Data processing: structural design – modeling – simulation – and em – Modeling by mathematical expression
Reexamination Certificate
2006-08-22
2006-08-22
Jones, Hugh (Department: 2128)
Data processing: structural design, modeling, simulation, and em
Modeling by mathematical expression
C703S006000, C702S019000
Reexamination Certificate
active
07096167
ABSTRACT:
A system and method for molecular dynamic simulation includes a database for storing data pertaining to at least one biomolecular system, a memory device for storing instructions for performing at least one algorithm having an electrostatic interaction calculating function and a multiple time step function, and subdividing forces on a basis of distance over which the forces act, and a processor for processing the data by executing the instructions in order to propagate the biomolecular system from a first set of coordinates to a second set of coordinates. The system and method significantly speed up the molecular dynamics simulation of biomolecular systems in which there are long-range and short-range electrostatic interactions and in which there are fast and slow motions, and make practicable the simulation of large protein solutions and thus, can be used to simulate protein folding and the binding of substrates to protein molecules.
REFERENCES:
Stuart et al.; Molecular dynamics with multiple time scales: the selection of efficient reference system propagators; JCP; pp. 1426-1436; 1996.
Deserno et al.; How to mesh up Ewald sums. ! A theoretical and numerical comparison of various particle mesh routines; JCP; pp. 7678-76-93; 1998.
Berne Bruce J.
Harder Edward
Xu Huafeng
Zhou Ruhong
Abzug, Esq. Jesse L.
International Business Machines - Corporation
Jones Hugh
McGinn IP Law Group PLLC
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