protein structure alignmentBayesian statisticsMCMCMultiple protein structure alignment is an important tool in computational biology, with numerous algorithms published in the past two decades. However, recently literature highlights a growing recognition of the inconsistencies among alignments from different ...
MOTIVATION: A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools. RESULTS: We describe COBALT, a constraint based alignment tool that im...
A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools. We describe COBALT, a constraint based alignment tool that implements a general ...
Protein sequence alignment is the task of identifying evolutionarily or structurally related positions in a collection of amino acid sequences. Although the protein alignment problem has been studied for several decades, many recent studies have demonstrated considerable progress in improving the accuracy ...
Multiple sequence alignments are the usual starting point for analyses of protein structure and evolution. For proteins with repeated, shuffled and missing domains, however, traditional multiple sequence alignment algorithms fail to provide an accurate view of homology between related proteins, because they...
Protein Pairwise Sequence Alignment The alignment tools are similar to the DNA alignment tools BLASTP, FASTA Main difference: instead of scoring match (+2) and mismatch (-1) we have similarity scores: Score s(i,j) > 0 if amino acids i and j have similar properties Score s(i,j) is ...
Multiple comparison or alignmentof protein sequences has become a fundamental tool in many different domains in modern molecular biology, from evolutionary... Thompson,D Julie,Linard,... - 《Plos One》 被引量: 206发表: 2011年 Identifying protein The vast majority of the biology of a newly seq...
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. We report the largest and most comprehensive comparison of protein structural alignment methods. Specifically, we evaluate six publicly available structure... R Kolodny,P Koehl,M Levitt - 《Journal of Molecular...
The MUMmer suite is a set of tools for pairwise genome alignment [92,106–108]. Themummertool from the suite works by first finding all maximal exact matches (MEMs) between a reference genome and a query genome longer than some minimum lengthlby using a suffix array [109]. MEMs which ar...
However, with the lack of sufficient ligand-protein complex structures, an experimental alignment is difficult or often impossible to obtain. Several computational 3D alignment tools have been developed by academic or commercial groups to address this challenge. Here, we present a new approach, MARS ...