Academic Journal
Assessment of Detection and Refinement Strategies for de novo Protein Structures using Force Field and Statistical Potentials
| العنوان: | Assessment of Detection and Refinement Strategies for de novo Protein Structures using Force Field and Statistical Potentials |
|---|---|
| المؤلفون: | Lee, Michael S., Olson, Mark A. |
| المساهمون: | ARMY MEDICAL RESEARCH INST OF INFECTIOUS DISEASES FORT DETRICK MD |
| المصدر: | DTIC |
| سنة النشر: | 2007 |
| المجموعة: | Defense Technical Information Center: DTIC Technical Reports database |
| مصطلحات موضوعية: | Biochemistry, Statistics and Probability, Atomic and Molecular Physics and Spectroscopy, PROTEINS, MOLECULAR STRUCTURE, DETECTION, MOLECULAR DYNAMICS, FOLDING, PREDICTIONS, DE NOVO STRUCTURE PREDICTIONS, RMSD(ROOT-MEAN-SQUARE-DEVIATION), PROTEIN STRUCTURE MODELS, PROTEIN STRUCTURE PREDICTION, STATISTICAL POTENTIALS, ALL-ATOM FORCE FIELDS |
| الوصف: | De novo predictions of protein structures at high resolution are challenged by the problem of detecting the native conformation from false energy minima. In this work, we provide an assessment of various detection and refinement protocols on a small subset of the second-generation all-atom Rosetta decoy set (Tsai, et al. Proteins 2003, 53, 76-87) by using an all-atom force field and a heavy-atom statistical potential. Detection schemes include minimization followed by conformational scoring and short-time molecular dynamics simulations. Refinement methods include temperature-based replica exchange molecular dynamics and a new computational unfold/refold procedure. Our results indicate that simple detection without any refinement is the best protocol for finding most native-like structures in the decoy set. The refinement techniques that we tested were generally unsuccessful in improving detection; however, they provided marginal improvements to some of the decoy structures. ; Prepared in collaboration with the Computational and Information Sciences Directorate, Army Research Lab., Aberdeen Proving Ground, MD. Published in the Journal of Chemical Theory and Computation, v3, p312-324, 2007. |
| نوع الوثيقة: | text |
| وصف الملف: | text/html |
| اللغة: | English |
| Relation: | http://www.dtic.mil/docs/citations/ADA468130 |
| الاتاحة: | http://www.dtic.mil/docs/citations/ADA468130 http://oai.dtic.mil/oai/oai?&verb=getRecord&metadataPrefix=html&identifier=ADA468130 |
| Rights: | Approved for public release; distribution is unlimited. |
| رقم الانضمام: | edsbas.132715FE |
| قاعدة البيانات: | BASE |
| الوصف غير متاح. |