SA M32K25

GSATools

Structural Alphabet M32K25

Structural Alphabet M32K25

 

The M32K25 is a Structural Alphabet (SA) derived by clustering all four-residue fragments of a high-resolution subset of the Protein Data Bank and extracting the high-density states as representative conformational states.

 

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Molecular Dynamics trajectory to Structural Alphabet strings

GSATools

 

GSATools is a set of programs that translate ensembles of protein conformations into alignments of structural strings using the M32K25 Structural Alphabet (SA). It is designed for the investigation of the conformational dynamics of local structures, the functional correlations between local and global motions and the mechanisms of allosteric communication. The software has been integrated into the GROMACS environment.

 

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CVSA

 

The CVSA is a novel Collective Variable based on the M32K25 Structural Alphabet (SA). It can be used to bias the sampling of backbone conformations of fragments in a protein towards experimentally preferred local states during MD simulations. The CVSA was implemented in a modified version of PLUMED.

 

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