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 کاملModeller: generation and refinement of homology-based protein structure models.
and forces, holds promise for future refinements when applied wholesale, but is already capable of producing valuable insight when applied to structural detail. Calculation of macromolecular energy and forces with quantum mechanics requires considerably increased computational effort, and its possible use in refinement remains very much a topic for exploratory research. On the other hand, calcu...
متن کاملA Knowledge-Based Method for Protein Structure Refinement and Prediction
The native conformation of a protein, in a given environment, is determined entirely by the various interatomic interactions dictated by the amino acid sequence (1-3). We describe here a knowledge-based approach for protein structure assessment and prediction. Using a well-defined set of high-resolution protein structures, we have derived statistical potentials, in the form of atom-pairwise dis...
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...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2012
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2011.11.3376