Abstract

Wearedevelopingnewalgorithmsfordeterminationofprotein structures via NMR spectroscopy. By using the protein folding algorithms developed in the Friesner laboratory, we expect to be able to determine low resolution structures (3-5A RMS)with a small number of distance constraints, which will be easily obtained from an initial set of NMR data. This low resolution structure will then allow new experiments to be designed efficiently so as to quickly resolve the remaining NOE peaks, thus substantially reducing the time necessary to produce a high resolution structure. Results thus far are quite encouraging, using simulated data sets for myoglobin, 1-CTF, and lysozyme.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR006892-10
Application #
6314227
Study Section
Project Start
2000-05-05
Project End
2002-04-30
Budget Start
1998-10-01
Budget End
1999-09-30
Support Year
10
Fiscal Year
2000
Total Cost
$43,625
Indirect Cost

  Institution

Name
Columbia University (N.Y.)
Department
Type
DUNS #
049179401
City
New York
State
NY
Country
United States
Zip Code
10027

  Publications

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