Macs in Chemistry

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JAMMING

Most of the available software to understand the relationship between the three-dimensional (3D) structure of a protein with its function, is based on the protein primary structure (i.e., protein sequence).
However there are many examples where this approach is not helpful. It is clear that protein function arises from the interaction among the protein's residues. Such interactions are observed when the protein folds in a three dimensional shape. This fact may explain that primary sequence alone can not identify every critical residues correctly. At the same time, highligths the need to develop approaches aimed to identify critical residues from protein 3D structures.
Although several approaches based on physics principles (e.g., electrostatics) have been reported to identify critical residues from the three dimensional structure of proteins (
3), there is a limited accessibility to software aimed to identify critical residues from protein structures. Network analysis on the other hand has been recently shown to be succesfull and complementary to protein sequence-based approaches, JAMMING provides a means to identify critical residues from protein 3D structures Efficient identification of critical residues based only on protein structure by network analysis Cusack M, Thibert B, Bredesen DE and del Rio G. 2007. PLoS ONE 2(5):e421
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