This proposal describes an NIH Research Resource devoted to the development of novel algorithms and software for theoretical simulations of biological systems. The core research team has expertise in quantum chemistry, statistical mechanics, molecular modeling, and biophysical theory; advances in all of these areas will be pursued and synthesized into integrated, user friendly simulation codes that will be distributed to the biophysical research community. Methodological improvements will arise both from new mathematical technology and from efficient exploitation of rapidly evolving computer architectures, including massively parallel machines. Resource participants have already developed four major simulation codes, which will form a base on which to build the new Resource software. Initial collaborative efforts will involve experimentalists whose work will benefit from the state of the art theoretical calculations on complex biological systems allowed by the Resource technology. Projects include modeling of enzymatic reactions, studies of the thermodynamics and photophysical properties of metal complexes bound to DNA, and X-ray crystallographic and NMR structural studies of proteins and nucleic acids. In subsequent years, the Resource software will be widely disseminated, with a national conference on biomolecular simulation serving as a forum for presenting advances achieved by the Resource and other research groups.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
1P41RR006892-01
Application #
3104340
Study Section
Special Emphasis Panel (SSS (F1))
Project Start
1991-09-30
Project End
1996-05-04
Budget Start
1991-09-30
Budget End
1992-05-04
Support Year
1
Fiscal Year
1991
Total Cost
Indirect Cost
Name
Columbia University (N.Y.)
Department
Type
Other Domestic Higher Education
DUNS #
064931884
City
New York
State
NY
Country
United States
Zip Code
10027
Halgren, Thomas A; Murphy, Robert B; Friesner, Richard A et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750-9
Friesner, Richard A; Banks, Jay L; Murphy, Robert B et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739-49
Baik, Mu-Hyun; Friesner, Richard A; Lippard, Stephen J (2003) Theoretical study of cisplatin binding to purine bases: why does cisplatin prefer guanine over adenine? J Am Chem Soc 125:14082-92
Baik, Mu-Hyun; Friesner, Richard A; Lippard, Stephen J (2002) Theoretical study on the stability of N-glycosyl bonds: why does N7-platination not promote depurination? J Am Chem Soc 124:4495-503
An, Yuling; Friesner, Richard A (2002) A novel fold recognition method using composite predicted secondary structures. Proteins 48:352-66
Gallicchio, Emilio; Zhang, Linda Yu; Levy, Ronald M (2002) The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. J Comput Chem 23:517-29
Friesner, R A; Dunietz, B D (2001) Large-scale ab initio quantum chemical calculations on biological systems. Acc Chem Res 34:351-8
Gherman, B F; Dunietz, B D; Whittington, D A et al. (2001) Activation of the C-H bond of methane by intermediate Q of methane monooxygenase: a theoretical study. J Am Chem Soc 123:3836-7
Standley, D M; Eyrich, V A; An, Y et al. (2001) Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment. Proteins Suppl 5:133-9
Eyrich, V A; Standley, D M; Friesner, R A (1999) Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set. J Mol Biol 288:725-42

Showing the most recent 10 out of 22 publications