TY - JOUR AU - Hawkins, T. AU - Kihara, D. PY - 2007 DA - 2007// TI - Function prediction of uncharacterized proteins JO - Journal of bioinformatics and computational biology VL - 5 UR - https://doi.org/10.1142/S0219720007002503 DO - 10.1142/S0219720007002503 ID - Hawkins2007 ER - TY - JOUR AU - Hawkins, T. AU - Chitale, M. AU - Kihara, D. PY - 2008 DA - 2008// TI - New paradigm in protein function prediction for large scale omics analysis JO - Mol BioSyst VL - 4 UR - https://doi.org/10.1039/b718229e DO - 10.1039/b718229e ID - Hawkins2008 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - Journal of molecular biology VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Pearson, W. R. PY - 1990 DA - 1990// TI - Rapid and sensitive sequence comparison with FASTP and FASTA JO - Methods in enzymology VL - 183 UR - https://doi.org/10.1016/0076-6879(90)83007-V DO - 10.1016/0076-6879(90)83007-V ID - Pearson1990 ER - TY - JOUR AU - Bru, C. AU - Courcelle, E. AU - Carrere, S. AU - Beausse, Y. AU - Dalmar, S. AU - Kahn, D. PY - 2005 DA - 2005// TI - The ProDom database of protein domain families: more emphasis on 3D JO - Nucleic acids research VL - 33 UR - https://doi.org/10.1093/nar/gki034 DO - 10.1093/nar/gki034 ID - Bru2005 ER - TY - JOUR AU - Finn, R. D. AU - Mistry, J. AU - Schuster-Bockler, B. AU - Griffiths-Jones, S. AU - Hollich, V. AU - Lassmann, T. PY - 2006 DA - 2006// TI - Pfam: clans, web tools and services JO - Nucleic acids research VL - 34 UR - https://doi.org/10.1093/nar/gkj149 DO - 10.1093/nar/gkj149 ID - Finn2006 ER - TY - JOUR AU - Hunter, S. AU - Apweiler, R. AU - Attwood, T. K. AU - Bairoch, A. AU - Bateman, A. AU - Binns, D. PY - 2009 DA - 2009// TI - InterPro: the integrative protein signature database JO - Nucleic acids research VL - 37 UR - https://doi.org/10.1093/nar/gkn785 DO - 10.1093/nar/gkn785 ID - Hunter2009 ER - TY - JOUR AU - Hawkins, T. AU - Luban, S. AU - Kihara, D. PY - 2006 DA - 2006// TI - Enhanced automated function prediction using distantly related sequences and contextual association by PFP JO - Protein Science VL - 15 UR - https://doi.org/10.1110/ps.062153506 DO - 10.1110/ps.062153506 ID - Hawkins2006 ER - TY - JOUR AU - Hawkins, T. AU - Chitale, M. AU - Luban, S. AU - Kihara, D. PY - 2009 DA - 2009// TI - PFP: automated prediction of gene ontology functional annotations with confidence scores using protein sequence data JO - Proteins: Structure, Function, and Bioinformatics VL - 74 UR - https://doi.org/10.1002/prot.22172 DO - 10.1002/prot.22172 ID - Hawkins2009 ER - TY - JOUR AU - Chitale, M. AU - Hawkins, T. AU - Park, C. AU - Kihara, D. PY - 2009 DA - 2009// TI - ESG: extended similarity group method for automated protein function prediction JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp309 DO - 10.1093/bioinformatics/btp309 ID - Chitale2009 ER - TY - JOUR AU - Martin, D. AU - Berriman, M. AU - Barton, G. PY - 2004 DA - 2004// TI - GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-178 DO - 10.1186/1471-2105-5-178 ID - Martin2004 ER - TY - JOUR AU - Khan, S. AU - Situ, G. AU - Decker, K. AU - Schmidt, C. J. PY - 2003 DA - 2003// TI - GoFigure: automated Gene Ontology annotation JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg338 DO - 10.1093/bioinformatics/btg338 ID - Khan2003 ER - TY - JOUR AU - Wass, M. N. AU - Sternberg, M. J. PY - 2008 DA - 2008// TI - ConFunc--functional annotation in the twilight zone JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn037 DO - 10.1093/bioinformatics/btn037 ID - Wass2008 ER - TY - JOUR AU - Engelhardt, B. E. AU - Jordan, M. I. AU - Muratore, K. E. AU - Brenner, S. E. PY - 2005 DA - 2005// TI - Protein molecular function prediction by Bayesian phylogenomics JO - PLoS Comput Biol VL - 1 UR - https://doi.org/10.1371/journal.pcbi.0010045 DO - 10.1371/journal.pcbi.0010045 ID - Engelhardt2005 ER - TY - JOUR AU - Krishnamurthy, N. AU - Brown, D. AU - Sj+¦lander, K. PY - 2007 DA - 2007// TI - FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function JO - BMC Evolutionary Biology VL - 7 UR - https://doi.org/10.1186/1471-2148-7-S1-S12 DO - 10.1186/1471-2148-7-S1-S12 ID - Krishnamurthy2007 ER - TY - JOUR AU - Storm, C. E. V. AU - Sonnhammer, E. L. L. PY - 2002 DA - 2002// TI - Automated ortholog inference from phylogenetic trees and calculation of orthology reliability JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.1.92 DO - 10.1093/bioinformatics/18.1.92 ID - Storm2002 ER - TY - JOUR AU - Brown, M. P. S. AU - Grundy, W. N. AU - Lin, D. AU - Cristianini, N. AU - Sugnet, C. W. AU - Furey, T. S. PY - 2000 DA - 2000// TI - Knowledge-based analysis of microarray gene expression data by using support vector machines JO - Proceedings of the National Academy of Sciences VL - 97 UR - https://doi.org/10.1073/pnas.97.1.262 DO - 10.1073/pnas.97.1.262 ID - Brown2000 ER - TY - JOUR AU - Eisen, M. B. AU - Spellman, P. T. AU - Brown, P. O. AU - Botstein, D. PY - 1998 DA - 1998// TI - Cluster analysis and display of genome-wide expression patterns JO - Proceedings of the National Academy of Sciences VL - 95 UR - https://doi.org/10.1073/pnas.95.25.14863 DO - 10.1073/pnas.95.25.14863 ID - Eisen1998 ER - TY - JOUR AU - Gao, L. AU - Li, X. AU - Guo, Z. AU - Zhu, M. AU - Li, Y. AU - Rao, S. PY - 2007 DA - 2007// TI - Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile JO - Sci China C Life Sci VL - 50 UR - https://doi.org/10.1007/s11427-007-0009-1 DO - 10.1007/s11427-007-0009-1 ID - Gao2007 ER - TY - JOUR AU - Khatri, P. AU - Dr-âghici, S. PY - 2005 DA - 2005// TI - Ontological analysis of gene expression data: current tools, limitations, and open problems JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti565 DO - 10.1093/bioinformatics/bti565 ID - Khatri2005 ER - TY - JOUR AU - van Noort, V. AU - Snel, B. AU - Huynen, M. A. PY - 2003 DA - 2003// TI - Predicting gene function by conserved co-expression JO - TRENDS in Genetics VL - 19 UR - https://doi.org/10.1016/S0168-9525(03)00056-8 DO - 10.1016/S0168-9525(03)00056-8 ID - van Noort2003 ER - TY - JOUR AU - Gherardini, P. F. AU - Helmer-Citterich, M. PY - 2008 DA - 2008// TI - Structure-based function prediction: approaches and applications JO - Briefings in functional genomics & proteomics VL - 7 UR - https://doi.org/10.1093/bfgp/eln030 DO - 10.1093/bfgp/eln030 ID - Gherardini2008 ER - TY - JOUR AU - Marti-Renom, M. AU - Rossi, A. AU - Al-Shahrour, F. AU - Davis, F. AU - Pieper, U. AU - Dopazo, J. PY - 2007 DA - 2007// TI - The AnnoLite and AnnoLyze programs for comparative annotation of protein structures JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-S4-S4 DO - 10.1186/1471-2105-8-S4-S4 ID - Marti-Renom2007 ER - TY - JOUR AU - Martin, A. C. R. AU - Orengo, C. A. AU - Hutchinson, E. G. AU - Jones, S. AU - Karmirantzou, M. AU - Laskowski, R. A. PY - 1998 DA - 1998// TI - Protein folds and functions JO - Structure VL - 6 UR - https://doi.org/10.1016/S0969-2126(98)00089-6 DO - 10.1016/S0969-2126(98)00089-6 ID - Martin1998 ER - TY - JOUR AU - Pal, D. AU - Eisenberg, D. PY - 2005 DA - 2005// TI - Inference of protein function from protein structure JO - Structure VL - 13 UR - https://doi.org/10.1016/j.str.2004.10.015 DO - 10.1016/j.str.2004.10.015 ID - Pal2005 ER - TY - JOUR AU - Ponomarenko, J. V. AU - Bourne, P. E. AU - Shindyalov, I. N. PY - 2005 DA - 2005// TI - Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology JO - Proteins: Structure, Function, and Bioinformatics VL - 58 UR - https://doi.org/10.1002/prot.20355 DO - 10.1002/prot.20355 ID - Ponomarenko2005 ER - TY - JOUR AU - Thornton, J. M. AU - Todd, A. E. AU - Milburn, D. AU - Borkakoti, N. AU - Orengo, C. A. PY - 2000 DA - 2000// TI - From structure to function: approaches and limitations JO - nature structural biology VL - 7 UR - https://doi.org/10.1038/80784 DO - 10.1038/80784 ID - Thornton2000 ER - TY - JOUR AU - Chikhi, R. AU - Sael, L. AU - Kihara, D. PY - 2010 DA - 2010// TI - Real-time ligand binding pocket database search using local surface descriptors JO - Proteins: Structure, Function, and Bioinformatics VL - 78 UR - https://doi.org/10.1002/prot.22715 DO - 10.1002/prot.22715 ID - Chikhi2010 ER - TY - JOUR AU - Sael, L. AU - Kihara, D. PY - 2010 DA - 2010// TI - Binding ligand prediction for proteins using partial matching of local surface patches JO - International Journal of Molecular Sciences VL - 11 UR - https://doi.org/10.3390/ijms11125009 DO - 10.3390/ijms11125009 ID - Sael2010 ER - TY - CHAP AU - Sael, L. AU - Chitale, M. AU - Kihara, D. PY - 2012 DA - 2012// TI - Structure- and sequence-based function prediction for non-homologous proteins. Journal of Structural and Functional Genomics BT - Journal of Structural and Functional Genomics ID - Sael2012 ER - TY - JOUR AU - Brun, C. AU - Chevenet, F. AU - Martin, D. AU - Wojcik, J. AU - Guenoche, A. AU - Jacq, B. PY - 2003 DA - 2003// TI - Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2003-5-1-r6 DO - 10.1186/gb-2003-5-1-r6 ID - Brun2003 ER - TY - JOUR AU - Chua, H. N. AU - Sung, W. K. AU - Wong, L. PY - 2006 DA - 2006// TI - Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl145 DO - 10.1093/bioinformatics/btl145 ID - Chua2006 ER - TY - JOUR AU - Letovsky, S. AU - Kasif, S. PY - 2003 DA - 2003// TI - Predicting protein function from protein/protein interaction data: a probabilistic approach JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg1026 DO - 10.1093/bioinformatics/btg1026 ID - Letovsky2003 ER - TY - JOUR AU - Nariai, N. AU - Kolaczyk, E. D. AU - Kasif, S. PY - 2007 DA - 2007// TI - Probabilistic protein function prediction from heterogeneous genome-wide data JO - PLoS One VL - 2 UR - https://doi.org/10.1371/journal.pone.0000337 DO - 10.1371/journal.pone.0000337 ID - Nariai2007 ER - TY - JOUR AU - Sharan, R. AU - Ulitsky, I. AU - Shamir, R. PY - 2007 DA - 2007// TI - Network-based prediction of protein function JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100129 DO - 10.1038/msb4100129 ID - Sharan2007 ER - TY - JOUR AU - Deng, M. AU - Tu, Z. AU - Sun, F. AU - Chen, T. PY - 2004 DA - 2004// TI - Mapping gene ontology to proteins based on protein-protein interaction data JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg500 DO - 10.1093/bioinformatics/btg500 ID - Deng2004 ER - TY - JOUR AU - Jeffery, C. J. PY - 1999 DA - 1999// TI - Moonlighting Proteins JO - Trends in Biochemical Sciences VL - 24 UR - https://doi.org/10.1016/S0968-0004(98)01335-8 DO - 10.1016/S0968-0004(98)01335-8 ID - Jeffery1999 ER - TY - JOUR AU - Jeffery, C. J. PY - 2003 DA - 2003// TI - Moonlighting Proteins: old proteins learning new tricks JO - TRENDS in Genetics VL - 19 UR - https://doi.org/10.1016/S0168-9525(03)00167-7 DO - 10.1016/S0168-9525(03)00167-7 ID - Jeffery2003 ER - TY - JOUR AU - Gancedo, C. AU - Flores, C. L. PY - 2008 DA - 2008// TI - Moonlighting proteins in yeasts JO - Microbiology and Molecular Biology Reviews VL - 72 UR - https://doi.org/10.1128/MMBR.00036-07 DO - 10.1128/MMBR.00036-07 ID - Gancedo2008 ER - TY - JOUR AU - Jeffery, C. J. PY - 2011 DA - 2011// TI - Proteins with neomorphic moonlighting functions in disease JO - IUBMB Life VL - 63 UR - https://doi.org/10.1002/iub.504 DO - 10.1002/iub.504 ID - Jeffery2011 ER - TY - JOUR AU - Ovadi, J. PY - 2011 DA - 2011// TI - Moonlighting Proteins in Neurological Disorders JO - IUBMB Life VL - 63 UR - https://doi.org/10.1002/iub.491 DO - 10.1002/iub.491 ID - Ovadi2011 ER - TY - JOUR AU - Huberts, D. H. E. W. AU - Klei, I. J. v. d. PY - 2010 DA - 2010// TI - Moonlighting proteins: an intriguing mode of multitasking JO - Biochim Biophys Acta VL - 1803 UR - https://doi.org/10.1016/j.bbamcr.2010.01.022 DO - 10.1016/j.bbamcr.2010.01.022 ID - Huberts2010 ER -