Prediction of long-range contacts from sequence profile

IEEE International Conference on Neural Networks - Conference Proceedings

Volumn , Issue , 2007, Pages 938-943

  Chen, Peng ^b,c,d   Wang, Bing ^b,c,d   Wong, Hau San ^d   Huang, De Shuang ^a,b  

^a IEEE

^b INSTITUTE OF INTELLIGENT MACHINES   (China)

^c UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^d CITY UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ARSENIC COMPOUNDS; ARTIFICIAL INTELLIGENCE; CLASSIFICATION (OF INFORMATION); CLASSIFIERS; COMPUTER NETWORKS; FORECASTING;

JOINT CONFERENCE; PROTEIN SEQUENCING;

NEURAL NETWORKS;

EID: 51749083506     PISSN: 10987576     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IJCNN.2007.4371084     Document Type: Conference Paper

References (29)

1. Sánchez, R. and Sali, A. (1997) Evaluation of comparative protein structure modeling by MODELLER -3. Proteins, Suppl. 1, 50-58.
2. Guex, N. and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresi., 18(15), 2714-2723.
3. Skolnick, J. and Kihara, D. (2001) Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins, 42(3), 319-331.
4. Panchenko, A. R., Marchler-Bauer, A. and Bryant S. H. (2000) Combination of threading potentials and sequence profiles improves fold recognition. J. Mol. Biol., 296, 1319-1331.
5. Simons, K. T., Strauss, C. and Baker, D. (2001) Prospects for ab initio protein structural genomics. J. Mol. Biol., 306, 1191-1199.
6. Huang, E. S., Samudrala, R. and Ponder, J. W. (1999) Ab Initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. J. Mol. Biol., 290, 267-281.
7. M. Niggemann and B. Steipe. (2000) Exploring local and non-local interactions for protein stability by structural motif engineering. J. Mol. Biol., 296, 181-195.
8. Fariselli, P. and Casadio, R. (1999) A neural network based predictor of residue contacts in proteins. Protein Engineering, 12(1), 15-21.
9. Vendruscolo, M., Kussell, E. and Domany, E. (1997) Recovery of protein structure from contact maps. Fold Des., 2, 295-306.
10. Vicatos, S., Boojala, V.B. Reddy and Kaznessis, Y. (2005) Prediction of distant residue contacts with the use of evolutionary information. PROTEINS: Structure, Function, and Bioinformatics, 58, 935-949.
11. Robert M. MacCallum. Striped sheets and protein contact prediction. (2004) Bioinformatics, 20(Suppl. 1), 224-231.
12. Fariselli, P., Olmea, O., Valencia, A. and Casadio, R. (2001) Prediction of contact maps with neural networks and correlated mutations. Protein Engineering , 14, 835-843.
13. Pollastri, G. and Baldi, P. (2002) Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics, 18(Suppl. 1), S62-S70.
14. Punta, M. and Rost, B. (2005) PROFcon: novel prediction of long-range contacts. Bioinformatics, 21(13), 2960-2968.
15. Wong, H.S., Cheung, Kkent K. T. and Horace, H. S. Ip. (2004) 3D head model classification by evolutionary optimization of the extended Gaussian image representation. Pattern Recognition, 37, 2307-2322.
16. Kittler, J. and Alkoot, F.M. (2003) Sum versus vote fusion in multiple classifier systems. IEEE Trans. Pattern Anal. Mach. Intell., 25 (1), 110-115.
17. Noguchi, T. and Akiyama, Y. (2003) PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. Nucleic Acids Res., 31, 492-493.
18. Glaser, F., Rosenberg, Y., Kessel, A., Tal Pupko and Ben-Tal, N. (2005) The ConSurf-HSSP Database: The Mapping of Evolutionary Conservation Among Homologs Onto PDB Structures. PROTEINS: Structure, Function, and Bioinformatics, 58, 610-617
19. Dodge, C., Schneider, R. and Sander, C. (1998). The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res., 26, 313-315.
20. Shindyalov, I.N. and Bourne, P.E. (2000) An alternative view of protein fold space. Proteins, 38, 247-260.
21. Baldi, P. and Brunak, S. (2001) Bioinformatics: The machine learning approach. The MIT Press, London, England, 29-42
22. Fischer, D., Rychlewski, L., Dunbrack, R. L., Jr.,Ortiz, A. R. and Elofsson, A. (2003) CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins: Structure,Function, and Genetics, 53, 503-516.
23. Rost, B. (1999) Twilight zone of protein sequence alignment. Protein Eng. 12, 85-94.
24. Chung, S. and Subbiah, S. (1996). A structural explanation for the twilight zone of protein sequence homology. Structure, 4, 1123-1127.
25. Wong, H.S., Cheung, Kkent K. T. and Horace, H. S. Ip. (2003) An Evolutionary Optimization Approach for 3D Human Head Model Classification. In: MIR'03, November 7, 2003, Berkeley, California, USA.
26. Vullo, A., Walsh, L. and Pollastri, G. (2006) A two-stage approach for improved prediction of residue contact maps. BMC Bioinformatics, 7:180
27. Kuncheva, L.I. (2004) Combing pattern classifiers: methods and algorithms. U.S.: Wiley.
28. Gromiha, M. M. and Selvaraj, S. (2004) Inter-residue interactions in proteins folding and stabiligy, Progress in Biophysics & Molecular Biology, 86, 235-277.
29. Leary, R.H., Rosen, J.B. and Jambeckz, P. (2004) An Optimal Structure-Discriminative Amino Acid Index for Protein Fold Recognition. Biophysical Journal, 86, 411-419