An efficient method for sampling the essential subspace of proteins

Journal of Biomolecular Structure and Dynamics

Volumn 13, Issue 4, 1996, Pages 615-625

  Amadei, A ^a   Linssen, A B M ^a   de Groot, B L ^a   van Aalten, D M F ^b   Berendsen, H J C ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONFORMATIONAL TRANSITION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE;

EID: 0029985860     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1996.10508874     Document Type: Article

References (16)

1. Amadei, A., Linssen, A. B.M., and Berendsen, H. J.C., 1993. Essential Dynamics of Proteins. Proteins:Str., Fund., and Gen., 17:412–425.
2. van Aalten, D. M.F., Amadei, A., Bywater, R., Findlay, J. B.C., Berendsen, H. J.C., Sander, C., and Stouten, P. F.W., A comparison of structural and dynamic properties of different simulation methods applied to SH3. Biophysical journal, Submitted to the
3. van Aalten, D. M.F., Amadei, A., Vriend, G., Linssen, A. B.M., Venema, G., Berendsen, H. J.C., and Eijsink, V. G.H., 1995. The essential dynamics of thermolysin - confirmation of hinge-bending motion and comparison of simulations in vacuum and water. Proteins:Str. Funct., and Gen., 22:45–54.
4. Scheek, R. M., van Nuland, N. A.J., de Groot, B. L., and Amadei, A., 1995. Structure from NMR and mol ecular dynamics:distance restraining inhibits motion in the essential subspace. J. Biomol. NMR., 6:106–111.
5. Romo, T. D., Clarage, J. B., Sorensen, D. C., and Phillips, G. N., Jr. 1995. Singular Value Decomposition Analysis of Time-Averaged Crystallographic Refinements. Proteins:Str., Fund., and Gen., 22:311–321.
6. Amadei, A., Linssen, A. B. M., de Groot, B. L., and Berendsen, H. J. C., 1995. “ Essential degrees of free dom of proteins. ”. In Modelling of Biomolecular Structures and Mechanisms Edited by:Pullmann, A., 85–93. The Netherlands Kluwer
7. Levitt, M., Sander, C., and Stern, P. S., 1985. Protein normal-mode dynamics-trypsin-inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol., 181:423–447.
8. Garcia, A. E., 1992. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett., 68:2696–2699.
9. van Nuland, Nico A.J., Hangyi, Ilona W., van Schaik, Rene C., Berendsen, Herman J.C., van Gunsteren, Wilfred F., Scheek, Ruud M., and Robillard, George T., 1994. The high-resolution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from NMR-NOE data. J. Mol. Biol., 237:544–559.
10. van Gunsteren, W. F., and Berendsen, H. J.C., 1987. Gromos manual. BIOMOS The Netherlands:Biomolecular Software, Laboratory of Physical Chemistry, University of Groningen.
11. 1983. Biopolymers, 22:2577–2637. Wolfgang Kabsch and Christian Sander, Dictionary of Protein Secondary Structure:Pattern recognition of Hydrogen-Bonded and Geometrical features
12. Laskowski, R. A., MacArthurand, M. W., Moss, D. S., and Thornton, J. M., 1993. PROCHECK:a program to check the stereochemical quality of protein structures. J. Appl Cryst., 26:283–291.
13. Vriend, G., 1990. WHAT IF:a molecular modeling and drug design program. J. Mol. Graph., 8:52–56.
14. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., and Hermans, J., 1981. Intermolecular Forces Edited by:Pullmann, B., 331Dordrecht:Reidel.
15. Berendsen, H. J.C., Postma, J. P.M., DiNola, A., and Haak, J. R., 1984. Molecular Dynamics With Coupling to an External Bath. J. Chem. Phys., 81:3684–3690.
16. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J.C., 1977. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints; Molecular Dynamics of n-Alkanes. J. Comp. Phys., 23:327–341.