SMD: Visual steering of molecular dynamics for protein design

被引：64

作者：

Leech, J ^{[1
]}

Prins, JF ^{[1
]}

Hermans, J ^{[1
]}

机构：

[1] UNIV N CAROLINA,SCH MED,CHAPEL HILL,NC 27515

来源：

IEEE COMPUTATIONAL SCIENCE & ENGINEERING | 1996年 / 3卷 / 04期

关键词：

D O I：

10.1109/99.556511

中图分类号：

TP301 [理论、方法];

学科分类号：

081202 ;

摘要：

SMD, a system for interactively steering molecular dynamics calculations of protein molecules, includes computation, visualization, and communication components. Biochemists can ''tug'' molecules into different shapes by specifying external forces in the graphical interface, which are added to internal forces representing atomic bonds and nonbonded interactions.

引用

页码：38 / 45

页数：8

共 10 条

[1] MICROFOLDING - CONFORMATIONAL PROBABILITY MAP FOR THE ALANINE DIPEPTIDE IN WATER FROM MOLECULAR-DYNAMICS SIMULATIONS [J].

ANDERSON, AG ;

HERMANS, J .

PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1988, 3 (04) :262-265

[2] MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH [J].

BERENDSEN, HJC ;

POSTMA, JPM ;

VANGUNSTEREN, WF ;

DINOLA, A ;

HAAK, JR .

JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) :3684-3690

[3]

BROOKS CL, 1988, ADV CHEM PHYSICS, V71, pCH1

[4]

BROOKS FP, 1990, ACM COMPUTER GRAPHIC, V24, P177

[5] Ligand binding: Molecular mechanics calculation of the streptavidin biotin rupture force [J].

Grubmuller, H ;

Heymann, B ;

Tavan, P .

SCIENCE, 1996, 271 (5251) :997-999

[6]

HERMANS J, 1994, SIGMA DOCUMENTATION

[7] INTERMOLECULAR FORCES AND ENERGIES BETWEEN LIGANDS AND RECEPTORS [J].

MOY, VT ;

FLORIN, EL ;

GAUB, HE .

SCIENCE, 1994, 266 (5183) :257-259

[8] MDSCOPE - A VISUAL COMPUTING ENVIRONMENT FOR STRUCTURAL BIOLOGY [J].

NELSON, M ;

HUMPHREY, W ;

KUFRIN, R ;

GURSOY, A ;

DALKE, A ;

KALE, L ;

SKEEL, R ;

SCHULTEN, K .

COMPUTER PHYSICS COMMUNICATIONS, 1995, 91 (1-3) :111-133

[9]

SURLES MC, 1994, PROTEIN SCI, V3, P198

[10]

SURLES MC, 1992, TR92016 UNC DEP COMP

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