Protein structure refinement by optimization
نویسندگان
چکیده
منابع مشابه
Protein structure refinement by optimization.
Knowledge-based protein potentials are simplified potentials designed to improve the quality of protein models, which is important as more accurate models are more useful for biological and pharmaceutical studies. Consequently, knowledge-based potentials often are designed to be efficient in ordering a given set of deformed structures denoted decoys according to how close they are to the releva...
متن کاملConditional optimization: a new formalism for protein structure refinement.
Conditional optimization allows unlabelled loose-atom refinement to be combined with extensive application of geometrical restraints. It offers an N-particle solution for the assignment of topology to loose atoms, with weighted gradients applied to all possibilities. For a simplified test structure consisting of a polyalanine four-helical bundle, this method shows a large radius of convergence ...
متن کاملGalaxyRefine: protein structure refinement driven by side-chain repacking
The quality of model structures generated by contemporary protein structure prediction methods strongly depends on the degree of similarity between the target and available template structures. Therefore, the importance of improving template-based model structures beyond the accuracy available from template information has been emphasized in the structure prediction community. The GalaxyRefine ...
متن کاملRefinement of protein dynamic structure: normal mode refinement.
An x-ray crystallographic refinement method, referred to as the normal mode refinement, is proposed. The Debye-Waller factor is expanded in terms of the effective normal modes whose amplitudes and eigenvectors are experimentally determined by the crystallographic refinement. In contrast to the conventional method, the atomic motions are treated generally as anisotropic and concerted. This metho...
متن کاملSolvent dramatically affects protein structure refinement.
One of the most challenging problems in protein structure prediction is improvement of homology models (structures within 1-3 A C(alpha) rmsd of the native structure), also known as the protein structure refinement problem. It has been shown that improvement could be achieved using in vacuo energy minimization with molecular mechanics and statistically derived continuously differentiable hybrid...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Proteins: Structure, Function, and Bioinformatics
سال: 2015
ISSN: 0887-3585
DOI: 10.1002/prot.24846