This work builds interactive computer software that lets users directly modify a protein's three-dimensional structure while the software maintains valid physical properties such as van der Waals separations, peptide geometry, and hydrogen bonds. This builds on Sculpt, a graphical modeling system that maintains these properties as one interactively moves atoms. Our intent is to maintain valid contacts and conformation while providing the user these additional interactive capabilities: 1. insert, delete, and substitute amino acids and disulfide bonds; 2. assemble chain segments with valid peptide geometry; 3. use interactive molecular mechanics to assist in arranging a valid conformation after the changes in 1 & 2; 4. decompose a model into regions with restricted, limited, or unrestricted atom motions; 5. move, bend, and twist secondary structure directly through an intuite 3D interface while modeling interactions with other atoms; 6. address needs specific to NMR, homology modeling, and de novo design. This Phase 2 proposal develops these algorithms, concentrates on interface issues, and tests the results with real modeling research. This work directly produces commercial software for molecular modeling. It also develops the foundation for software products for de novo drug design, structure determination based on NMR and crystallography, nucleic acid modeling, and education.

Proposed Commercial Applications

This work directly produces commercial software for molecular modeling. It also develops the foundation for software products for de novo drug design, structure determination based on NMR and crystallography- nucleic acid modeling, and education.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Small Business Innovation Research Grants (SBIR) - Phase II (R44)
Project #
5R44GM051732-03
Application #
2459592
Study Section
Special Emphasis Panel (ZRG7-SSS-6 (07))
Project Start
1994-08-01
Project End
1999-07-31
Budget Start
1997-08-01
Budget End
1999-07-31
Support Year
3
Fiscal Year
1997
Total Cost
Indirect Cost
Name
Interactive Simulations
Department
Type
DUNS #
City
San Diego
State
CA
Country
United States
Zip Code
92121