CONFOLD: Residue-residue contact-guidedab initioprotein folding
نویسندگان
چکیده
منابع مشابه
Residue-Residue Contact Prediction Based on Evolutionary Computation
In this study, a novel residue-residue contacts prediction approach based on evolutionary computation is presented. The prediction is based on four amino acids properties. In particular, we consider the hydrophobicity, the polarity, the charge and residues size. The prediction model consists of a set of rules that identifies contacts between amino acids.
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A contact map is a 2D derivative of the 3D structure of proteins, containing various residue-residue (RR) contacts within the structure. Contact maps can be used for the reconstruction of structure with high accuracy and can be predicted from the amino acid sequence. Therefore understanding the various properties of contact maps is an important step in protein structure prediction. For investig...
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A neural network method (SPINE-2D) is introduced to provide a sequence-based prediction of residue-residue contact maps. This method is built on the success of SPINE in predicting secondary structure, residue solvent accessibility, and backbone torsion angles via large-scale training with overfit protection and a two-layer neural network. SPINE-2D achieved a 10-fold cross-validated accuracy of ...
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Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regi...
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Contact sites between amino acids characterize important structural features of a protein. We investigated characteristics of contact sites in a representative set of proteins and their relations between protein class or topology. For this purpose, we used a non-redundant set of 5872 protein domains, identically categorized by CATH and SCOP databases. The proteins represented alpha, beta, and a...
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ژورنال
عنوان ژورنال: Proteins: Structure, Function, and Bioinformatics
سال: 2015
ISSN: 0887-3585
DOI: 10.1002/prot.24829