TY - JOUR AU - Copley, R. R. AU - Doerks, T. AU - Letunic, I. AU - Bork, P. PY - 2002 DA - 2002// TI - Protein domain analysis in the era of complete genomes JO - FEBS Letters VL - 513 UR - https://doi.org/10.1016/S0014-5793(01)03289-6 DO - 10.1016/S0014-5793(01)03289-6 ID - Copley2002 ER - TY - JOUR AU - Levitt, M. AU - Chothia, C. PY - 1976 DA - 1976// TI - Structural patterns in globular proteins JO - Nature VL - 261 UR - https://doi.org/10.1038/261552a0 DO - 10.1038/261552a0 ID - Levitt1976 ER - TY - JOUR AU - Kong, L. AU - Ranganathan, S. PY - 2004 DA - 2004// TI - Delineation of modular proteins: Domain boundary prediction from sequence information JO - Briefings in Bioinformatics VL - 5 UR - https://doi.org/10.1093/bib/5.2.179 DO - 10.1093/bib/5.2.179 ID - Kong2004 ER - TY - JOUR AU - Suyama, M. AU - Ohara, O. PY - 2003 DA - 2003// TI - DomCut: prediction of inter-domain linker regions in amino acid sequences JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg031 DO - 10.1093/bioinformatics/btg031 ID - Suyama2003 ER - TY - JOUR AU - Contreras-Moreira, B. AU - Bates, P. A. PY - 2002 DA - 2002// TI - Domain Fishing: A first step in protein comparative modelling JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.8.1141 DO - 10.1093/bioinformatics/18.8.1141 ID - Contreras-Moreira2002 ER - TY - JOUR AU - Wheelan, S. J. AU - Marchler-Bauer, A. AU - Bryant, S. H. PY - 2000 DA - 2000// TI - Domain size distributions can predict domain boundaries JO - Bioinformatics VL - 16 UR - https://doi.org/10.1093/bioinformatics/16.7.613 DO - 10.1093/bioinformatics/16.7.613 ID - Wheelan2000 ER - TY - JOUR AU - Gracy, J. AU - Argos, P. PY - 1998 DA - 1998// TI - DOMO: A new database of aligned protein domains JO - Trends Biochem Sci VL - 23 UR - https://doi.org/10.1016/S0968-0004(98)01294-8 DO - 10.1016/S0968-0004(98)01294-8 ID - Gracy1998 ER - TY - CHAP AU - Veretnik, S. AU - Shindyalov, I. N. ED - Xu, Y. ED - Xu, D. ED - Liang, J. PY - 2006 DA - 2006// BT - Computational Methods for Domain Partitioning in Protein Structures in Computational Methods for Protein Structure and Modeling ID - Veretnik2006 ER - TY - JOUR AU - Friedberg, I. AU - Jaroszewski, L. AU - Ye, Y. AU - Godzik, A. PY - 2004 DA - 2004// TI - The interplay of fold recognition and experimental structure determination in structural genomics JO - Curr Opin Struct Biol VL - 14 UR - https://doi.org/10.1016/j.sbi.2004.04.005 DO - 10.1016/j.sbi.2004.04.005 ID - Friedberg2004 ER - TY - JOUR AU - Marsden, R. L. AU - Lewis, T. A. AU - Orengo, C. A. PY - 2007 DA - 2007// TI - Towards a comprehensive structural coverage of completed genomics: a structural genomics viewpoint JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-86 DO - 10.1186/1471-2105-8-86 ID - Marsden2007 ER - TY - JOUR AU - Yoo, P. D. AU - Zhou, B. B. AU - Zomaya, A. Y. PY - 2008 DA - 2008// TI - Machine learning techniques for protein secondary structure prediction: an overview and evaluation JO - Journal of Current Bioinformatics VL - 3 UR - https://doi.org/10.2174/157489308784340676 DO - 10.2174/157489308784340676 ID - Yoo2008 ER - TY - JOUR AU - Baldi, P. AU - Pollastri, G. PY - 2002 DA - 2002// TI - A machine learning strategy for protein analysis JO - Intelligent Systems in Biology VL - 17 ID - Baldi2002 ER - TY - JOUR AU - Baldi, P. AU - Brunak, S. AU - Frasconi, P. AU - Soda, G. AU - Pollastri, G. PY - 1999 DA - 1999// TI - Exploiting the past and the future in protein secondary structure prediction JO - Bioinformatics VL - 15 UR - https://doi.org/10.1093/bioinformatics/15.11.937 DO - 10.1093/bioinformatics/15.11.937 ID - Baldi1999 ER - TY - JOUR AU - Punta, M. AU - Rost, B. PY - 2005 DA - 2005// TI - PROFcon: novel prediction of long-range contacts JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti454 DO - 10.1093/bioinformatics/bti454 ID - Punta2005 ER - TY - JOUR AU - Chen, J. AU - Chaudhari, N. S. PY - 2007 DA - 2007// TI - Cascaded Bidirectional Recurrent Neural Networks for Protein Secondary Structure Prediction JO - IEEE/ACM Trans Comput Biol Bioinform VL - 4 UR - https://doi.org/10.1109/tcbb.2007.1055 DO - 10.1109/tcbb.2007.1055 ID - Chen2007 ER - TY - JOUR AU - Altschul, S. AU - Madden, T. AU - Schaffer, A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. 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 - Yoo, P. D. AU - Sikder, A. AU - Taheri, J. AU - Zhou, B. B. AU - Zomaya, A. PY - 2008 DA - 2008// TI - DomNet: Protein Domain Boundary Prediction Using Enhanced General Regression Network and New Profiles JO - IEEE Transactions on NanoBioscience VL - 7 UR - https://doi.org/10.1109/TNB.2008.2000747 DO - 10.1109/TNB.2008.2000747 ID - Yoo2008 ER - TY - JOUR AU - Cheng, J. AU - Sweredoski, M. AU - Baldi, P. PY - 2006 DA - 2006// TI - DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks JO - Data Mining and Knowledge Discovery VL - 13 UR - https://doi.org/10.1007/s10618-005-0023-5 DO - 10.1007/s10618-005-0023-5 ID - Cheng2006 ER - TY - JOUR AU - Marchler-Bauer, A. PY - 2005 DA - 2005// TI - CDD: a Conserved Domain Database for protein classification JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki069 DO - 10.1093/nar/gki069 ID - Marchler-Bauer2005 ER - TY - JOUR AU - Marsden, R. L. AU - McGuffin, L. J. AU - Jones, D. T. PY - 2002 DA - 2002// TI - Rapid protein domain assignment from amino acid sequence using predicted secondary structure JO - Protein Science VL - 11 UR - https://doi.org/10.1110/ps.0209902 DO - 10.1110/ps.0209902 ID - Marsden2002 ER - TY - CHAP AU - Dietterich, T. G. AU - Bakiri, G. PY - 1995 DA - 1995// TI - Machine Learning bias, statistical bias and statistical variance of decision tree algorithms BT - Dept Comput Sci ID - Dietterich1995 ER - TY - CHAP AU - Baldi, P. AU - Brunak, S. PY - 2001 DA - 2001// BT - Bioinformatics: The machine learning approach PB - MIT Press CY - Cambridge, Mass ID - Baldi2001 ER - TY - JOUR AU - Rost, B. AU - Sander, C. PY - 1994 DA - 1994// TI - Combining evolutionary information and neural networks to predict protein secondary structure JO - Proteins VL - 19 UR - https://doi.org/10.1002/prot.340190108 DO - 10.1002/prot.340190108 ID - Rost1994 ER - TY - JOUR AU - Jones, D. T. PY - 1999 DA - 1999// TI - Protein secondary structure prediction based on position-specific scoring matrices JO - J Mol Biol VL - 292 UR - https://doi.org/10.1006/jmbi.1999.3091 DO - 10.1006/jmbi.1999.3091 ID - Jones1999 ER - TY - JOUR AU - Ginalski, K. AU - Elofsson, A. AU - Fischer, D. AU - Rychlewski, L. PY - 2003 DA - 2003// TI - 3D-Jury: a simple approach to improve protein structure predictions JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg124 DO - 10.1093/bioinformatics/btg124 ID - Ginalski2003 ER - TY - JOUR AU - Sim, J. AU - Kim, S. -. Y. AU - Lee, J. PY - 2005 DA - 2005// TI - PRODO: Prediction of Protein Domain Boundaries using Neural Networks JO - Proteins VL - 59 UR - https://doi.org/10.1002/prot.20442 DO - 10.1002/prot.20442 ID - Sim2005 ER - TY - JOUR AU - Pollastri, G. AU - Przybylski, D. AU - Rost, B. AU - Baldi, P. PY - 2002 DA - 2002// TI - Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles JO - Proteins VL - 47 UR - https://doi.org/10.1002/prot.10082 DO - 10.1002/prot.10082 ID - Pollastri2002 ER - TY - JOUR AU - Yoo, P. D. AU - Ho, S. AU - Zhou, B. B. AU - Zomaya, A. Y. PY - 2008 DA - 2008// TI - SiteSeek: Protein Post-Translational Modification Analysis Using Adaptive Locality-Effective Kernel Methods and New Profiles JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-272 DO - 10.1186/1471-2105-9-272 ID - Yoo2008 ER - TY - JOUR AU - Yoo, P. D. AU - Sikder, A. R. AU - Zhou, B. B. AU - Zomaya, A. Y. PY - 2008 DA - 2008// TI - Improved general regression network for protein domain boundary prediction JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-S1-S12 DO - 10.1186/1471-2105-9-S1-S12 ID - Yoo2008 ER - TY - JOUR AU - Bujnicki, J. M. AU - Elofsson, A. AU - Fischer, D. AU - Rychlewski, L. PY - 2001 DA - 2001// TI - Structure prediction meta server JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.8.750 DO - 10.1093/bioinformatics/17.8.750 ID - Bujnicki2001 ER - TY - JOUR AU - Sim, J. AU - Kim, S. -. Y. AU - Lee, J. PY - 2005 DA - 2005// TI - PRODO: Prediction of Protein Domain Boundaries using Neural Networks JO - Proteins VL - 59 UR - https://doi.org/10.1002/prot.20442 DO - 10.1002/prot.20442 ID - Sim2005 ER - TY - JOUR AU - Notredame, C. PY - 2002 DA - 2002// TI - Recent progress in multiple sequence alignment: a survey JO - Phar-Macogenomics VL - 3 ID - Notredame2002 ER - TY - JOUR AU - Edgar, R. C. AU - Batzoglou, S. PY - 2006 DA - 2006// TI - Multiple sequence alignment JO - Current Opinion in Structural Biology VL - 16 UR - https://doi.org/10.1016/j.sbi.2006.04.004 DO - 10.1016/j.sbi.2006.04.004 ID - Edgar2006 ER - TY - JOUR AU - Edgar, R. C. AU - Sjölander, K. PY - 2004 DA - 2004// TI - A comparison of scoring functions for protein sequence profile alignment JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth090 DO - 10.1093/bioinformatics/bth090 ID - Edgar2004 ER - TY - JOUR AU - Thompson, J. D. AU - Plewniak, F. AU - Poch, O. PY - 1999 DA - 1999// TI - A comprehensive comparison of multiple sequence alignment programs JO - Nucleic Acids Research VL - 27 UR - https://doi.org/10.1093/nar/27.13.2682 DO - 10.1093/nar/27.13.2682 ID - Thompson1999 ER - TY - JOUR AU - Liu, J. AU - Rost, B. PY - 2004 DA - 2004// TI - Sequence-based prediction of protein domains JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh684 DO - 10.1093/nar/gkh684 ID - Liu2004 ER - TY - JOUR AU - Joshi, R. R. PY - 2007 DA - 2007// TI - A Decade of Computing to Traverse the Labyrinth of Protein Domains JO - Current Bioinformatics VL - 2 UR - https://doi.org/10.2174/157489307780618213 DO - 10.2174/157489307780618213 ID - Joshi2007 ER - TY - JOUR AU - Wetlaufer, D. B. PY - 1973 DA - 1973// TI - Nucleation, rapid folding, and globular intrachain regions in proteins JO - Proc Nat Acad Sci USA VL - 70 UR - https://doi.org/10.1073/pnas.70.3.697 DO - 10.1073/pnas.70.3.697 ID - Wetlaufer1973 ER - TY - JOUR AU - George, R. A. AU - Heringa, J. PY - 2002 DA - 2002// TI - SnapDRAGON: a method to delineate protein structural domains from sequence data JO - Journal of molecular biology VL - 316 UR - https://doi.org/10.1006/jmbi.2001.5387 DO - 10.1006/jmbi.2001.5387 ID - George2002 ER - TY - JOUR AU - Taylor, W. R. PY - 1999 DA - 1999// TI - Protein structural domain identification JO - Protein Eng VL - 12 UR - https://doi.org/10.1093/protein/12.3.203 DO - 10.1093/protein/12.3.203 ID - Taylor1999 ER - TY - JOUR AU - Holland, T. A. AU - Veretnik, S. AU - Shindyalov, I. N. AU - Bourne, P. E. PY - 2006 DA - 2006// TI - Partitioning Protein Structures into Domains: Why Is It so Difficult? JO - J Mol Biol VL - 361 UR - https://doi.org/10.1016/j.jmb.2006.05.060 DO - 10.1016/j.jmb.2006.05.060 ID - Holland2006 ER - TY - JOUR AU - Pearl, F. M. G. AU - Lee, D. AU - Bray, J. E. AU - Sillitoe, I. AU - Todd, A. E. AU - Harrison, A. P. AU - Thornton, J. M. AU - Orengo, C. A. PY - 2000 DA - 2000// TI - Assigning genomic sequences to CATH JO - Nucleic Acids Research VL - 28 UR - https://doi.org/10.1093/nar/28.1.277 DO - 10.1093/nar/28.1.277 ID - Pearl2000 ER - TY - JOUR AU - Andreeva, A. AU - Howorth, D. AU - Brenner, S. E. AU - Hubbard, T. J. AU - Chothia, C. AU - Murzin, A. G. PY - 2004 DA - 2004// TI - SCOP database in 2004: refinements integrate structure and sequence family data JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh039 DO - 10.1093/nar/gkh039 ID - Andreeva2004 ER - TY - JOUR AU - Berman, H. M. AU - Westbrook, J. AU - Feng, Z. AU - Gilliland, G. AU - Bhat, T. N. AU - Weissig, H. AU - Shindylov, I. N. AU - Bourne, P. E. PY - 2000 DA - 2000// TI - The Protein Data Bank JO - Nucleic Acids Research VL - 28 UR - https://doi.org/10.1093/nar/28.1.235 DO - 10.1093/nar/28.1.235 ID - Berman2000 ER - TY - JOUR AU - Pollastri, G. AU - Baldi, P. AU - Fariselli, P. AU - Casadio, R. PY - 2002 DA - 2002// TI - Prediction of coordination number and relative solvent accessibility in proteins JO - Proteins VL - 47 UR - https://doi.org/10.1002/prot.10069 DO - 10.1002/prot.10069 ID - Pollastri2002 ER - TY - JOUR AU - Bairoch, A. AU - Boeckman, B. PY - 1991 DA - 1991// TI - The SWISS-PROT protein sequence data bank JO - Nucleic Acids Res VL - 19 UR - https://doi.org/10.1093/nar/19.suppl.2247 DO - 10.1093/nar/19.suppl.2247 ID - Bairoch1991 ER - TY - JOUR AU - Hu, H. AU - Pan, Y. PY - 2004 DA - 2004// TI - Improved Protein Secondary Structure Prediction Using Support Vector Machine with a New Encoding Scheme and an Advanced Tertiary Classifier JO - IEEE Trans Nanobioscience VL - 3 UR - https://doi.org/10.1109/TNB.2004.837906 DO - 10.1109/TNB.2004.837906 ID - Hu2004 ER - TY - JOUR AU - Kim, H. AU - Park, H. PY - 2003 DA - 2003// TI - Protein secondary structure prediction based on an improved support vector machines approach JO - Protein Engineering VL - 16 UR - https://doi.org/10.1093/protein/gzg072 DO - 10.1093/protein/gzg072 ID - Kim2003 ER - TY - JOUR AU - Korenberg, M. J. AU - David, R. AU - Hunter, I. W. AU - Solomon, J. E. PY - 2000 DA - 2000// TI - Automatic classification of protein sequences into structure/function groups via parallel cascade identification: a feasibility study JO - Ann Biomed Eng VL - 28 UR - https://doi.org/10.1114/1.1289470 DO - 10.1114/1.1289470 ID - Korenberg2000 ER - TY - JOUR AU - Jang, H. H. AU - Kim, S. Y. AU - Park, S. K. AU - Jeon, H. S. AU - Lee, Y. M. AU - Jung, J. H. AU - Lee, S. Y. AU - Chae, H. B. AU - Jung, Y. J. AU - Lee, K. O. AU - Lim, C. O. AU - Chung, W. S. AU - Bahk, J. D. AU - Yun, D. AU - Cho, M. J. AU - Lee, S. Y. PY - 2006 DA - 2006// TI - Phosphorylation and concomitant structural changes in human 2-Cys peroxiredoxin isotype I differentially regulate its peroxidase and molecular chaperone functions JO - FEBS Letters VL - 580 UR - https://doi.org/10.1016/j.febslet.2005.12.030 DO - 10.1016/j.febslet.2005.12.030 ID - Jang2006 ER - TY - JOUR AU - Li, C. AU - Ibrahim, H. R. AU - Sugimoto, Y. AU - Hatta, H. AU - Aoki, T. PY - 2004 DA - 2004// TI - Improvement of Functional Properties of Egg White Protein through Phosphorylation by Dry-Heating in the Presence of Pyrophosphate JO - J Agric Food Chem VL - 52 UR - https://doi.org/10.1021/jf0498259 DO - 10.1021/jf0498259 ID - Li2004 ER - TY - CHAP AU - David, R. PY - 2000 DA - 2000// TI - Applications of nonlinear system identification to protein structural prediction BT - MSc thesis PB - MIT CY - Cambridge ID - David2000 ER - TY - JOUR AU - Rose, G. D. AU - Geselowitz, A. R. AU - Lesser, G. J. AU - Lee, R. H. AU - Zehfus, M. H. PY - 1985 DA - 1985// TI - Hydrophobicity of amino acid residues in globular proteins JO - Science VL - 229 UR - https://doi.org/10.1126/science.4023714 DO - 10.1126/science.4023714 ID - Rose1985 ER - TY - JOUR AU - Korenberg, M. J. AU - David, R. AU - Hunter, I. W. AU - Solomon, J. E. PY - 2000 DA - 2000// TI - Automatic classification of protein sequences into structure/function groups via parallel cascade identification: a feasibility study JO - Ann Biomed Eng VL - 28 UR - https://doi.org/10.1114/1.1289470 DO - 10.1114/1.1289470 ID - Korenberg2000 ER - TY - JOUR AU - Zhang, B. AU - Zhihang, C. AU - Murphey, Y. L. PY - 2005 DA - 2005// TI - Protein secondary structure prediction using machine learning JO - Proc of IEEE Conf on Neural Networks (IJCNN) VL - 1 ID - Zhang2005 ER - TY - CHAP AU - Hochreiter, S. AU - Bengio, Y. AU - Frasconi, P. AU - Schmidhuber, S. ED - Kremer, S. C. ED - Kolen, J. F. PY - 2001 DA - 2001// TI - Gradient flow in recurrent nets: the difficulty of learning long-term dependencies BT - A Field Guide to Dynamical Recurrent Neural Networks ID - Hochreiter2001 ER - TY - JOUR AU - Bengio, Y. AU - Simard, P. AU - Frasconi, P. PY - 1994 DA - 1994// TI - Learning long-term dependencies with Gradient descent is difficult JO - IEEE Trans Neural Netw VL - 5 UR - https://doi.org/10.1109/72.279181 DO - 10.1109/72.279181 ID - Bengio1994 ER - TY - JOUR AU - Hochreiter, S. AU - Schmidhuber, J. PY - 1997 DA - 1997// TI - Long Shot-Term Memory JO - Neural Computation VL - 9 UR - https://doi.org/10.1162/neco.1997.9.8.1735 DO - 10.1162/neco.1997.9.8.1735 ID - Hochreiter1997 ER - TY - JOUR AU - Gers, F. AU - Schraudolph, N. AU - Schmidhuber, J. PY - 2002 DA - 2002// TI - Learning precise timing with LSTM recurrent networks JO - Machine Learning Research VL - 3 ID - Gers2002 ER - TY - JOUR AU - Jordan, M. I. AU - Jacobs, R. A. PY - 1994 DA - 1994// TI - Hierarchical mixtures of experts and the EM algorithm JO - Neural Comp VL - 6 UR - https://doi.org/10.1162/neco.1994.6.2.181 DO - 10.1162/neco.1994.6.2.181 ID - Jordan1994 ER - TY - JOUR AU - Radzicka, A. AU - Wolfenden, R. PY - 1988 DA - 1988// TI - Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-Octanol, and neutral aqueous solution JO - Biochemistry VL - 27 UR - https://doi.org/10.1021/bi00405a042 DO - 10.1021/bi00405a042 ID - Radzicka1988 ER -