A comprehensive system for evaluation of remote sequence similarity detection

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Qi, Yuan ^b,c   Sadreyev, Ruslan I ^a   Wang, Yong ^b   Kim, Bong Hyun ^b   Grishin, Nick V ^a,b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE ANALYSIS; COMPREHENSIVE EVALUATION; COMPREHENSIVE SYSTEM; PERFORMANCE ASPECTS; SENSITIVITY AND SPECIFICITY; SEQUENCE SIMILARITY; SIMILARITY DETECTION; STRUCTURE PREDICTION;

ALIGNMENT; BENCHMARKING; PROTEINS; TOOLS;

QUALITY CONTROL;

ACCURACY; ALGORITHM; ARTICLE; BIOINFORMATICS; EVALUATION RESEARCH; INTERMETHOD COMPARISON; METHODOLOGY; PREDICTION; PROTEIN DOMAIN; PROTEIN STRUCTURE; QUALITATIVE ANALYSIS; QUALITY CONTROL; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS; AMINO ACID SEQUENCE; AUTOMATED PATTERN RECOGNITION; CHEMISTRY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT;

PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; CONSERVED SEQUENCE; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 35348932100     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-314     Document Type: Article

References (50)

1. Burley SK An overview of structural genomics Nat Struct Biol 2000, 7 Suppl:932-934 10.1038/80697 11103991
2. Todd AE Marsden RL Thornton JM Orengo CA Progress of structural genomics initiatives: An analysis of solved target structures J Mol Biol 2005, 348(5):1235-1260 10.1016/j.jmb.2005.03.037 15854658
3. Sadreyev RI Grishin NV Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds BMC Struct Biol 2006, 6:6 1444916 16549009 10.1186/1472-6807-6-6
4. Xie L Bourne PE Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models PLoS Comput Biol 2005, 1(3):e31 1188274 16118666 10.1371/journal.pcbi.0010031
5. Elofsson A A study on protein sequence alignment quality Proteins 2002, 46(3):330-339 10.1002/prot.10043 11835508
6. Elofsson A Sonnhammer EL A comparison of sequence and structure protein domain families as a basis for structural genomics Bioinformatics 1999, 15(6):480-500 10.1093/bioinformatics/15.6.480 10383473
7. Ohlson T Wallner B Elofsson A Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods Proteins 2004, 57(1):188-197 10.1002/prot.20184 15326603
8. Sauder JM Arthur JW Dunbrack RL Jr. Large-scale comparison of protein sequence alignment algorithms with structure alignments Proteins 2000, 40(1):6-22 10.1002/ (SICI)1097-0134(20000701)40:1<6::AID-PROT30>3.0.CO;2-7 10813826
9. Wallner B Elofsson A All are not equal: A benchmark of different homology modeling programs Protein Sci 2005, 14(5):1315-1327 10.1110/ ps.041253405 15840834
10. Wang G Dunbrack RL Jr. Scoring profile-to-profile sequence alignments Protein Sci 2004, 13(6):1612-1626 10.1110/ps.03601504 15152092
11. Pearson WR Sierk ML The limits of protein sequence comparison? Curr Opin Struct Biol 2005, 15(3):254-260 10.1016/j.sbi.2005.05.005 15919194
12. Murzin AG Brenner SE Hubbard T Chothia C SCOP: A structural classification of proteins database for the investigation of sequences and structures J Mol Biol 1995, 247(4):536-540 10.1006/jmbi.1995.0159 7723011
13. Orengo CA Michie AD Jones S Jones DT Swindells MB Thornton JM CATH - a hierarchic classification of protein domain structures Structure 1997, 5(8):1093-1108 10.1016/S0969-2126(97)00260-8 9309224
14. Holm L Sander C Dali: A network tool for protein structure comparison Trends Biochem Sci 1995, 20(11):478-480 10.1016/S0968-0004(00)89105-7 8578593
15. Holm L Sander C Mapping the protein universe Science 1996, 273(5275):595-603 10.1126/science.273.5275.595 8662544
16. Moult J Fidelis K Rost B Hubbard T Tramontano A Critical assessment of methods of protein structure prediction (CASP) - round 6 Proteins 2005, 61(Suppl 7):3-7 10.1002/prot.20716 16187341
17. Fischer D Rychlewski L Dunbrack RL Jr. Ortiz AR Elofsson A CAFASP3: The third critical assessment of fully automated structure prediction methods Proteins 2003, 53(Suppl 6):503-516 10.1002/prot.10538 14579340
18. 6th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction http://predictioncenter.org/casp6/
19. Zemla A LGA: A method for finding 3D similarities in protein structures Nucleic Acids Res 2003, 31(13):3370-3374 168977 12824330 10.1093/nar/ gkg571
20. Zemla A Venclovas Moult J Fidelis K Processing and evaluation of predictions in CASP4 Proteins 2001, Suppl 5:13-21 10.1002/prot.10052 11835478
21. Rychlewski L Fischer D LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction Protein Sci 2005, 14(1):240-245 10.1110/ps.04888805 15608124
22. Eyrich VA Marti-Renom MA Przybylski D Madhusudhan MS Fiser A Pazos F Valencia A Sali A Rost B EVA: Continuous automatic evaluation of protein structure prediction servers Bioinformatics 2001, 17(12):1242-1243 10.1093/bioinformatics/17.12.1242 11751240
23. Pei J Grishin NV MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information Nucleic Acids Res 2006, 34(16):4364-4374 1636350 16936316 10.1093/nar/gkl514
24. Pei J Grishin NV PROMALS: Towards accurate multiple sequence alignments of distantly related proteins Bioinformatics 2007, 17267437
25. Schaffer AA Aravind L Madden TL Shavirin S Spouge JL Wolf YI Koonin EV Altschul SF Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements Nucleic Acids Res 2001, 29(14):2994-3005 55814 11452024 10.1093/nar/29.14.2994
26. Chung R Yona G Protein family comparison using statistical models and predicted structural information BMC Bioinformatics 2004, 5:183 544344 15563734 10.1186/1471-2105-5-183
27. Zhu J Weng Z FAST: A novel protein structure alignment algorithm Proteins 2005, 58(3):618-627 10.1002/prot.20331 15609341
28. Paccanaro A Casbon JA Saqi MA Spectral clustering of protein sequences Nucleic Acids Res 2006, 34(5):1571-1580 1409676 16547200 10.1093/nar/ gkj515
29. Soding J Protein homology detection by HMM-HMM comparison Bioinformatics 2005, 21(7):951-960 10.1093/bioinformatics/bti125 15531603
30. Siew N Elofsson A Rychlewski L Fischer D MaxSub: An automated measure for the assessment of protein structure prediction quality Bioinformatics 2000, 16(9):776-785 10.1093/bioinformatics/16.9.776 11108700
31. Leslie CS Eskin E Cohen A Weston J Noble WS Mismatch string kernels for discriminative protein classification Bioinformatics 2004, 20(4):467-476 10.1093/bioinformatics/btg431 14990442
32. Anantharaman V Aravind L Diversification of catalytic activities and ligand interactions in the protein fold shared by the sugar isomerases, eIF2B, DeoR transcription factors, acyl-CoA transferases and methenyltetrahydrofolate synthetase J Mol Biol 2006, 356(3):823-842 10.1016/j.jmb.2005.11.031 16376935
33. Cheek S Qi Y Krishna SS Kinch LN Grishin NV 4SCOPmap: Automated assignment of protein structures to evolutionary superfamilies BMC Bioinformatics 2004, 5:197 544345 15598351 10.1186/1471-2105-5-197
34. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25(17):3389-3402 146917 9254694 10.1093/ nar/25.17.3389
35. Sadreyev R Grishin N COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance J Mol Biol 2003, 326(1):317-336 10.1016/S0022-2836(02)01371-2 12547212
36. FTP site with a benchmark set for the evaluation of remote sequence similarity detection ftp://iole.swmed.edu/pub/evaluation/
37. Brenner SE Koehl P Levitt M The ASTRAL compendium for protein structure and sequence analysis Nucleic Acids Res 2000, 28(1):254-256 102434 10592239 10.1093/nar/28.1.254
38. Chandonia JM Hon G Walker NS Lo Conte L Koehl P Levitt M Brenner SE The ASTRAL Compendium in 2004 Nucleic Acids Res 2004, 32 Database issue D189-92 308768 14681391 10.1093/nar/gkh034
39. Zhang Y Skolnick J Scoring function for automated assessment of protein structure template quality Proteins 2004, 57(4):702-710 10.1002/ prot.20264 15476259
40. Dayhoff MO Atlas of protein sequence and structure Silver Spring, Md.,, National Biomedical Research Foundation. 1978 v.
41. Jones DT Protein secondary structure prediction based on position-specific scoring matrices J Mol Biol 1999, 292(2):195-202 10.1006/jmbi.1999.3091 10493868
42. Kabsch W Sander C Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22(12):2577-2637 10.1002/bip.360221211 6667333
43. Chandonia JM Karplus M New methods for accurate prediction of protein secondary structure Proteins 1999, 35(3):293-306 10.1002/ (SICI)1097-0134(19990515)35:3<293::AID-PROT3>3.0.CO;2-L 10328264
44. Zemla A Venclovas C Fidelis K Rost B A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment Proteins 1999, 34(2):220-223 10.1002/ (SICI)1097-0134(19990201)34:2<220::AID-PROT7>3.0.CO;2-K 10022357
45. Bryson K McGuffin LJ Marsden RL Ward JJ Sodhi JS Jones DT Protein structure prediction servers at University College London Nucleic Acids Res 2005, 33(Web Server issue):W36-8 1160171 15980489 10.1093/nar/gki410
46. Joachims T Making large-Scale SVM Learning Practical Advances in kernel methods: Support vector learning Cambridge, Mass., MIT Press Schölkopf B, Burges CJC, Smola AJ 1999
47. Kolodny R Koehl P Levitt M Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures J Mol Biol 2005, 346(4):1173-1188 10.1016/j.jmb.2004.12.032 15701525
48. Holm L Sander C Dictionary of recurrent domains in protein structures Proteins 1998, 33(1):88-96 10.1002/ (SICI)1097-0134(19981001)33:1<88::AID-PROT8>3.0.CO;2-H 9741847
49. Ginalski K Grishin NV Godzik A Rychlewski L Practical lessons from protein structure prediction Nucleic Acids Res 2005, 33(6):1874-1891 1074308 15805122 10.1093/nar/gki327
50. Yona G Levitt M Within the twilight zone: A sensitive profile-profile comparison tool based on information theory J Mol Biol 2002, 315(5):1257-1275 10.1006/jmbi.2001.5293 11827492