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.
Patch for PLUMED 1.3:
R scripts for data analysis:
python script to convert PDB atom names from ffAMBER to ROSETTA:
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