Low-homology protein threading

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چکیده

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Low-homology protein threading

MOTIVATION The challenge of template-based modeling lies in the recognition of correct templates and generation of accurate sequence-template alignments. Homologous information has proved to be very powerful in detecting remote homologs, as demonstrated by the state-of-the-art profile-based method HHpred. However, HHpred does not fare well when proteins under consideration are low-homology. A p...

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Protein Threading

The most important in silico methods, to exploit the amount of new genomic data, are based on the concept of homology. The principle of homology-based analysis is to identify a homology relationship between a new protein and a protein whose function is known. For remote homologs, sequence alignment methods fail. In such a case one aligns the sequence of a new protein with the 3D structures of k...

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Protein threading by learning.

By using techniques borrowed from statistical physics and neural networks, we determine the parameters, associated with a scoring function, that are chosen optimally to ensure complete success in threading tests in a training set of proteins. These parameters provide a quantitative measure of the propensities of amino acids to be buried or exposed and to be in a given secondary structure and ar...

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Boosting Protein Threading Accuracy

Protein threading is one of the most successful protein structure prediction methods. Most protein threading methods use a scoring function linearly combining sequence and structure features to measure the quality of a sequence-template alignment so that a dynamic programming algorithm can be used to optimize the scoring function. However, a linear scoring function cannot fully exploit interdep...

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FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling

Ligand virtual screening is a widely used tool to assist in new pharmaceutical discovery. In practice, virtual screening approaches have a number of limitations, and the development of new methodologies is required. Previously, we showed that remotely related proteins identified by threading often share a common binding site occupied by chemically similar ligands. Here, we demonstrate that acro...

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2010

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/btq192