Method for Sampling Alpha-Helical Protein Backbones
We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible 3-D arrangements of the constituent helices. We produce a library of possible folds for 25 helical protein cores. In each case the method finds significant numbers of conformations close to the native structure. In addition we assign coordinates to all atoms for 4 of the 25 proteins. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of structures (0.02%--82%) within 6A of the native structure. The method's speed and efficiency make it a valuable contribution towards the goal of predicting protein structure.
- Research Organization:
- Stanford University, Stanford, CA (US)
- Sponsoring Organization:
- DOE/AP; Sloan Foundation (US)
- DOE Contract Number:
- FG03-97ER62440
- OSTI ID:
- 760875
- Journal Information:
- Journal of Molecular Biology, Other Information: Submitted to Journal of Molecular Biology; PBD: 22 Feb 2000
- Country of Publication:
- United States
- Language:
- English
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