New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations

被引:601
作者
Darden, T
Perera, L
Li, LP
Pedersen, L
机构
[1] NIEHS, Res Triangle Pk, NC 27709 USA
[2] Univ N Carolina, Dept Chem, Chapel Hill, NC 27599 USA
来源
STRUCTURE WITH FOLDING & DESIGN | 1999年 / 7卷 / 03期
关键词
D O I
10.1016/S0969-2126(99)80033-1
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 [生物化学与分子生物学]; 081704 [应用化学];
摘要
[No abstract available]
引用
收藏
页码:R55 / R60
页数:6
相关论文
共 57 条
[1]
A novel mode of DNA recognition by a β-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA [J].
Allen, MD ;
Yamasaki, K ;
Ohme-Takagi, M ;
Tateno, M ;
Suzuki, M .
EMBO JOURNAL, 1998, 17 (18) :5484-5496
[2]
Simulations of the molecular dynamics of nucleic acids [J].
Auffinger, P ;
Westhof, E .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 1998, 8 (02) :227-236
[3]
Vertical-scanning mutagenesis of a critical tryptophan in the minor groove binding track of HIV-1 reverse transcriptase - Molecular nature of polymerase-nucleic acid interactions [J].
Beard, WA ;
Bebenek, K ;
Darden, TA ;
Li, L ;
Prasad, R ;
Kunkel, TA ;
Wilson, SH .
JOURNAL OF BIOLOGICAL CHEMISTRY, 1998, 273 (46) :30435-30442
[4]
Cheatham TE, 1996, J MOL BIOL, V259, P434
[5]
MOLECULAR-DYNAMICS SIMULATIONS ON SOLVATED BIOMOLECULAR SYSTEMS - THE PARTICLE MESH EWALD METHOD LEADS TO STABLE TRAJECTORIES OF DNA, RNA, AND PROTEINS [J].
CHEATHAM, TE ;
MILLER, JL ;
FOX, T ;
DARDEN, TA ;
KOLLMAN, PA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (14) :4193-4194
[6]
Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution [J].
Cheatham, TE ;
Brooks, BR .
THEORETICAL CHEMISTRY ACCOUNTS, 1998, 99 (05) :279-288
[7]
Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT](2) in the presence of hexaamminecobalt(III) [J].
Cheatham, TE ;
Kollman, PA .
STRUCTURE, 1997, 5 (10) :1297-1311
[8]
PARTICLE MESH EWALD - AN N.LOG(N) METHOD FOR EWALD SUMS IN LARGE SYSTEMS [J].
DARDEN, T ;
YORK, D ;
PEDERSEN, L .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (12) :10089-10092
[9]
Long-range electrostatic effects in biomolecular simulations [J].
Darden, TA ;
Toukmaji, A ;
Pedersen, LG .
JOURNAL DE CHIMIE PHYSIQUE ET DE PHYSICO-CHIMIE BIOLOGIQUE, 1997, 94 (7-8) :1346-1364
[10]
SIMULATION OF ELECTROSTATIC SYSTEMS IN PERIODIC BOUNDARY-CONDITIONS .1. LATTICE SUMS AND DIELECTRIC-CONSTANTS [J].
DELEEUW, SW ;
PERRAM, JW ;
SMITH, ER .
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 1980, 373 (1752) :27-56