Generation of pseudonative protein structures for threading

Proteins: Structure, Function and Genetics

Volumn 28, Issue 4, 1997, Pages 522-529

  Hamprecht, Fred A ^a   Scott, Walter ^a   Van Gunsteren, Wilfred F ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Empirical energy function; Protein fold recognition; Protein folding force field; Protein structure prediction

Indexed keywords

ARTICLE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; THREE DIMENSIONAL IMAGING;

COMPUTER SIMULATION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 0030746122     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199708)28:4<522::AID-PROT6>3.0.CO;2-B     Document Type: Article

References (21)

1. Crippen, G.M., Snow, M.E. A 1.8 Å Resolution potential function for protein folding. Biopolymers 29:1479-1489, 1990.
2. Jones, D., Thornton, J. Protein fold recognition. J. Comp-Aided Mol. Design 7:439-456, 1993.
3. Sippl, M.J. Boltzmann's principle, knowledge-based mean fields and protein folding. An Approach to the computational determination of protein structures. J Comp-Aided Mol. Design 7:473-501, 1993.
4. Wodak, S.J., Rooman, M.J. Generating and testing protein folds. Curr. Opin. Struct. Biol. 3:247-259, 1993.
5. Bryant, S.H., Altschul, S.F. Statistics of sequence-structure threading. Curr. Opin. Struct. Biol. 5:236-244, 1995.
6. Ouzounis, C., Sander, C., Scharf, M., Schneider, R. Prediction of protein structure by evaluation of sequence-structure fitness: Aligning sequences to contact profiles derived from 3D structures. J. Mol. Biol. 232:805-825, 1993.
7. Bowie, J.U., Lüthy, R., Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164-170, 1991.
8. Mosimann, S., Meleshko, R., James, M.N.G. A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins 23:301-317, 1995.
9. Lemer, C.M.-R., Rooman, M.J., Wodak, S.J. Protein structure prediction by threading methods: Evaluation of current techniques. Proteins 23:337-355, 1995.
10. Madej, T., Gibrat, J.-F., Bryant, S.H. Threading a database of protein cores. Proteins 23:356-369, 1995.
11. Flockner, H., Braxenthaler, M., Lackner, P., Jaritz, M., Ortner, M., Sippl, M.J. Progress in fold recognition. Proteins 23:376-386, 1995.
12. Jones, D.T., Miller, R.T., Thornton, J.M. Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins 23:387-397, 1995.
13. Defay, T., Cohen, F.E. Evaluation of current techniques for ab initio protein structure prediction. Proteins 23:431-445, 1995.
14. Crippen, G.M., Maiorov, V.N. How many protein folding motifs are there? J. Mol. Biol. 252:144-151, 1995.
15. Maiorov, V.N., Crippen, G.M. Learning about protein-folding via potential functions. Proteins 20:167-173, 1994.
16. Ulrich, P., Scott, W., van Gunsteren, W.F., Torda, A.E. Protein structure prediction force fields: parametrization with quasi newtonian dynamics. Proteins 27:367-384, 1996.
17. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
18. Maiorov, V.N., Crippen, G.M. Contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol. 227:876-888, 1992.
19. Rost, B., Sander, C. Progress of ID structure prediction at last. Proteins 23:295-300, 1995.
20. Shortle, D. Protein fold recognition. Struct. Biol. 2:91-93, 1995.
21. Hobohm, U., Sander, C. Enlarged representative set of protein structures. Prot. Sci. 3:522-524, 1994.