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Bioinformatics, v.21 no.11, 2005년, pp.2667 - 2673
Han, Sangjo (The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.) , Lee, Byung-chul (The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.) , Yu, Seung Taek (Department of Biosystems, Korea Advanced Institute of Science and Technology Daejeon, 305-701, Korea) , Jeong, Chan-seok (Department of Biosystems, Korea Advanced Institute of Science and Technology Daejeon, 305-701, Korea) , Lee, Soyoung (Department of Biosystems, Korea Advanced Institute of Science and Technology Daejeon, 305-701, Korea) , Kim, Dongsup (*To whom correspondence should be addressed.)
Motivation: Currently, the most accurate fold-recognition method is to perform profile–profile alignments and estimate the statistical significances of those alignments by calculating Z-score or E-value. Although this scheme is reliable in recognizing relatively close homologs related at the family level, it has difficulty in finding the remote homologs that are related at the superfamily or fold level.Results: In this paper, we present an alternative method to estimate the significance of the alignments. The alignment between a query protein and a template of length n in the fold library is transformed into a feature vector of length n + 1, which is then evaluated by support vector machine (SVM). The output from SVM is converted to a posterior probability that a query sequence is related to a template, given SVM output. Results show that a new method shows significantly better performance than PSI-BLAST and profile–profile alignment with Z-score scheme. While PSI-BLAST and Z-score scheme detect 16 and 20% of superfamily-related proteins, respectively, at 90% specificity, a new method detects 46% of these proteins, resulting in more than 2-fold increase in sensitivity. More significantly, at the fold level, a new method can detect 14% of remotely related proteins at 90% specificity, a remarkable result considering the fact that the other methods can detect almost none at the same level of specificity.Contact: kds@kaist.ac.kr
0305-1048 Nucleic Acids Research 25 17 3389 1997 10.1093/nar/25.17.3389
0036-8075 Science Bowie 253 5016 164 1991 10.1126/science.1853201
0305-1048 Nucleic Acids Research Chandonia 32 90001 D189 2004 10.1093/nar/gkh034
1367-4803 Bioinformatics 20 16 2860 2004 10.1093/bioinformatics/bth300
0887-3585 Proteins Elofsson 46 3 330 2002 10.1002/prot.10043
0959-440X Current opinion in structural biology Friedberg 14 3 307 2004 10.1016/j.sbi.2004.04.005
0097-8485 Computers & chemistry Gribskov 20 1 25 1996 10.1016/S0097-8485(96)80004-0
0027-8424 PNAS 100 5 2386 2003 10.1073/pnas.2628030100
1367-4803 Bioinformatics Hou 19 17 2294 2003 10.1093/bioinformatics/btg317
0887-3585 Proteins Hou 57 3 518 2004 10.1002/prot.20221
0022-2836 Journal of molecular biology Hua 308 2 397 2001 10.1006/jmbi.2001.4580
1066-5277 Journal of computational biology : a journal of computational molecular cell biology Jaakkola 7 1-2 95 2000 10.1089/10665270050081405
0022-2836 Journal of molecular biology Jones 287 4 797 1999 10.1006/jmbi.1999.2583
0027-8424 PNAS Karlin 87 6 2264 1990 10.1073/pnas.87.6.2264
0022-2836 Journal of molecular biology Kelley 299 2 499 2000 10.1006/jmbi.2000.3741
1741-0126 Protein Engineering Design and Selection Kim 16 9 641 2003 10.1093/protein/gzg081
1066-5277 Journal of computational biology : a journal of computational molecular cell biology Liao 10 6 857 2003 10.1089/106652703322756113
0305-1048 Nucleic Acids Research McGuffin 32 90001 D196 2004 10.1093/nar/gkh043
0022-2836 Journal of molecular biology Murzin 247 4 536 1995 10.1006/jmbi.1995.0159
0887-3585 Proteins Ohlson 57 1 188 2004 10.1002/prot.20184
0022-2836 Journal of molecular biology Park 273 1 349 1997 10.1006/jmbi.1997.1288
0022-2836 Journal of molecular biology Przybylski 341 1 255 2004 10.1016/j.jmb.2004.05.041
0022-2836 Journal of molecular biology Qian 313 4 673 2001 10.1006/jmbi.2001.5079
0961-8368 Protein Science Rychlewski 9 2 232 2000 10.1110/ps.9.2.232
0022-2836 Journal of molecular biology Sadreyev 326 1 317 2003 10.1016/S0022-2836(02)01371-2
0022-2836 Journal of molecular biology Shi 310 1 243 2001 10.1006/jmbi.2001.4762
0022-2836 Journal of molecular biology Tress 330 4 705 2003 10.1016/S0022-2836(03)00622-3
1367-4803 Bioinformatics 20 14 2228 2004 10.1093/bioinformatics/bth232
0887-3585 Proteins Wallner 54 2 342 2004 10.1002/prot.10565
0027-8424 PNAS 101 17 6559 2004 10.1073/pnas.0308067101
0887-3585 Proteins Xu 40 3 343 2000 10.1002/1097-0134(20000815)40:3<343::AID-PROT10>3.0.CO;2-S
0022-2836 Journal of molecular biology Yona 315 5 1257 2002 10.1006/jmbi.2001.5293
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