CPHmodels-3.0-remote homology modeling using structure-guided sequence profiles

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Nielsen, Morten ^a   Lundegaard, Claus ^a   Lund, Ole ^a   Petersen, Thomas Nordahl ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE 8;

ACCURACY; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENE INTERACTION; GENE TARGETING; GENETIC ALGORITHM; PERFORMANCE MEASUREMENT SYSTEM; PRIORITY JOURNAL; QUALITY CONTROL; RELIABILITY; SCORING SYSTEM; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; ALGORITHM; INTERNET; PROTEIN FOLDING; REPRODUCIBILITY; SEQUENCE ANALYSIS; STRUCTURAL HOMOLOGY;

ALGORITHMS; INTERNET; PROTEIN FOLDING; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN; USER-COMPUTER INTERFACE;

EID: 77954293798     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq535     Document Type: Article

References (16)

1. Rost,B. and Sander,C. (1993) Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc. Natl Acad. Sci. USA, 90, 7558-7562.
2. Soding,J., Biegert,A. and Lupas,A.N. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res., 33(Web Server issue), W244-W248.
3. Bennett-Lovsey,R.M., Herbert,A.D., Sternberg,M.J.E. and Kelley,L.A. (2008) Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins, 70, 611-625.
4. Jaroszewski,L., Rychlewski,L. and Godzik,A. (2000) Improving the quality of twilight-zone alignments. Protein Sci., 9, 1487-1496.
5. Petersen,T.N., Lundegaard,C., Nielsen,M., Bohr,H., Bohr,J., Brunak,S., Gippert,G.P. and Lund,O. (2000) Prediction of protein secondary structure at 80% accuracy. Proteins, 41, 17-20.
6. Dor,O. and Zhou,Y. (2007) Real-SPINE: an integrated system of neural networks for real-value prediction of protein structural properties. Proteins, 68, 76-81.
7. Petersen,B., Petersen,T.N., Andersen,P., Nielsen,M. and Lundegaard,C. (2009) A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct. Biol., 9, 51.
8. Altschul,S.F. and Koonin,E.V. (1998) Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases. TIBS, 23, 444-447.
9. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
10. Hobohm,U., Scharf,M., Schneider,R. and Sander,C. (1992) Selection of representative protein data sets. Protein Sci., 1, 409-417.
11. Levitt,M. (1992) Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol., 226, 507-533.
12. Levitt,M., Hirshberg,M., Sharon,R. and Daggett,V. (1995) Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Computer Physics Comm., 91, 215-231.
13. Sali,A., Potterton,L., Yuan,F., van Vlijmen,H. and Karplus,M. (1995) Evaluation of comparative protein modelling by MODELLER. Proteins, 23, 318-326.
14. Ginalski,K., Elofsson,A., Fischer,D. and Rychlewski,L. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics, 19, 1015-1018.
15. Larsson,P., Wallner,B., Lindahl,E. and Elofsson,A. (2008) Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci., 17, 990-1002.
16. Cheng,J. (2008) A multi-template combination algorithm for protein comparative modeling. BMC Struct. Biol., 8, 18.