The CVSA [1] 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.


Patch for PLUMED 1.3:


R scripts for data analysis:


python script to convert PDB atom names from ffAMBER to ROSETTA:



1. Pandini A, Fornili A: “Using Local States to Drive the Sampling of Global Conformations in Proteins”. Journal of Chemical Theory and ComputationDOI: 10.1021/acs.jctc.5b00992. PubMed URL

2. Pandini A*, Fornili A, Fraternali F, Kleinjung J*: “GSATools: analysis of allosteric communication and functional local motions using a Structural Alphabet”. Bioinformatics 29(16):2053-2055, 2013. PubMed URL

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. PubMed URL

4. Pandini A, Fornili A, Kleinjung J*: “Structural alphabets derived from attractors in conformational space”. BMC Bioinformatics 11(1):97, 2010. PubMed URL