ConClus - search of conservative clusters in protein families

  

Alignment (example):

Threshold of distance (Å)
Minimal size of Clud clusters (residues)
Minimal size of global clusters (residues)


Definitions

Alignment

An alignment of a set of structures is a set of positions, to each position some atoms from different structures correspond. In this service, only CA-atoms are included into alignments.

In a text representation of an alignment, all CA-atoms of the residues that are at the same position in different sequences form a position of the alignment (i.e., the first letters of the sequences form one position, the second ones — another position, etc.).

Hydrophobic cluseters and core

Hydrophobic cluster of a single protein structure is a separated pool of nonpolar atoms. Usually there is the biggest cluster in the protein called hydrophobic core. Hydrophobic clusters are constructed with CluD program (see also overview of its algorithm).

Conserved hydrophobic core

It is known that the conserved features of a structure generally are the most constitutive in biological sense. In our case, aminoacid residues forming conserved clusters and first of all conserved hydrophobic core are expected to be important for determination of the domain fold. ConClus program is able to detect of conservative hydrophobic clusters for a family of related protein domains or just for a set of aligned proteins.


Algorithm: Andrei Alexeevski, Sergei Spirin, Yury Pekov
Programming: Yury Pekov
Contact: yurapekov@gmail.com

The work was partly supported by the Russian Foundation for Basic Research, grant 09–04–92743

© S&S 2011