Structural Fragments in Protein Model Refinement
نویسندگان
چکیده
منابع مشابه
Model of protein fragments and statistical potentials
We discuss a model of protein conformations where the conformations are combinations of short fragments from some small set. For these fragments we consider a distribution of frequencies of occurrence of pairs (sequence of amino acids, conformation), averaged over some balls in the spaces of sequences and conformations. These frequencies can be estimated due to smallness of the ε–entropy of the...
متن کاملStructural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide im...
متن کاملProtein Fragments: Functional and Structural Roles of Their Coevolution Networks
Small protein fragments, and not just residues, can be used as basic building blocks to reconstruct networks of coevolved amino acids in proteins. Fragments often enter in physical contact one with the other and play a major biological role in the protein. The nature of these interactions might be multiple and spans beyond binding specificity, allosteric regulation and folding constraints. Inde...
متن کاملAssembling novel protein folds from super-secondary structural fragments.
The results of applying a fragment-based protein tertiary structure prediction method to the prediction of 14 CASP5 target domains are described. The method is based on the assembly of supersecondary structural fragments taken from highly resolved protein structures using a simulated annealing algorithm. A number of good predictions for proteins with novel folds were produced, although not alwa...
متن کاملLattice model refinement of protein structures
To find the best lattice model representation of a given full atom protein structure is a hard computational problem. Several greedy methods have been suggested where results are usually biased and leave room for improvement. In this paper we formulate and implement a Constraint Programming method to refine such lattice structure models. We show that the approach is able to provide better quali...
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: Protein & Peptide Letters
سال: 2008
ISSN: 0929-8665
DOI: 10.2174/092986608785849263