The CVSA  is a novel Collective Variable based on the M32K25 Structural Alphabet [2-4]. It can be used to bias the sampling of backbone conformations of fragments in a protein towards experimentally preferred local states during MD simulations. Biasing the sampling of local states has a wide range of potential applications, going from protein folding to protein design and to the study of conformational changes based on large local rearrangements such as hinged motions, secondary structure transitions or loop remodelling. The CVSA was implemented in a modified version of PLUMED 1.3. A patch for the program is provided alongside R and python scripts for data analysis.
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3. Pandini A☯*, Fornili A☯, Fraternali F, Kleinjung J*: “Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics”. FASEB J 26(2):868-81, 2012. PubMedURL
4. Pandini A, Fornili A, Kleinjung J*: “Structural alphabets derived from attractors in conformational space”. BMC Bioinformatics 11(1):97, 2010. PubMedURL