Princeton University

D.e. Shaw Research, LLC

Shaw, David E.

John Klepeis

David E Shaw

Ron Dror

Christodoulos A Floudas

Michael Eastwood

Yibing Shan

A method and a corresponding software and a system for processing a charge distribution according to a spreading function and a predefined operation are described.

Grid based computation for multiple body simulation.

The present invention provides a novel four stage ab initio approach for predicting the tertiary structure of polypeptides. The methods of the invention combine the classical and modern views of protein folding, while using free energy calculations and integer linear optimization to predict helical and &bgr;-sheet structures. Derivation of restraints, detailed atomistic modeling, and a deterministic global optimization method, &agr;BB, coupled with torsion angle dynamics, form the basis for the final tertiary structure prediction. The performance of the methods of the invention is illustrated using several different polypeptides.

Methods of ab initio prediction of &agr; helices, &bgr; sheets, and polypeptide tertiary structures

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New Fairfield, CT, United States of America

John Klepeis