Practical limits of function prediction JO - Proteins VL - 41 UR - https://doi.org/3.0.CO;2-S DO - 3.0.CO;2-S ID - Devos2000 ER - TY - JOUR AU - Attwood, T. K. PY - 2000 DA - 2000// TI - The quest to deduce protein function from sequence: the role of pattern databases JO - International Journal of Biochemistry and Cell Biology VL - 32 UR - https://doi.org/10.1016/S1357-2725(99)00106-5 DO - 10.1016/S1357-2725(99)00106-5 ID - Attwood2000 ER - TY - JOUR AU - Liu, B. AU - Wang, X. AU - Lin, L. AU - Dong, Q. AU - Wang, X. PY - 2008 DA - 2008// TI - A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis JO - Bioinformatics VL - 9 ID - Liu2008 ER - TY - JOUR AU - Jensen, L. J. AU - Gupta, R. AU - Blom, N. AU - Devos, D. AU - Tamames, J. AU - Kesmir, C. AU - Nielsen, H. AU - Stærfeldt, H. H. AU - Rapacki, K. AU - Workman, C. AU - Andersen, C. A. F. AU - Knudsen, S. AU - Krogh, A. AU - Valencia, A. AU - Brunak, S. PY - 2002 DA - 2002// TI - Prediction of human protein function form post-translational modifications and localization features JO - J Mol Biol VL - 319 UR - https://doi.org/10.1016/S0022-2836(02)00379-0 DO - 10.1016/S0022-2836(02)00379-0 ID - Jensen2002 ER - TY - JOUR AU - Wu, C. H. PY - 1997 DA - 1997// TI - Artificial neural networks for molecular sequence analysis JO - Comput Chem VL - 21 UR - https://doi.org/10.1016/S0097-8485(96)00038-1 DO - 10.1016/S0097-8485(96)00038-1 ID - Wu1997 ER - TY - JOUR AU - Mooney, C. AU - Wang, Y. H. AU - Pollastri, G. PY - 2011 DA - 2011// TI - SCLpred: protein subcellular localization prediction by N-to-1 neural networks JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr494 DO - 10.1093/bioinformatics/btr494 ID - Mooney2011 ER - TY - JOUR AU - Savoiardo, C. AU - Fariselli, P. AU - Casadio, R. PY - 2011 DA - 2011// TI - Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr549 DO - 10.1093/bioinformatics/btr549 ID - Savoiardo2011 ER - TY - JOUR AU - Rost, B. AU - Sander, C. PY - 1993 DA - 1993// TI - Improved prediction of protein secondary structure by use of sequence profiles and neural networks JO - Proc Natl Acad Sci USA VL - 90 UR - https://doi.org/10.1073/pnas.90.16.7558 DO - 10.1073/pnas.90.16.7558 ID - Rost1993 ER - TY - JOUR AU - Suzek, B. AU - Huang, H. AU - McGarvey, P. AU - Mazumder, R. AU - Wu, C. PY - 2007 DA - 2007// TI - Uniref: comprehensive and non-redundant uniprot reference clusters JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm098 DO - 10.1093/bioinformatics/btm098 ID - Suzek2007 ER - TY - JOUR AU - Pollastri, G. AU - McLysaght, A. PY - 2004 DA - 2004// TI - Porter: a new, accurate server for protein secondary structure prediction JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti203 DO - 10.1093/bioinformatics/bti203 ID - Pollastri2004 ER - TY - JOUR AU - Baú, D. AU - Martin, A. AU - Mooney, C. AU - Vullo, A. AU - Walsh, I. AU - Pollastri, G. PY - 2006 DA - 2006// TI - Distill: a suite of web servers for the prediction of one-, two-and three-dimensional structural features of proteins JO - BMC bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-402 DO - 10.1186/1471-2105-7-402 ID - Baú2006 ER - TY - JOUR AU - Pollastri, G. AU - Martin, A. AU - Mooney, C. AU - Vullo, A. PY - 2007 DA - 2007// TI - Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information JO - BMC Bioinformatics VL - 8 ID - Pollastri2007 ER - TY - JOUR AU - Mooney, C. AU - Pollastri PY - 2009 DA - 2009// TI - Beyond the twilight zone: automated prediction of structural properties of proteins by recursive neural networks and remote homology information JO - Proteins VL - 77 UR - https://doi.org/10.1002/prot.22429 DO - 10.1002/prot.22429 ID - Mooney2009 ER - TY - JOUR AU - Baldi, P. AU - Pollastri, G. PY - 2003 DA - 2003// TI - The principled design of large-scale recursive neural network architectures-dag-rnns and the protein structure prediction problem JO - The Journal of Machine Learning Research VL - 4 ID - Baldi2003 ER - TY - CHAP AU - Walsh, I. AU - Vullo, A. AU - Pollastri, G. PY - 2009 DA - 2009// TI - Recursive neural networks for undirected graphs for learning molecular endpoints BT - Pattern Recognition in Bioinformatics UR - https://doi.org/10.1007/978-3-642-04031-3_34 DO - 10.1007/978-3-642-04031-3_34 ID - Walsh2009 ER - TY - JOUR AU - Gribskov, M. AU - McLachlan, A. D. AU - Eisenberg, D. PY - 1987 DA - 1987// TI - Profile analysis: detection of distantly related proteins JO - Proc Natl Acad Sci USA VL - 84 UR - https://doi.org/10.1073/pnas.84.13.4355 DO - 10.1073/pnas.84.13.4355 ID - Gribskov1987 ER - TY - JOUR AU - Ganfornina, M. D. AU - Sánchez, D. PY - 1999 DA - 1999// TI - Generation of evolutionary novelty by functional shift JO - BioEssays VL - 21 UR - https://doi.org/3.0.CO;2-T DO - 3.0.CO;2-T ID - Ganfornina1999 ER - TY - JOUR AU - Vullo, A. AU - Walsh, I. AU - Pollastri, G. PY - 2006 DA - 2006// TI - A two-stage approach for improved prediction of residue contact maps JO - BMC bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-180 DO - 10.1186/1471-2105-7-180 ID - Vullo2006 ER - TY - JOUR AU - Walsh, I. AU - Baù, D. AU - Martin, A. AU - Mooney, C. AU - Vullo, A. AU - Pollastri, G. PY - 2009 DA - 2009// TI - Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks JO - BMC structural biology VL - 9 UR - https://doi.org/10.1186/1472-6807-9-5 DO - 10.1186/1472-6807-9-5 ID - Walsh2009 ER -