TM-align: a protein structure alignment algorithm based on the TM-score
نویسندگان
چکیده
منابع مشابه
TM-align: a protein structure alignment algorithm based on the TM-score
We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is approximately 4 times faster than CE and 20 times faster than DALI and SAL. On average, the resulting structure alignments have higher accuracy and coverage than those provided by these most often-us...
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MOTIVATION Accurate comparisons of different protein structures play important roles in structural biology, structure prediction and functional annotation. The root-mean-square-deviation (RMSD) after optimal superposition is the predominant measure of similarity due to the ease and speed of computation. However, global RMSD is dependent on the length of the protein and can be dominated by diver...
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MOTIVATION Protein structure similarity is often measured by root mean squared deviation, global distance test score and template modeling score (TM-score). However, the scores themselves cannot provide information on how significant the structural similarity is. Also, it lacks a quantitative relation between the scores and conventional fold classifications. This article aims to answer two ques...
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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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In this paper, a fast automatic NP alignment technique developed for MetaMorpho TM is presented. MetaMorpho TM is an EBMT-based translation memory that stores not only full sentence pairs but also NP pairs in its database of translations. In order to fulfill speed requirements of a translation memory (segments have to be stored quickly), in the proposed NP alignment algorithm time consuming sta...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2005
ISSN: 1362-4962
DOI: 10.1093/nar/gki524