Abstract
A new algorithm is presented allows protein specificity residues to be assigned from multiple sequence alignments alone. This information can be used, amongst other things, to infer protein functions.
Highlights
The diversity of biologic phenomena arises from the complexity and specificity of biomolecular interactions
We tested the robustness of the results for many protein families, with representative results for two protein families in Additional data file 1
We conclude that the assignment of sequences to subfamilies is reasonably consistent with prior biologic knowledge and that the selection of characteristic residues is reasonably stable in the range A = 0.6 to 0.9
Summary
The diversity of biologic phenomena arises from the complexity and specificity of biomolecular interactions. Nucleic acid and protein polymers encode and express biologic information through the specific sequence of polymer units (residues). Changes in sequence alter intermolecular communication and affect the phenotype and can lead to disease [1,2,3,4,5,6]. Detailed understanding (quantitative and predictive description) of how such molecular changes affect cellular and organismic function lies at the heart of molecular and systems biology. Our ability to predict the biologic and medical consequences of human genetic variation and to design therapeutic interventions can benefit hugely from such detailed understanding. We are motivated to develop further our ability to identify functionally specific residues in protein molecules
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