Long timescale simulations

被引：104

作者：

Daggett, V ^{[1
]}

机构：

[1] Univ Washington, Dept Med Chem, Seattle, WA 98195 USA

来源：

CURRENT OPINION IN STRUCTURAL BIOLOGY | 2000年 / 10卷 / 02期

关键词：

D O I：

10.1016/S0959-440X(00)00062-2

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Computers are becoming increasingly fast, making it possible to perform simulations of macromolecules on timescales that were previously inaccessible. Questions have arisen concerning how well we are keeping up with computer power and the state of the art with respect to long molecular dynamics simulations in solvent. More importantly however, simulations of macromolecules are performed to aid the understanding of biochemical phenomena. So, what are we learning from longer simulations and are they providing reliable insight into protein dynamics, conformational behavior and function?

引用

页码：160 / 164

页数：5

共 37 条

[1] Allen M. P., 1987, COMPUTER SIMULATIONS, DOI [10.1093/oso/9780198803195.001.0001, DOI 10.1093/OSO/9780198803195.001.0001]
[2] Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains
Alonso, DOV
Daggett, V
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (01) : 133 - 138
[3] Alonso DOV, 1998, PROTEIN SCI, V7, P860
[4] MOLECULAR-DYNAMICS SIMULATIONS OF PROTEIN UNFOLDING AND LIMITED REFOLDING - CHARACTERIZATION OF PARTIALLY UNFOLDED STATES OF UBIQUITIN IN 60-PERCENT METHANOL AND IN WATER
ALONSO, DOV
DAGGETT, V
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1995, 247 (03) : 501 - 520
[5] Long-range electrostatic effects on peptide folding
Åqvist, J
[J]. FEBS LETTERS, 1999, 457 (03) : 414 - 418
[6] Absence of a stable intermediate on the folding pathway of protein A
Bai, YW
Karimi, A
Dyson, HJ
Wright, PE
[J]. PROTEIN SCIENCE, 1997, 6 (07) : 1449 - 1457
[7] FIRST-PRINCIPLES CALCULATION OF THE FOLDING FREE-ENERGY OF A 3-HELIX BUNDLE PROTEIN
BOCZKO, EM
BROOKS, CL
[J]. SCIENCE, 1995, 269 (5222) : 393 - 396
[8] Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway
Bond, CJ
Wong, KB
Clarke, J
Fersht, AR
Daggett, V
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (25) : 13409 - 13413
[9] THE STABILITY AND UNFOLDING OF AN IGG BINDING-PROTEIN BASED UPON THE B-DOMAIN OF PROTEIN-A FROM STAPHYLOCOCCUS-AUREUS PROBED BY TRYPTOPHAN SUBSTITUTION AND FLUORESCENCE SPECTROSCOPY
BOTTOMLEY, SP
POPPLEWELL, AG
SCAWEN, M
WAN, T
SUTTON, BJ
GORE, MG
[J]. PROTEIN ENGINEERING, 1994, 7 (12): : 1463 - 1470
[10] Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin
Caves, LSD
Evanseck, JD
Karplus, M
[J]. PROTEIN SCIENCE, 1998, 7 (03) : 649 - 666

← 1 2 3 4 →