Boston University

The United States of America As Represented by the Department of Health

Charles DeLisi

James L Cornette

Jay A Berzofsky

Michael Silverman

Sandor Vajda

Hanah Margalit

Benjamin L King

Rakefet Rosenfeld

Ugur Sezerman

Kemp B Cease

Cecilia S Ouyang

A method, performed on a computer (10), for generating representations of a molecule, both two- and three-dimensional, is provided. The method includes establishing X, Y, and Z coordinate axes for the molecule to be modeled such that a rectangular region is established with sides parallel to the coordinate axes. The method also includes establishing a grid of coordinates on the X, Y, and Z coordinates axes with a grid mesh size of sufficient resolution to identify atom points of the molecule and solvent points. Next, the method includes identifying surface points which form a trace in one dimension in each Z cross-section, and generating tracing instructions for each Z cross-section by tracing along the surface points in the trace in each Z cross-section and writing the X, Y coordinates to instructions for controlling a computer display or for controlling a computer controlled milling machine. The method also includes generating on a computer display a two-dimensional grid and surface geometry for the molecule including atom identifications using the tracing steps for each Z cross-section. Additionally, the method includes cutting sheets representative of each Z cross-section with the milling instructions and assembling the sheets into three-dimensional models representative of the molecule.

Molecular modeling method and system

A method for computing the conformation and location that a protein fragment will obtain in binding to the active site of a receptor is provided. The invention relates to both the computation of conformation and location of natural ligands within an active site and the design of artificial ligands with useful binding characteristics.

General strategy for vaccine and drug design

This invention relates to the identification of short peptide segments of AIDS virus proteins which elicit T cellular immunity, and to a method of inducing cellular immunity to native proteins of the AIDS virus by immunization with short synthetic peptides. Five potential peptides have been identified by searching for regions which can fold as a maximally amphipathic helix. These may be useful to include in either a synthetic peptide- or recombinant fragment- based vaccine.

Synthetic peptides sharing sequence homology with the HIV envelope

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Boston, MA, United States of America

Charles DeLisi