Solving protein structures using molecular replacement via protein fragments

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4578 LNAI, Issue , 2007, Pages 627-634

  Gubbi, Jayavardhana ^a   Parker, Michael ^b   Palaniswami, Marimuthu ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b ST VINCENT'S INSTITUTE OF MEDICAL RESEARCH   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; PROBLEM SOLVING; X RAY CRYSTALLOGRAPHY;

MODEL GENERATION; MOLECULAR REPLACEMENT; PROTEIN DATA BANK (PDB);

PROTEINS;

EID: 37249071840     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-73400-0_80     Document Type: Conference Paper

References (24)

1. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acids Research 28, 235-242 (2000)
2. Abola, E., Kuhn, P., Earnest, T., Stevens, R.C: Automation of x-ray crystallography. Nature structural biology, Structural Genomic Supplement, 973-977 (2000)
3. Lamzin, V.S., Perrakis, A.: Current state of automated crystallographic data analysis. Nature structural biology, Structural Genomic Supplement, 978-981 (2000)
4. Drenth, J.: Principles of Protein X-Ray Crystallography, 2nd edn. Springer, New York (1999)
5. Rhodes, G.: Crystallography Made Crystal Clear, 2nd edn. Academic Press, San Diego (2000)
6. Rossmann, M.G., Blow, D.M.: The detection of sub-units within the crystallographic asymmetric unit. Acta Crystallographica 15, 24-31 (1962)
7. Jones, D.T.: Evaluating the potential of using fold-recognition models for molecular replacement. Acta Crystallographica D57, 1428-1434 (2001)
8. Rost, B.: Twilight zone of protein sequence alignments. Protein Engineering 12(2), 85-94 (1999)
9. Schwarzenbacher, R., Godzik, A., Grzenchnik, S.K., Jaroszewski, L.: The importance of alignment accuracy for molecular replacement. Acta Crystallographica D60, 1229-1236 (2004)
10. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallographica Section D, 50(5), pp.760-763 (1994)
11. McCoy, A.J.: Solving structures of protein complexes by mlecular replacement with Phaser. Acta Crystallographica D63, 32-41 (2007)
12. Read, R.J.: Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallographica D57, 1373-1382 (2001)
13. Navaza, G.: AMORE: an automated package for molecular replacement. Acta Crystallographica A50, 157-163 (1994)
14. Vagin, A., Teplyakov, A.: MOLREP: an automated program for molecular replacement. Journal of Applied Crystallography 30, 1022-1025 (1997)
15. Claude, J.-B., Suhre, K., Notredame, C., Claverie, C., Abergel, J.M.: CaspR: a webserver for automated molecular replacement using homology modelling. Nucleic Acids Research 32, W606-W609 (2004)
16. Bahar, M., et al.: Others. SPINE workshop on automated X-ray analysis: a progress report. Acta Crystallographica D62, 1170-1183 (2006)
17. Long, F., Vagin, A.A., Murshudov, G.N.: Complete automation of molecular replacement in BALBES. CCP4 Study Weekend (Abstract, 2007)
18. Strop, P., Brzustowicz, M.R., Brunger, A.T.: Ab initio molecular replacement phasing for symmetric helical membrane proteins. Acta Crystallographica D63, 188-196 (2007)
19. Webster, G., Hilgenfeld, R.: An evolutionary computational approach to the phase problem in macromolecular X-ray crystallography. Acta Crystallographica A57, 351-358 (2001)
20. Cowtan, K.: Modified Phased Translation Functions and their application to Molecular-Fragment location. Acta Crystallographica D54, 750-756 (1998)
21. Terwilliger, T.C.: Automated main-chain model building by template matching and iterative fragment extension, Acta Crystallographica D59, 38-44 (2003)
22. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., Thornton, J.M.: Cath- a hierarchic classification of protein domain structures. Structure 5(8), 1093-1108 (1997)
23. Gubbi, J., Shilton, A., Parker, M., Palaniswami, M.: Protein topology classification using two-stage support vector machines. Genome Informatics 17(2), 259-269 (2006)
24. Guex, N., Peitsch, M.C.: SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18, 2714-2723 (1997)