Matt: Local Flexibility Aids Protein Multiple Structure Alignment
نویسندگان
چکیده
منابع مشابه
Matt: Local Flexibility Aids Protein Multiple Structure Alignment
Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geome...
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Although many algorithms have been developed so far for structure alignment problem based on either distancebased methods or vector-based methods, such as iterative dynamical programming, Monte Carlo simulation, graph theory, and mean field equations, only a few methods are published for multiple structure alignment, such as progressive structure alignment and Monte Carlo optimization. In this ...
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If we know the structures of the proteins A and B, and the function of protein A, then if we can detect structural similarity between A and B by producing an alignment between them, it can help us infer functionality of B. The problem of protein structure alignment is essentially similar to the sequence alignment; the fact that we have to do structural alignment in 3-d adds to the complexity of...
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Protein threading, a method employed in protein three-dimensional (3D) structure prediction was only proposed in the early 1990's although predicting protein 3D structure from its given amino acid sequence has been around since 1970's. Here we describe a protein threading method/system that we have developed based on multiple protein structure alignment. In order to compute multiple structure a...
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This paper describes three weighting schemes for improving the accuracy of progressive multiple sequence alignment methods: (1) global profile pre-processing, to capture for each sequence information about other sequences in a profile before the actual multiple alignment takes place; (2) local pre-processing; which incorporates a new protocol to only use non-overlapping local sequence regions t...
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ژورنال
عنوان ژورنال: PLoS Computational Biology
سال: 2008
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.0040010