Abstract
The link between biological form and function is well known, and is assumed to hold true at the molecular level. Since identifying similar protein structures is the first step in identifying similar functions, much effort has been placed in developing methods to detect structural similarity. Several methods exist, including: SCOP [8], the DALI algorithm (from the FSSP Database [6]), the VAST algorithm (from the MMDB database [5]), and Root Mean Square (RMS) superimposition [9]. The latter three provide quantitative metrics describing protein similarity on an objective, continuous scale. Statistical analyses can then be performed on similarity scores for a set of proteins, to obtain a plot of ‘protein structure space’ [7]. Before such analyses are done however, one must be sure that the metric used accurately represents similarity.
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Adams, D.C., Naylor, G.J.P. (2003). A Comparison of Methods for Assessing the Structural Similarity of Proteins. In: Guerra, C., Istrail, S. (eds) Mathematical Methods for Protein Structure Analysis and Design. Lecture Notes in Computer Science(), vol 2666. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-44827-3_6
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DOI: https://doi.org/10.1007/978-3-540-44827-3_6
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