STALK users guide | Zendy

David Levine | Zendy; M. Facello | Zendy; P. Hallstrom | Zendy; G. Reeder | Zendy; Brian P. Walenz | Zendy; F. Stevens | Zendy

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STALK users guide

Author(s) -

David Levine,

M. Facello,

P. Hallstrom,

G. Reeder,

Brian P. Walenz,

F. Stevens

Publication year - 1996

Publication title -

osti oai (u.s. department of energy office of scientific and technical information)

Language(s) - English

Resource type - Reports

DOI - 10.2172/379000

Subject(s) - intermolecular force , computer science , stalk , molecular dynamics , genetic algorithm , molecule , docking (animal) , virtual reality , space (punctuation) , energy minimization , chemistry , human–computer interaction , computational chemistry , biology , machine learning , medicine , nursing , organic chemistry , horticulture , operating system

STALK is a system that models molecular docking between two proteins. A problem is posed as an optimization problem where the objective is to minimize the free energy of the molecular system by maximizing the intermolecular interaction energy between the molecules. The possible number of conformations between the two molecules can be very large. A parallel genetic algorithm (GA) is used to explore the conformation space and identify the low-energy molecular configurations. The CAVE, a virtual reality environment, can be used to visualize and interact with the systems while it is executing

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