LOOPER: A molecular mechanics-based algorithm for protein loop prediction

Protein Engineering, Design and Selection

Volumn 21, Issue 2, 2008, Pages 91-100

  Spassov, Velin Z ^a   Flook, Paul K ^a   Yan, Lisa ^a  

^a ACCELRYS INC   (United States)

Author keywords

Conformational sampling; Energy minimization; Force field; Protein loops; Protein modeling

Indexed keywords

CONFORMATIONS; MOLECULAR MECHANICS; MONTE CARLO METHODS; OPTIMIZATION; PARAMETER ESTIMATION;

CONFORMATIONAL SAMPLING; ENERGY MINIMIZATION; FORCE FIELDS; PROTEIN LOOPS; PROTEIN MODELING;

PROTEINS;

ALANINE; GLYCINE; PROTEIN;

AB INITIO CALCULATION; ALGORITHM; ANALYTICAL PARAMETERS; ARTICLE; ATOM; COMPUTER MODEL; ENERGY; MOLECULAR MECHANICS; MONTE CARLO METHOD; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; SAMPLING; SCORING SYSTEM; STANDARD; VALIDATION PROCESS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PREDICTIVE VALUE OF TESTS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 39749085824     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzm083     Document Type: Article

References (23)

1. Bashford,D. and Case,D.A. (2000) Annual Review of Physical Chemistry, 51, 129-152.
2. Brooks,B., Bruccoleri,R.E., Olafson,B.D., States,D.J., Swaminathan,S. and Karplus,M. (1983) J. Comput. Chem., 4, 187-217.
3. Bruccoleri,R.E. and Karplus,M. (1987) Biopolymers, 26, 137-168.
4. Brunger,A.T. and Karplus,M. (1988) Proteins, 4, 148-156.
5. Chothia,C. and Lesk,A.M. (1987) J. Mol. Biol., 196, 901-917.
6. Chothia,C., Lesk,A.M., Levitt,M., Amit,A.G., Mariuzza,R.A., Phillips,S.E. and Poljak,R.J. (1986) Science, 233, 755-758.
7. Deane,C.M. and Blundell,T.L. (2001) Protein Sci., 10, 599-612.
8. Dominy,B.N. and Brooks,C.L., III (1999) J. Phys. Chem. B, 103, 3765-3773.
9. Fiser,A., Do,R.K. and Sali,A. (2000) Protein Sci., 9, 1753-1773.
10. Greer,J. (1980) Proc. Natl. Acad. Sci. USA, 77, 3393-3397.
11. Jacobson,M.P., Pincus,D.L., Rapp,C.S., Day,T.J., Honig,B., Shaw,D.E. and Friesner,R.A. (2004) Proteins, 55, 351-367.
12. Michalsky,E., Goede,A. and Preissner,R. (2003) Protein Eng., 16, 979-985.
13. Momany,F. and Rone,R. (1992) J. Comp. Chem., 13, 888-900.
14. Moult,J. and James,M.N. (1986) Proteins, 1, 146-163.
15. Ramachandran,G.E., Ramakrisnan,C. and Sasisekharan,V. (1963) J. Mol. Biol., 7, 95-99.
16. Rohl,C.A., Strauss,C.E., Chivian,D. and Baker,D. (2004) Proteins, 55, 656-677.
17. Spassov,V., Yan,L. and Szalma,S.Z. (2002) J. Phys. Chem. B, 106, 8726-8738.
18. Spassov,V.Z., Yan,L. and Flook,P.K. (2007) Protein Sci., 16, 494-506.
19. Still,W.C., Tempczyk,A., Hawley,R.C. and Hendrickson,T. (1990) J. Am. Chem. Soc., 112, 6127-6129.
20. Sudarsanam,S., DuBose,R.F., March,C.J. and Srinivasan,S. (1995) Protein Sci., 4, 1412-1420.
21. van Vlijmen,H.W. and Karplus,M. (1997) J. Mol. Biol., 267, 975-1001.
22. Xiang,Z., Soto,C.S. and Honig,B. (2002) Proc. Natl. Acad. Sci. USA, 99, 7432-7437.
23. Zhu,K., Pincus,D.L., Zhao,S. and Friesner,R.A. (2006) Proteins, 65, 438-452.