Making optimal use of empirical energy functions: Force-field parameterization in crystal space

Proteins: Structure, Function and Genetics

Volumn 57, Issue 4, 2004, Pages 678-683

  Krieger, Elmar ^a   Darden, Tom ^b   Nabuurs, Sander B ^a   Finkelstein, Alexei ^c   Vriend, Gert ^a  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^c INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

PROTON;

ACCURACY; ARTICLE; COMPUTER PROGRAM; CRYSTAL; ENERGY; FORCE; MOLECULAR DYNAMICS; MOLECULAR MODEL; PH; PRIORITY JOURNAL; PROTEIN FOLDING; SIMULATION; STRUCTURE ANALYSIS; X RAY ANALYSIS;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEINS; RIBONUCLEASE T1; STRUCTURAL HOMOLOGY, PROTEIN; THERMODYNAMICS;

EID: 10344223464     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20251     Document Type: Article

References (31)

1. Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol 2002;9:646-652.
2. de Groot BL, van Aalten DM, Scheek RM, Amadei A, Vriend G, Berendsen HJ. Prediction of protein conformational freedom from distance constraints. Proteins 1997;29:240-251.
3. el-Bastawissy E, Knaggs MH, Gilbert IH. Molecular dynamics simulations of wild-type and point mutation human prion protein at normal and elevated temperature. J Mol Graph Model 2001;20:145-154.
4. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Jr., Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J Am Chem Soc 1995;117:5179-5197.
5. MacKerell Jr., A.D., Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
6. Van Gunsteren WF, Billeter SR, Eising AA, Hünenberger PH, Krüger P, Mark AE, Scott WRP, Tironi IG. Biomolecular simulation: The GROMOS96, manual and user guide. vdf Hochschulverlag, ETH Zürich; 1996.
7. Tramontano A, Leplae R, Morea V. Analysis and assessment of comparative modeling predictions in CASP4. Proteins 2001; Suppl.5:22-38.
8. Sanchez R, Sali A. ModBase: a database of comparative protein structure models. Bioinformatics 1999;15:1060-1061.
9. Peitsch MC, Schwede T, Guex N. Automated protein modelling- the proteome in 3D. Pharmacogenomics 2000;1:257-266.
10. Teichmann SA, Murzin AG, Chothia C. Determination of protein function, evolution and interactions by structural genomics. Curr Opin Struct Biol 2001;11:354-363.
11. Huang ES, Subbiah S, Tsai J, Levitt M. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. J Mol Biol 1996;257:716-725.
12. Lee MR, Tsai J, Baker D, Kollman PA. Molecular dynamics in the endgame of protein structure prediction. J Mol Biol 2001;313:417-430.
13. Wang J, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comp Chem 2000;21:1049-1074.
14. Ren P, Ponder JW. Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J Comp Chem 2002;23:1497-1506.
15. Krieger E, Koraimann G, Vriend G. Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing force field. Proteins 2002;47:393-402.
16. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
17. Vassylyev DG, Katayanagi K, Ishikawa K, Tsujimoto-Hirano M, Danno M, Pahler A, Matsumoto O, Matsushima M, Yoshida H, Morikawa K. Crystal structures of ribonuclease F1 of Fusarium moniliforme in its free form and in complex with 2′GMP. J Mol Biol 1993;230:979-996.
18. Hooft RWW, Sander C, Vriend G. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins 1996;26:363-376.
19. Hooft RWW, Sander C, Scharf M, Vriend G. The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. Comput Appl Biosci 1996;12:525-529.
20. Hooft RWW, Sander C, Vriend G. Verification of protein structures: side-chain planarity. J Appl Cryst 1996;29:714-716.
21. Vriend G. WHAT IF-A molecular modeling and drug design program. J Mol Graph 1990;8:52-56.
22. Walser R, Hunenberger PH, Van Gunsteren WF. Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal. Proteins 2001;43:509-519.
23. Essman U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys 1995;103:8577-8593.
24. Van Gunsteren WF, Karplus M. Protein dynamics in solution and in a crystalline environment: a molecular dynamics study. Biochemistry 1982;21:2259-2274.
25. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
26. Eastman P, Pellegrini M, Doniach S. Protein flexibility in solution and in crystals. J Chem Phys 1999;110:10141-10152.
27. Liu H, Elstner M, Kaxiras E, Frauenheim T, Hermans J, Yang W. Quantum mechanics simulation of protein dynamics on long timescale. Proteins 2001;44:484-489.
28. Krieger E, Vriend G. Models@Home: distributed computing in bioinformatics using a screensaver based approach. Bioinformatics 2002;18:315-318.
29. Engh RA, Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr A 1991;47:392-400.
30. Hooft RWW, Vriend G, Sander C, Abola EE. Errors in protein structures. Nature 1996;381:272-272.
31. Clarage JB, Romo T, Andrews BK, Pettitt BM, Phillips GNJ. A sampling problem in molecular dynamics simulations of macromolecules. Proc Natl Acad Sci USA 1995;92:3288.