Improving sequence-based fold recognition by using 3D model quality assessment

Bioinformatics

Volumn 21, Issue 17, 2005, Pages 3509-3515

  Pettitt, Chris S ^a   McGuffin, Liam J ^a   Jones, David T ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUALITY CONTROL; SEQUENCE ANALYSIS; STRUCTURAL BIOINFORMATICS; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

EID: 24144437430     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti540     Document Type: Article

References (28)

1. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Bujnicki,J.M. et al. (2001) LiveBench-1: Continuous benchmarking of protein structure prediction servers. Protein Sci., 10, 352-361.
3. Cristobal,S. et al. (2001) A study of quality measures for protein threading models. BMC Bioinformatics, 2, 2-5.
4. Ginalski,K. et al. (2003) ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res., 31, 3804-3807.
5. Hendlich,M. et al. (1990) Identification of native protein folds amongst a large number of incorrect models - the calculation of low-energy conformations from potentials of mean force. J. Mol. Biol. 216, 167-180.
6. Holm,L. and Sander,C. (1992) Evaluation of protein models by atomic solvation preferences. J. Mol. Biol., 225, 93-105.
7. Jaroszewski,L. et al. (2000) Improving the quality of twilight-zone alignments. Protein Sci., 9, 1487-1496.
8. Jones,D.T. (1999) GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol., 287 797-815.
9. Jones,D.T. et al. (1992) A new approach to protein fold recognition. Nature, 358, 86-89.
10. Karplus,K. et al. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
11. Karplus,K. et al. (2003) Combining local-structure, fold-recognition and new-fold methods for protein structure prediction. Proteins, 53, 491-496.
12. Kelley,L.A. et al. (2000) Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol., 299 499-520.
13. Lee,M.R. et al. (2001) Molecular dynamics in the endgame of protein structure prediction. J. Mol. Biol., 313, 417-430.
14. Li,W. et al. (2002) Sequence clustering strategies improve remote homology recognitions while reducing search times. Protein Eng., 15, 643-649.
15. Lundstrom,J. et al. (2001) Pcons: A neural-network-based consensus predictor that improves fold recognition. Protein Sci., 10, 2354-2362.
16. McGuffin,L.J. and Jones,D.T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19, 874-881.
17. Moult,J. et al. (2003) Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins, 53, 334-349.
18. Petrey,D. et al. (2003) Using multiple structure alignments, fast model building and energetic analysis in fold recognition and homology modeling. Proteins, 53, 430-435.
19. Rychlewski,L. et al. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci., 9, 776-785.
20. Rychlewski,L. et al. (2003) LiveBench-6: Large-scale automated evaluation of protein structure prediction servers. Proteins, 53, 524-527.
21. Siew,N. et al. (2000) MaxSub: An automated measure for the assessment of protein structure prediction quality. Bioinformatics 16, 776-785.
22. Sippl,M.J. (1995) Knowledge based potentials for proteins. Curr. Opin. Struct. Biol., 5, 229-235.
23. Sussman,J.L. et al. (1998) Protein Data Bank (PDB): Database of three-dimensional structural information of biological macromolecules. Acta Crystallogr. D Biol Crystallogr., 1, 1078-1084.
24. Venclovas,C. et al. (2003) Assessment of progress over the CASP experiments. Proteins, 53, 585-595.
25. Wallin,S. et al. (2003) Testing similarity measures with continuous and discrete protein models. Proteins, 50, 144-157.
26. Wallner,B. and Elofsson,A. (2003) Can correct protein models be identified? Protein Sci., 12, 1073-1086.
27. Zemla,A. (2003) Lga: A method for finding 3D similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.
28. Zhang,Y. and Skolnick,J. (2004) SPICKER: A clustering approach to identify near-native protein folds. J. Comput. Chem., 25, 865-871.