Evaluating the usefulness of protein structure models for molecular replacement

Bioinformatics

Volumn 21, Issue SUPPL. 2, 2005, Pages

  Giorgetti, Alejandro ^a   Raimondo, Domenico ^a   Miele, Adriana Erica ^a   Tramontano, Anna ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; BIOINFORMATICS; COMPUTER MODEL; CORRELATION ANALYSIS; INTERNET; METHODOLOGY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN QUALITY; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 27544504227     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1112     Document Type: Article

References (23)

1. Bernstein,F.C. et al. (1977) The Protein Data Bank. A computer-based archival file for macromolecular structures. Eur. J. Biochem., 80, 319-324.
2. Claude,J. et al. (2004) CaspR: A web server for automated molecular replacement using homology modelling. Nucleic Acids Res., 32, W606-W609.
3. Collaborative Computational Project Number 4. (1994) The CCP4 suite: programs for protein crystallography. Acta Cryst., D50, 760-763.
4. Cozzetto,D. et al. (2005) Ten years of predictions... and counting. FEBS J., 272, 1-2.
5. Eisenberg,D. et al. (1997) Verify3d: Assessment of protein models with three-dimensional profiles. Methods Enzymol., 277, 396-404.
6. Hooft,R.W.W. et al. (1996) Errors in protein structures. Nature, 381, 272-272.
7. Jones,D.T. (2001) Evaluating the potential of using fold-recognition models for molecular replacement. Acta Crystallogr., D57, 1428-1434.
8. Laskowski,R.A. et al. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
9. Morris,R.J. et al. (2002) ARP/wARP's model building algorithms. I. The main chain. Acla Crystallogr., D58, 968-975.
10. Moult,J. et al. (1995) A large-scale experiment to assess protein structure prediction methods. Proteins, 23, ii-v.
11. Moult,J. et al. (1997) Critical assessment of methods of protein structure prediction (CASP): Round II. Proteins, (suppl. 1), 2-6.
12. Moult,J. et al. (2001) Critical assessment of methods of protein structure prediction (CASP): Round III. Proteins, (suppl. 3), 2-6.
13. Moult,J. et al. (2001) Critical assessment of methods of protein structure prediction (CASP): Round IV. Proteins, (suppl. 5), 2-6.
14. Moult,J. et al. (2003) Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins, 53 (suppl. 6), 334-339.
15. Murshudov,G.N. et al. (1997) Refinement of macromolecular structure by maximum likelyhood method. Acta Crystallogr., A50, 1131-1137.
16. Navaza,J. (1994) AMoRe: And automatic package for molecular replacement. Acta Crystallogr., D53, 240-255.
17. Potterton,E. et al. (2003) A graphical user interface to the CCP4 program suite. Acta Crystallogr., D59, 1131-1137.
18. Rossmann,M.G. and Blow,D.M. (1962) The detection of sub-units within the crystallographic asymmetric unit. Acta Crystallogr., 15, 24-31.
19. Turkenburg,J.P. and Dodson,E.J. (1996) Modern developments in molecular replacement. Curr. Opin. Struct. Biol., 6, 604-610.
20. Vagin,A.A. and Teplyakov,A. (1997) MOLREP: An automated program for molecular replacement. Appl. Crystallogr., 30, 1022-1025.
21. Valencia,A. (2005) Protein refinement: A new challenge for CASP in its 10th anniversary. Bioinformatics, 21, 277.
22. Wilmanns,M. and Nilges,M. (1996) Molecular replacement with NMR models using distance-derived pseudo B factors. Acta Crystallogr., D52, 937-982.
23. Zemla,A. (2003) LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.