Copyright (C) 2010, 2011 Zhang Initiative Research Unit,

Advance Science Institute, RIKEN

2-1 Hirosawa, Wako, Saitama 351-0198, Japan

This program is free software: you can redistribute it and/or modify

it under the terms of the GNU Lesser General Public License as published by

the Free Software Foundation, either version 3 of the License, or

(at your option) any later version.

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License

along with this program. If not, see http://www.gnu.org/licenses/.

IF YOU USE THIS SOFTWARE, PLEASE CITE THE CORRESPONDING PUBLICATION:

@article{Berenger2011, author = {Berenger, Francois and Zhou, Yong and Shrestha, Rojan and Zhang, Kam Y. J.}, title = {Entropy-accelerated exact clustering of protein decoys}, volume = {27}, number = {7}, pages = {939-945}, year = {2011}, doi = {10.1093/bioinformatics/btr072}, URL = {http://bioinformatics.oxfordjournals.org/content/27/7/939.abstract}, journal = {Bioinformatics}, }

Preconditions:

The alignment expected by the Durandal software is 1 to 1. For example, if 2 structures A and B are to be optimally superposed before computing the CARMSD, both PDB files (A.pdb and B.pdb) must have same numbers of alpha carbons. The first alpha carbon in A.pdb will be matched to the first alpha carbon in B.pdb. The second alpha carbon in A.pdb will be matched to the second alpha carbon in B.pdb. And so on until the end of both files. If it is not the case, please edit all your PDB files in advance.

Output format (cluster listings):

Use the -v option to get easily readable cluster listings. Then, the output will look like this:

pole position centers(5): ./pdbs/02.pdb ./pdbs/03.pdb ./pdbs/05.pdb ./pdbs/07.pdb ./pdbs/09.pdb members(3): ./pdbs/01.pdb ./pdbs/03.pdb ./pdbs/07.pdb members(3): ./pdbs/02.pdb ./pdbs/05.pdb ./pdbs/09.pdb members(2): ./pdbs/00.pdb ./pdbs/06.pdb members(2): ./pdbs/04.pdb ./pdbs/08.pdb

A cluster is listed after a 'members(N):' line. The first PDB of the cluster is the cluster center, other PDBs are cluster members.

Clusters are listed in a biggest-first (most members) order.

The 'pole position centers(N):' and following lines indicate that there were other possible biggest clusters; only their centers are listed.