What is the probability of a chance prediction of a protein structure with an rmsd of 6 Å?

Folding and Design

Volumn 3, Issue 2, 1998, Pages 141-147

  Reva, Boris A ^a,c   Finkelstein, Alexei V ^b   Skolnick, Jeffrey ^c  

^a INSTITUTE OF MATHEMATICAL PROBLEMS OF BIOLOGY   (Russian Federation)

^b INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Protein structure prediction; Protein like structure; rmsd distribution; Threading

Indexed keywords

EID: 0000939821     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(98)00019-4     Document Type: Article

References (19)

1. Dunbrack, R.L., Jr., et al., & Cohen, F.E. (1997). Meeting review: the second meeting on the critical assessment of techniques for protein structure prediction (CASP2). Fold. Des. 2, R27-R42.
2. Kabsch, W. (1978). A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A 34, 827-828.
3. Lesk, A.M. (1986). A toolkit for computational molecular biology. II. On the optimal superposition of two sets of coordinates. Acta Crystallogr. A 42, 110-113.
4. Chothia C. & Lesk, A.M. (1986). The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823-826.
5. Dandekar, T. & Argos, P. (1994). Folding the mainchain of small proteins with the genetic algorithm. J. Mol. Biol. 236, 844-861.
6. Dandekar, T. & Argos, P. (1996). Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions. J. Mol. Biol. 266, 645-660.
7. Skolnick, J., Kolinski, A. & Ortiz, A. (1997). MONSSTER: a method for folding globular proteins with a small number of distance restraints. J. Mol. Biol. 265, 217-241.
8. Cohen, F. & Sternberg, M.J.E. (1980). On the prediction of protein structure: the significance of the root-mean-square deviation J. Mol. Biol. 138, 321-333.
9. Maiorov, V.N. & Crippen, G.M. (1994) Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins. J. Mol. Biol. 235, 625-634.
10. Hendlich, M., et al., & Sippl, M. (1990). Identification of native protein folds amongst a large number of incorrect models. J. Mol. Biol. 216, 167-180.
11. Maiorov, V.N. & Crippen, G.M. (1995). Size-independent comparison of protein three-dimensional structures. Proteins 22, 273-283.
12. Hobohm, U., Scharf, M., Schneider, R. & Sander, C. (1992). Selection of a representative set of structures from the Brookhaven Protein Data Bank. Protein Sci. 1, 409-417.
13. Smith, T. & Watermann, M. (1981). Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
14. Murzin, A., Brenner, S., Hubbrad, T. & Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
15. Finkelstein, A.V. (1987). Program FITT for rmsd calculation. Institute of Protein Research, Russian Academy of Sciences.
16. Mathews, J. & Walker, B.L. (1964). Mathematical Methods of Physics. W.A. Benjamin, Inc. New York.
17. Press, W.H., Teukolsky, S.A., Vetterling, W.T. & Flannery, B.P. (1994). Numeric Recipes in FORTRAN. Cambridge University Press.
18. Shakhnovich, E.I. & Gutin, A.M. (1989). Formation of unique structure in polypeptide chains: theoretical investigation with the aid of a replica approach. Biophys. Chem. 34, 187-199.
19. Wall, F., Seitz, A.W., Chin, J.C. & de Gennes, P.G. (1978). Statistics of self-avoiding walks confined to strips and capillaries. Proc. Natl Acad. Sci. USA 75, 2069-2070.