TY - JOUR AU - Rost, B. AU - Sander, C. PY - 1992 DA - 1992// TI - Jury returns on structure prediction JO - Nat VL - 360 UR - https://doi.org/10.1038/360540b0 DO - 10.1038/360540b0 ID - Rost1992 ER - TY - JOUR AU - Rost, B. AU - Sander, C. PY - 1993 DA - 1993// TI - Prediction of protein secondary structure at better than 70% accuracy JO - J Mol Biol VL - 232 UR - https://doi.org/10.1006/jmbi.1993.1413 DO - 10.1006/jmbi.1993.1413 ID - Rost1993 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 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 - Barton, G. J. PY - 1995 DA - 1995// TI - Protein secondary structure prediction JO - Curr Opin Struct Biol VL - 5 UR - https://doi.org/10.1016/0959-440X(95)80099-9 DO - 10.1016/0959-440X(95)80099-9 ID - Barton1995 ER - TY - JOUR AU - Chandonia, J. -. M. AU - Karplus, M. PY - 1995 DA - 1995// TI - Neural networks for secondary structure and structural class predictions JO - Protein Sci VL - 4 UR - https://doi.org/10.1002/pro.5560040214 DO - 10.1002/pro.5560040214 ID - Chandonia1995 ER - TY - JOUR AU - Mehta, P. K. AU - Heringa, J. AU - Argos, P. PY - 1995 DA - 1995// TI - A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70% JO - Protein Sci VL - 4 UR - https://doi.org/10.1002/pro.5560041208 DO - 10.1002/pro.5560041208 ID - Mehta1995 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 Struct Funct Genet VL - 19 UR - https://doi.org/10.1002/prot.340190108 DO - 10.1002/prot.340190108 ID - Rost1994 ER - TY - JOUR AU - Solovyev, V. V. AU - Salamov, A. A. PY - 1994 DA - 1994// TI - Predicting a-helix and b-strand segments of globular proteins JO - Comput Appl Biol Sci VL - 10 ID - Solovyev1994 ER - TY - JOUR AU - Frishman, D. AU - Argos, P. PY - 1995 DA - 1995// TI - Knowledge-based protein secondary structure assignment JO - Proteins Struct Funct Genet VL - 23 UR - https://doi.org/10.1002/prot.340230412 DO - 10.1002/prot.340230412 ID - Frishman1995 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 - Bigelow, H. AU - Petrey, D. AU - Liu, J. AU - Przybylski, D. AU - Rost, B. PY - 2004 DA - 2004// TI - Predicting transmembrane beta-barrels in proteomes JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh580 DO - 10.1093/nar/gkh580 ID - Bigelow2004 ER - TY - JOUR AU - Rost, B. AU - Casadio, R. AU - Fariselli, P. PY - 1996 DA - 1996// TI - Topology prediction for helical transmembrane proteins at 86% accuracy JO - Protein Sci VL - 5 UR - https://doi.org/10.1002/pro.5560050824 DO - 10.1002/pro.5560050824 ID - Rost1996 ER - TY - JOUR AU - Rost, B. AU - Casadio, R. AU - Fariselli, P. AU - Sander, C. PY - 1995 DA - 1995// TI - Transmembrane helix prediction at 95% accuracy JO - Protein Sci VL - 4 UR - https://doi.org/10.1002/pro.5560040318 DO - 10.1002/pro.5560040318 ID - Rost1995 ER - TY - JOUR AU - Rost, B. AU - Sander, C. PY - 1994 DA - 1994// TI - Conservation and prediction of solvent accessibility in protein families JO - Proteins Struct Funct Genet VL - 20 UR - https://doi.org/10.1002/prot.340200303 DO - 10.1002/prot.340200303 ID - Rost1994 ER - TY - JOUR AU - Radivojac, P. AU - Obradovic, Z. AU - Smith, D. K. AU - Zhu, G. AU - Vucetic, S. AU - Brown, C. J. AU - Lawson, J. D. AU - Dunker, A. K. PY - 2004 DA - 2004// TI - Protein flexibility and intrinsic disorder JO - Protein Sci VL - 13 UR - https://doi.org/10.1110/ps.03128904 DO - 10.1110/ps.03128904 ID - Radivojac2004 ER - TY - JOUR AU - Schlessinger, A. AU - Rost, B. PY - 2005 DA - 2005// TI - Protein flexibility and rigidity predicted from sequence JO - Proteins VL - 61 UR - https://doi.org/10.1002/prot.20587 DO - 10.1002/prot.20587 ID - Schlessinger2005 ER - TY - JOUR AU - Punta, M. AU - Rost, B. PY - 2005 DA - 2005// TI - PROFcon: novel prediction of long-range contacts JO - Bioinform VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti454 DO - 10.1093/bioinformatics/bti454 ID - Punta2005 ER - TY - JOUR AU - Peng, K. AU - Vucetic, S. AU - Radivojac, P. AU - Brown, C. J. AU - Dunker, A. K. AU - Obradovic, Z. PY - 2005 DA - 2005// TI - Optimizing long intrinsic disorder predictors with protein evolutionary information JO - J Bioinforma Comput Biol VL - 3 UR - https://doi.org/10.1142/S0219720005000886 DO - 10.1142/S0219720005000886 ID - Peng2005 ER - TY - JOUR AU - Schlessinger, A. AU - Liu, J. AU - Rost, B. PY - 2007 DA - 2007// TI - Natively unstructured loops differ from other loops JO - PLoS Comput Biol VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030140 DO - 10.1371/journal.pcbi.0030140 ID - Schlessinger2007 ER - TY - JOUR AU - Schlessinger, A. AU - Punta, M. AU - Rost, B. PY - 2007 DA - 2007// TI - Natively unstructured regions in proteins identified from contact predictions JO - Bioinform VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm349 DO - 10.1093/bioinformatics/btm349 ID - Schlessinger2007 ER - TY - JOUR AU - Nair, R. AU - Rost, B. PY - 2003 DA - 2003// TI - Better prediction of sub-cellular localization by combining evolutionary and structural information JO - Proteins VL - 53 UR - https://doi.org/10.1002/prot.10507 DO - 10.1002/prot.10507 ID - Nair2003 ER - TY - JOUR AU - Nair, R. AU - Rost, B. PY - 2005 DA - 2005// TI - Mimicking cellular sorting improves prediction of subcellular localization JO - J Mol Biol VL - 348 UR - https://doi.org/10.1016/j.jmb.2005.02.025 DO - 10.1016/j.jmb.2005.02.025 ID - Nair2005 ER - TY - JOUR AU - Marino Buslje, C. AU - Teppa, E. AU - Domenico, T. AU - Delfino, J. M. AU - Nielsen, M. PY - 2010 DA - 2010// TI - Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification JO - PLoS Comput Biol VL - 6 UR - https://doi.org/10.1371/journal.pcbi.1000978 DO - 10.1371/journal.pcbi.1000978 ID - Marino Buslje2010 ER - TY - JOUR AU - Ofran, Y. AU - Rost, B. PY - 2007 DA - 2007// TI - Protein-protein interaction hot spots carved into sequences JO - PLoS Comput Biol VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030119 DO - 10.1371/journal.pcbi.0030119 ID - Ofran2007 ER - TY - JOUR AU - Ofran, Y. AU - Rost, B. PY - 2007 DA - 2007// TI - ISIS: interaction sites identified from sequence JO - Bioinform VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl303 DO - 10.1093/bioinformatics/btl303 ID - Ofran2007 ER - TY - JOUR AU - Adzhubei, I. A. AU - Schmidt, S. AU - Peshkin, L. AU - Ramensky, V. E. AU - Gerasimova, A. AU - Bork, P. AU - Kondrashov, A. S. AU - Sunyaev, S. R. PY - 2010 DA - 2010// TI - A method and server for predicting damaging missense mutations JO - Nat Methods VL - 7 UR - https://doi.org/10.1038/nmeth0410-248 DO - 10.1038/nmeth0410-248 ID - Adzhubei2010 ER - TY - JOUR AU - Bromberg, Y. AU - Rost, B. PY - 2007 DA - 2007// TI - SNAP: predict effect of non-synonymous polymorphisms on function JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm238 DO - 10.1093/nar/gkm238 ID - Bromberg2007 ER - TY - JOUR AU - Hayat, S. AU - Sander, C. AU - Marks, D. S. AU - Elofsson, A. PY - 2015 DA - 2015// TI - All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences JO - Proc Natl Acad Sci VL - 112 UR - https://doi.org/10.1073/pnas.1419956112 DO - 10.1073/pnas.1419956112 ID - Hayat2015 ER - TY - JOUR AU - Marks, D. S. AU - Colwell, L. J. AU - Sheridan, R. AU - Hopf, T. A. AU - Pagnani, A. AU - Zecchina, R. AU - Sander, C. PY - 2011 DA - 2011// TI - Protein 3D structure computed from evolutionary sequence variation JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0028766 DO - 10.1371/journal.pone.0028766 ID - Marks2011 ER - TY - JOUR AU - Marks, D. S. AU - Hopf, T. A. AU - Sander, C. PY - 2012 DA - 2012// TI - Protein structure prediction from sequence variation JO - Nat Biotechnol VL - 30 UR - https://doi.org/10.1038/nbt.2419 DO - 10.1038/nbt.2419 ID - Marks2012 ER - TY - JOUR AU - Morcos, F. AU - Pagnani, A. AU - Lunt, B. AU - Bertolino, A. AU - Marks, D. S. AU - Sander, C. AU - Zecchina, R. AU - Onuchic, J. N. AU - Hwa, T. AU - Weigt, M. PY - 2011 DA - 2011// TI - Direct-coupling analysis of residue coevolution captures native contacts across many protein families JO - Proc Natl Acad Sci VL - 108 UR - https://doi.org/10.1073/pnas.1111471108 DO - 10.1073/pnas.1111471108 ID - Morcos2011 ER - TY - JOUR AU - Suzek, B. E. AU - Wang, Y. AU - Huang, H. AU - McGarvey, P. B. AU - Wu, C. H. AU - UniProt, C. PY - 2015 DA - 2015// TI - UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches JO - Bioinform VL - 31 UR - https://doi.org/10.1093/bioinformatics/btu739 DO - 10.1093/bioinformatics/btu739 ID - Suzek2015 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaeffer, 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 - Nucleic 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 - Remmert, M. AU - Biegert, A. AU - Hauser, A. AU - Soding, J. PY - 2012 DA - 2012// TI - HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1818 DO - 10.1038/nmeth.1818 ID - Remmert2012 ER - TY - JOUR AU - Steinegger, M. AU - Meier, M. AU - Mirdita, M. AU - Vohringer, H. AU - Haunsberger, S. J. AU - Soding, J. PY - 2019 DA - 2019// TI - HH-suite3 for fast remote homology detection and deep protein annotation JO - BMC Bioinform VL - 20 UR - https://doi.org/10.1186/s12859-019-3019-7 DO - 10.1186/s12859-019-3019-7 ID - Steinegger2019 ER - TY - JOUR AU - Steinegger, M. AU - Söding, J. PY - 2017 DA - 2017// TI - MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets JO - Nat Biotechnol VL - 35 UR - https://doi.org/10.1038/nbt.3988 DO - 10.1038/nbt.3988 ID - Steinegger2017 ER - TY - JOUR AU - Dunker, A. K. AU - Babu, M. M. AU - Barbar, E. AU - Blackledge, M. AU - Bondos, S. E. AU - Dosztanyi, Z. AU - Dyson, H. J. AU - Forman-Kay, J. AU - Fuxreiter, M. AU - Gsponer, J. PY - 2013 DA - 2013// TI - What's in a name? Why these proteins are intrinsically disordered JO - Intrinsically Disord Proteins VL - 1 UR - https://doi.org/10.4161/idp.24157 DO - 10.4161/idp.24157 ID - Dunker2013 ER - TY - JOUR AU - Uversky, V. N. AU - Radivojac, P. AU - Iakoucheva, L. M. AU - Obradovic, Z. AU - Dunker, A. K. PY - 2007 DA - 2007// TI - Prediction of intrinsic disorder and its use in functional proteomics JO - Methods Mol Biol VL - 408 UR - https://doi.org/10.1007/978-1-59745-547-3_5 DO - 10.1007/978-1-59745-547-3_5 ID - Uversky2007 ER - TY - STD TI - Perdigao N, Heinrich J, Stolte C, Sabir KS, Buckley MJ, Tabor B, Signal B, Gloss BS, Hammang CJ, Rost B, et al. Unexpected features of the dark proteome. Proc Natl Acad Sci U S A. 2015. ID - ref39 ER - TY - JOUR AU - Schafferhans, A. AU - O'Donoghue, S. I. AU - Heinzinger, M. AU - Rost, B. PY - 2018 DA - 2018// TI - Dark proteins important for cellular function JO - Proteomics VL - 18 UR - https://doi.org/10.1002/pmic.201800227 DO - 10.1002/pmic.201800227 ID - Schafferhans2018 ER - TY - STD TI - Peters ME, Neumann M, Iyyer M, Gardner M, Clark C, Lee K, Zettlemoyer L: Deep contextualized word representations. arXiv 2018,.https://arxiv.org/abs/1802.05365. UR - https://arxiv.org/abs/1802.05365 ID - ref41 ER - TY - JOUR AU - Asgari, E. AU - Mofrad, M. R. PY - 2015 DA - 2015// TI - Continuous distributed representation of biological sequences for deep proteomics and genomics JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0141287 DO - 10.1371/journal.pone.0141287 ID - Asgari2015 ER - TY - STD TI - Mikolov T, Chen K, Corrado G, Dean J: Efficient estimation of word representations in vector space. ArXiv 2013,https://arxiv.org/abs/1301.3781. UR - https://arxiv.org/abs/1301.3781 ID - ref43 ER - TY - JOUR AU - Schils, E. AU - Pd, H. PY - 1993 DA - 1993// TI - Characteristics of sentence length in running text JO - Literary Linguist Comput VL - 8 UR - https://doi.org/10.1093/llc/8.1.20 DO - 10.1093/llc/8.1.20 ID - Schils1993 ER - TY - JOUR AU - Hochreiter, S. AU - Schmidhuber, J. PY - 1997 DA - 1997// TI - Long short-term memory JO - Neural Comput 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 - STD TI - Klausen MS, Jespersen MC, Nielsen H, Jensen KK, Jurtz VI, Sonderby CK, Sommer MOA, Winther O, Nielsen M, Petersen B, et al. NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning. Proteins. 2019. ID - ref46 ER - TY - JOUR AU - Almagro Armenteros, J. J. AU - Sonderby, C. K. AU - Sonderby, S. K. AU - Nielsen, H. AU - Winther, O. PY - 2017 DA - 2017// TI - DeepLoc: prediction of protein subcellular localization using deep learning JO - Bioinform VL - 33 UR - https://doi.org/10.1093/bioinformatics/btx548 DO - 10.1093/bioinformatics/btx548 ID - Almagro Armenteros2017 ER - TY - JOUR AU - Anfinsen, C. B. PY - 1973 DA - 1973// TI - Principles that govern the folding of protein chains JO - Sci VL - 181 UR - https://doi.org/10.1126/science.181.4096.223 DO - 10.1126/science.181.4096.223 ID - Anfinsen1973 ER - TY - JOUR AU - Buchan, D. W. AU - Jones, D. T. PY - 2018 DA - 2018// TI - Improved protein contact predictions with the MetaPSICOV2 server in CASP12 JO - Proteins VL - 86 UR - https://doi.org/10.1002/prot.25379 DO - 10.1002/prot.25379 ID - Buchan2018 ER - TY - JOUR AU - Evans, R. AU - Jumper, J. AU - Kirkpatrick, J. AU - Sifre, L. AU - Green, T. AU - Qin, C. AU - Zidek, A. AU - Nelson, A. AU - Bridgland, A. AU - Penedones, H. PY - 2018 DA - 2018// TI - De novo structure prediction with deeplearning based scoring JO - Annu Rev Biochem VL - 77 ID - Evans2018 ER - TY - STD TI - Rives A, Goyal S, Meier J, Guo D, Ott M, Zitnick CL, Ma J, Fergus R. Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. bioRxiv. 2019:622803. ID - ref51 ER - TY - JOUR AU - Chou, K. C. AU - Wu, Z. C. AU - Xiao, X. PY - 2011 DA - 2011// TI - iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0018258 DO - 10.1371/journal.pone.0018258 ID - Chou2011 ER - TY - JOUR AU - Lvd, M. AU - Hinton, G. PY - 2008 DA - 2008// TI - Visualizing data using t-SNE JO - J Mach Learn Res VL - 9 ID - Lvd2008 ER - TY - JOUR AU - Fox, N. K. AU - Brenner, S. E. AU - Chandonia, J. -. M. PY - 2013 DA - 2013// TI - SCOPe: structural classification of proteins—extended, integrating SCOP and ASTRAL data and classification of new structures JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1240 DO - 10.1093/nar/gkt1240 ID - Fox2013 ER - TY - JOUR AU - Kosloff, M. AU - Kolodny, R. PY - 2008 DA - 2008// TI - Sequence-similar, structure-dissimilar protein pairs in the PDB JO - Proteins VL - 71 UR - https://doi.org/10.1002/prot.21770 DO - 10.1002/prot.21770 ID - Kosloff2008 ER - TY - STD TI - Dai Z, Yang Z, Yang Y, Cohen WW, Carbonell J, Le QV, Salakhutdinov R: Transformer-xl: Attentive language models beyond a fixed-length context. arXiv preprint arXiv:190102860 2019. ID - ref56 ER - TY - STD TI - Devlin J, Chang M-W, Lee K, Toutanova K: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:181004805 2018. ID - ref57 ER - TY - STD TI - Yang Z, Dai Z, Yang Y, Carbonell J, Salakhutdinov R, Le QV: XLNet: Generalized Autoregressive Pretraining for Language Understanding. arXiv preprint arXiv:190608237 2019. ID - ref58 ER - TY - JOUR AU - AlQuraishi, M. PY - 2019 DA - 2019// TI - ProteinNet: a standardized data set for machine learning of protein structure JO - BMC Bioinform VL - 20 UR - https://doi.org/10.1186/s12859-019-2932-0 DO - 10.1186/s12859-019-2932-0 ID - AlQuraishi2019 ER - TY - JOUR AU - Bairoch, A. PY - 2000 DA - 2000// TI - The ENZYME database in 2000 JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.304 DO - 10.1093/nar/28.1.304 ID - Bairoch2000 ER - TY - JOUR AU - Velankar, S. AU - Dana, J. M. AU - Jacobsen, J. AU - Ginkel, G. AU - Gane, P. J. AU - Luo, J. AU - Oldfield, T. J. AU - O’donovan, C. AU - Martin, M. -. J. AU - Kleywegt, G. J. PY - 2012 DA - 2012// TI - SIFTS: structure integration with function, taxonomy and sequences resource JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1258 DO - 10.1093/nar/gks1258 ID - Velankar2012 ER - TY - JOUR AU - Heffernan, R. AU - Yang, Y. AU - Paliwal, K. AU - Zhou, Y. PY - 2017 DA - 2017// TI - Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility JO - Bioinform VL - 33 UR - https://doi.org/10.1093/bioinformatics/btx218 DO - 10.1093/bioinformatics/btx218 ID - Heffernan2017 ER - TY - JOUR AU - Wang, S. AU - Li, W. AU - Liu, S. AU - Xu, J. PY - 2016 DA - 2016// TI - RaptorX-property: a web server for protein structure property prediction JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw306 DO - 10.1093/nar/gkw306 ID - Wang2016 ER - TY - JOUR AU - Wang, S. AU - Peng, J. AU - Ma, J. AU - Xu, J. PY - 2016 DA - 2016// TI - Protein secondary structure prediction using deep convolutional neural fields JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep18962 DO - 10.1038/srep18962 ID - Wang2016 ER - TY - JOUR AU - Drozdetskiy, A. AU - Cole, C. AU - Procter, J. AU - Barton, G. J. PY - 2015 DA - 2015// TI - JPred4: a protein secondary structure prediction server JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gkv332 DO - 10.1093/nar/gkv332 ID - Drozdetskiy2015 ER - TY - JOUR AU - Berman, H. M. AU - Westbrook, J. AU - Feng, Z. AU - Gilliland, G. AU - Bhat, T. N. AU - Weissig, H. AU - Shindyalov, I. N. AU - Bourne, P. E. PY - 2000 DA - 2000// TI - The protein data bank JO - Nucleic Acids Res 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 - Wang, G. AU - Dunbrack, R. L. PY - 2003 DA - 2003// TI - PISCES: a protein sequence culling server JO - Bioinform VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg224 DO - 10.1093/bioinformatics/btg224 ID - Wang2003 ER - TY - JOUR AU - Kabsch, W. AU - Sander, C. PY - 1983 DA - 1983// TI - Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features JO - Biopolym VL - 22 UR - https://doi.org/10.1002/bip.360221211 DO - 10.1002/bip.360221211 ID - Kabsch1983 ER - TY - JOUR AU - Yang, Y. AU - Gao, J. AU - Wang, J. AU - Heffernan, R. AU - Hanson, J. AU - Paliwal, K. AU - Zhou, Y. PY - 2016 DA - 2016// TI - Sixty-five years of the long march in protein secondary structure prediction: the final stretch? JO - Brief Bioinform VL - 19 ID - Yang2016 ER - TY - JOUR AU - Cuff, J. A. AU - Barton, G. J. PY - 1999 DA - 1999// TI - Evaluation and improvement of multiple sequence methods for protein secondary structure prediction JO - Proteins Struct Funct Genet VL - 34 UR - https://doi.org/3.0.CO;2-4 DO - 3.0.CO;2-4 ID - Cuff1999 ER - TY - JOUR AU - Abriata, L. A. AU - Tamò, G. E. AU - Monastyrskyy, B. AU - Kryshtafovych, A. AU - Dal Peraro, M. PY - 2018 DA - 2018// TI - Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods JO - Proteins VL - 86 UR - https://doi.org/10.1002/prot.25423 DO - 10.1002/prot.25423 ID - Abriata2018 ER - TY - JOUR AU - Goldberg, T. AU - Hamp, T. AU - Rost, B. PY - 2012 DA - 2012// TI - LocTree2 predicts localization for all domains of life JO - Bioinform VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts390 DO - 10.1093/bioinformatics/bts390 ID - Goldberg2012 ER - TY - JOUR AU - Blum, T. AU - Briesemeister, S. AU - Kohlbacher, O. PY - 2009 DA - 2009// TI - MultiLoc2: integrating phylogeny and gene ontology terms improves subcellular protein localization prediction JO - BMC Bioinform VL - 10 UR - https://doi.org/10.1186/1471-2105-10-274 DO - 10.1186/1471-2105-10-274 ID - Blum2009 ER - TY - JOUR AU - Briesemeister, S. AU - Blum, T. AU - Brady, S. AU - Lam, Y. AU - Kohlbacher, O. AU - Shatkay, H. PY - 2009 DA - 2009// TI - SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins JO - J Proteome Res VL - 8 UR - https://doi.org/10.1021/pr900665y DO - 10.1021/pr900665y ID - Briesemeister2009 ER - TY - JOUR AU - Yu, C. S. AU - Chen, Y. C. AU - Lu, C. H. AU - Hwang, J. K. PY - 2006 DA - 2006// TI - Prediction of protein subcellular localization JO - Proteins VL - 64 UR - https://doi.org/10.1002/prot.21018 DO - 10.1002/prot.21018 ID - Yu2006 ER - TY - JOUR AU - Horton, P. AU - Park, K. J. AU - Obayashi, T. AU - Fujita, N. AU - Harada, H. AU - Adams-Collier, C. J. AU - Nakai, K. PY - 2007 DA - 2007// TI - WoLF PSORT: protein localization predictor JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm259 DO - 10.1093/nar/gkm259 ID - Horton2007 ER - TY - JOUR AU - Briesemeister, S. AU - Rahnenfuhrer, J. AU - Kohlbacher, O. PY - 2010 DA - 2010// TI - YLoc - an interpretable web server for predicting subcellular localization JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq477 DO - 10.1093/nar/gkq477 ID - Briesemeister2010 ER - TY - JOUR AU - Boutet, E. AU - Lieberherr, D. AU - Tognolli, M. AU - Schneider, M. AU - Bansal, P. AU - Bridge, A. J. AU - Poux, S. AU - Bougueleret, L. AU - Xenarios, I. PY - 2016 DA - 2016// TI - UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: how to use the entry view JO - Methods Mol Biol VL - 1374 UR - https://doi.org/10.1007/978-1-4939-3167-5_2 DO - 10.1007/978-1-4939-3167-5_2 ID - Boutet2016 ER - TY - JOUR AU - Fu, L. AU - Niu, B. AU - Zhu, Z. AU - Wu, S. AU - Li, W. PY - 2012 DA - 2012// TI - CD-HIT: accelerated for clustering the next-generation sequencing data JO - Bioinform VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts565 DO - 10.1093/bioinformatics/bts565 ID - Fu2012 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 - Bioinform VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl158 DO - 10.1093/bioinformatics/btl158 ID - Li2006 ER - TY - JOUR AU - Moussa, M. AU - Mandoiu, I. I. PY - 2018 DA - 2018// TI - Single cell RNA-seq data clustering using TF-IDF based methods JO - BMC Genomics VL - 19 UR - https://doi.org/10.1186/s12864-018-4922-4 DO - 10.1186/s12864-018-4922-4 ID - Moussa2018 ER - TY - JOUR AU - Bailey, T. L. AU - Boden, M. AU - Buske, F. A. AU - Frith, M. AU - Grant, C. E. AU - Clementi, L. AU - Ren, J. AU - Li, W. W. AU - Noble, W. S. PY - 2009 DA - 2009// TI - MEME SUITE: tools for motif discovery and searching JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp335 DO - 10.1093/nar/gkp335 ID - Bailey2009 ER - TY - JOUR AU - Bernard, G. AU - Chan, C. X. AU - Ragan, M. A. PY - 2016 DA - 2016// TI - Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep28970 DO - 10.1038/srep28970 ID - Bernard2016 ER - TY - JOUR AU - Hamp, T. AU - Rost, B. PY - 2015 DA - 2015// TI - Evolutionary profiles improve protein-protein interaction prediction from sequence JO - Bioinform VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv077 DO - 10.1093/bioinformatics/btv077 ID - Hamp2015 ER - TY - JOUR AU - Kuang, R. AU - Ie, E. AU - Wang, K. AU - Wang, K. AU - Siddiqi, M. AU - Freund, Y. AU - Leslie, C. PY - 2005 DA - 2005// TI - Profile-based string kernels for remote homology detection and motif extraction JO - J Bioinforma Comput Biol VL - 3 UR - https://doi.org/10.1142/S021972000500120X DO - 10.1142/S021972000500120X ID - Kuang2005 ER - TY - STD TI - Leslie C, Eskin E, Weston J, Noble WS: Mismatch string kernels for SVM protein classification. Bioinform 2003:in press. ID - ref86 ER - TY - JOUR AU - Nakai, K. AU - Horton, P. PY - 1999 DA - 1999// TI - PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization JO - Trends Biochem Sci VL - 24 UR - https://doi.org/10.1016/S0968-0004(98)01336-X DO - 10.1016/S0968-0004(98)01336-X ID - Nakai1999 ER - TY - JOUR AU - Noble, W. S. AU - Kuang, R. AU - Leslie, C. AU - Weston, J. PY - 2005 DA - 2005// TI - Identifying remote protein homologs by network propagation JO - FEBS J VL - 272 UR - https://doi.org/10.1111/j.1742-4658.2005.04947.x DO - 10.1111/j.1742-4658.2005.04947.x ID - Noble2005 ER - TY - JOUR AU - Asgari, E. AU - McHardy, A. C. AU - Mofrad, M. R. K. PY - 2019 DA - 2019// TI - Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX) JO - Sci Rep VL - 9 UR - https://doi.org/10.1038/s41598-019-38746-w DO - 10.1038/s41598-019-38746-w ID - Asgari2019 ER - TY - JOUR AU - Kim, S. AU - Lee, H. AU - Kim, K. AU - Kang, J. PY - 2018 DA - 2018// TI - Mut2Vec: distributed representation of cancerous mutations JO - BMC Med Genet VL - 11 ID - Kim2018 ER - TY - STD TI - Xu Y, Song J, Wilson C, Whisstock JC. PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction. Sci Rep. 2018;8. ID - ref91 ER - TY - JOUR AU - Bojanowski, P. AU - Grave, E. AU - Joulin, A. AU - Mikolov, T. PY - 2017 DA - 2017// TI - Enriching word vectors with subword information JO - Trans Assoc Comput Linguist VL - 5 UR - https://doi.org/10.1162/tacl_a_00051 DO - 10.1162/tacl_a_00051 ID - Bojanowski2017 ER - TY - STD TI - Pennington J, Socher R, Manning C: Glove: Global vectors for word representation. In: Proceedings of the 2014 conference on empirical methods in natural language processing (EMNLP): 2014. 1532–1543. ID - ref93 ER - TY - STD TI - Kim Y, Jernite Y, Sontag D, Rush AM: Character-aware neural language models. In: Thirtieth AAAI Conference on Artificial Intelligence: 2016. ID - ref94 ER - TY - STD TI - Reddi SJ, Kale S, Kumar S: On the convergence of adam and beyond. arXiv preprint arXiv:190409237 2019. ID - ref95 ER - TY - STD TI - Kingma DP, Ba J: Adam: A method for stochastic optimization. arXiv preprint arXiv:14126980 2014. ID - ref96 ER - TY - JOUR AU - Srivastava, N. AU - Hinton, G. AU - Krizhevsky, A. AU - Sutskever, I. AU - Salakhutdinov, R. PY - 2014 DA - 2014// TI - Dropout: a simple way to prevent neural networks from overfitting JO - J Mach Learn Res VL - 15 ID - Srivastava2014 ER - TY - JOUR AU - Henikoff, S. AU - Henikoff, J. G. PY - 1992 DA - 1992// TI - Amino acid substitution matrices from protein blocks JO - Proc Natl Acad Sci VL - 89 UR - https://doi.org/10.1073/pnas.89.22.10915 DO - 10.1073/pnas.89.22.10915 ID - Henikoff1992 ER - TY - STD TI - Ioffe S, Szegedy C: Batch normalization: Accelerating deep network training by reducing internal covariate shift. arXiv preprint arXiv:150203167 2015. ID - ref99 ER - TY - JOUR AU - Matthews, B. W. PY - 1975 DA - 1975// TI - Comparison of the predicted and observed secondary structure of T4 phage lysozyme JO - Biochim Biophys Acta VL - 405 UR - https://doi.org/10.1016/0005-2795(75)90109-9 DO - 10.1016/0005-2795(75)90109-9 ID - Matthews1975 ER - TY - JOUR AU - Gorodkin, J. PY - 2004 DA - 2004// TI - Comparing two K-category assignments by a K-category correlation coefficient JO - Comput Biol Chem VL - 28 UR - https://doi.org/10.1016/j.compbiolchem.2004.09.006 DO - 10.1016/j.compbiolchem.2004.09.006 ID - Gorodkin2004 ER -