Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins |
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Authors: | Thomas Madej Anna R Panchenko Jie Chen Stephen H Bryant |
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Affiliation: | (1) Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Building 38A, Bethesda, Maryland 20894, USA |
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Abstract: | Background To discover remote evolutionary relationships and functional similarities between proteins, biologists rely on comparative sequence analysis, and when structures are available, on structural alignments and various measures of structural similarity. The measures/scores that have most commonly been used for this purpose include: alignment length, percent sequence identity, superposition RMSD and their different combinations. More recently, we have introduced the "Homologous core structure overlap score" (HCS) and the "Loop Hausdorff Measure" (LHM). Along with these we also consider the "gapped structural alignment score" (GSAS), which was introduced earlier by other researchers. |
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