Protein structure prediction by all-atom free-energy refinement |
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Authors: | Abhinav Verma Wolfgang Wenzel |
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Affiliation: | (1) Institute for Scientific Computing, Forschungszentrum Karlsruhe, Karlsruhe, Germany;(2) Institute for Nanotechnology, Forschungszentrum Karlsruhe, Karlsruhe, Germany |
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Abstract: | Background The reliable prediction of protein tertiary structure from the amino acid sequence remains challenging even for small proteins. We have developed an all-atom free-energy protein forcefield (PFF01) that we could use to fold several small proteins from completely extended conformations. Because the computational cost of de-novo folding studies rises steeply with system size, this approach is unsuitable for structure prediction purposes. We therefore investigate here a low-cost free-energy relaxation protocol for protein structure prediction that combines heuristic methods for model generation with all-atom free-energy relaxation in PFF01. |
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