Structural Alphabet M32K25

 

The M32K251-2 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. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the SA are equivalent to the conformational attractors of this space and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness.

Download

Structural Alphabet M32K25:

M32K25.pdb

Original data set of representative proteins:

MK.dataset.txt

Original test set for validation of protein structure reconstruction:

MK.testset.txt

 

References

 

1 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

 

2 Pandini A, Fornili A, Kleinjung J

"Structural alphabets derived from attractors in conformational space"

BMC Bioinformatics 11(1):97, 2010

PubMed   URL