Enhancing the accuracy, the efficiency and the scope of free energy simulations

被引:70
作者
Rodinger, T [1 ]
Pomès, R [1 ]
机构
[1] Hosp Sick Children, Toronto, ON M5G 1X8, Canada
基金
加拿大健康研究院; 加拿大自然科学与工程研究理事会;
关键词
D O I
10.1016/j.sbi.2005.03.001
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
Many different methods exist for computing free energy changes from molecular simulations. Recent advances have led to improvements in the theoretical framework underlying these calculations, as well as in the accuracy and sampling efficiency of the algorithms. Novel methods combining the advantages afforded by various existing approaches offer promising strategies and open up new perspectives to help elucidate the physical basis of important biological processes.
引用
收藏
页码:164 / 170
页数:7
相关论文
共 78 条
[1]   Developing an energy landscape for the novel function of a (β/α)8 barrel:: Ammonia conduction through HisF [J].
Amaro, R ;
Tajkhorshid, E ;
Luthey-Schulten, Z .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (13) :7599-7604
[2]   EFFICIENT ESTIMATION OF FREE-ENERGY DIFFERENCES FROM MONTE-CARLO DATA [J].
BENNETT, CH .
JOURNAL OF COMPUTATIONAL PHYSICS, 1976, 22 (02) :245-268
[3]   FREE-ENERGY VIA MOLECULAR SIMULATION - APPLICATIONS TO CHEMICAL AND BIOMOLECULAR SYSTEMS [J].
BEVERIDGE, DL ;
DICAPUA, FM .
ANNUAL REVIEW OF BIOPHYSICS AND BIOPHYSICAL CHEMISTRY, 1989, 18 :431-492
[4]   Generalized ensembles serve to improve the convergence of free energy simulations [J].
Bitetti-Putzer, R ;
Yang, W ;
Karplus, M .
CHEMICAL PHYSICS LETTERS, 2003, 377 (5-6) :633-641
[5]   Absolute binding free energies: A quantitative approach for their calculation [J].
Boresch, S ;
Tettinger, F ;
Leitgeb, M ;
Karplus, M .
JOURNAL OF PHYSICAL CHEMISTRY B, 2003, 107 (35) :9535-9551
[6]   Calculation of cyclodextrin binding affinities: Energy, entropy, and implications for drug design [J].
Chen, W ;
Chang, CE ;
Gilson, MK .
BIOPHYSICAL JOURNAL, 2004, 87 (05) :3035-3049
[7]  
Chipot C, 2002, MOL SIMULAT, V28, P1, DOI 10.1080/08927020211974
[8]   Nonequilibrium measurements of free energy differences for microscopically reversible Markovian systems [J].
Crooks, GE .
JOURNAL OF STATISTICAL PHYSICS, 1998, 90 (5-6) :1481-1487
[9]   Calculating free energies using average force [J].
Darve, E ;
Pohorille, A .
JOURNAL OF CHEMICAL PHYSICS, 2001, 115 (20) :9169-9183
[10]   Transition path sampling [J].
Dellago, C ;
Bolhuis, PG ;
Geissler, PL .
ADVANCES IN CHEMICAL PHYSICS, VOL 123, 2002, 123 :1-78