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Updated: Aug 7, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Maximum entropy weighting of aligned sequences of proteins or DNA
1Laboratory of Molecular Biology, Cambridge, England.
Abstract:
In a family of proteins or other biological sequences like DNA the various subfamilies are often very unevenly represented. For this reason a scheme for assigning weights to each sequence can greatly improve performance at tasks such as database searching with profiles or other consensus models based on multiple alignments. A new weighting scheme for this type of database search is proposed. In a statistical description of the searching problem it is derived from the maximum entropy principle. It can be proved that, in a certain sense, it corrects for uneven representation. It is shown that finding the maximum entropy weights is an easy optimization problem for which standard techniques are applicable.
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