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Protein Structure Alignment by Incremental COMBINATORIAL EXTENSION of the Optimal Path.

           Authors:   Shindyalov I.N., Bourne P.E. 

             e-mail:   {shindyal,bourne}@sdsc.edu

              URL:   http://ce.sdsc.edu/ce.html	

Copyright (c) 1997-2001 The Regents of the University of California All Rights Reserved

Permission to use, copy, modify and distribute any part of this CE software for educational, research and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies.

Those desiring to incorporate this CE Software into commercial products or use for commercial purposes should contact the Technology Transfer Office, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0910, Ph: (858) 534-5815, FAX: (858) 534-7345.

IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS CE SOFTWARE, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

THE CE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE UNIVERSITY OF CALIFORNIA MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE CE SOFTWARE WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS.

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How to compile and run the software.

1. To compile CE software in this directory, use command:

$ gmake

or

$ make

2. To run CE software:

$ mkdir -p scratch/
$ CE - pdb_file1 chain_id1 pdb_file2 chain_id2 scratch/

Note: '-' can be used for chain id1 and chain id2 for iterative comparison of all chains parsed from the corresponding files.

3. Examples

$ mkdir -p scratch/
$ CE - 4hhb.pdb A 1hba.pdb B scratch
$ CE - 4hhb.pdb - 1hba.pdb - scratch

4. Interpreting results:

Structure Alignment Calculator, version 1.02, last modified: Mar 13, 2003.

CE Algorithm, version 1.00, 1998.

Chain 1: 4hhb.pdb:A (Size=141) 
Chain 2: 1hba.pdb:B (Size=146)

Alignment length = 139 Rmsd = 1.36A Z-Score = 6.5 Gaps = 8(5.8%) CPU = 0s Sequence identities = 43.2%

Chain 1:    1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDL------SHGSAQVKGHGKKVAD
Chain 2:    2 HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPRTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG

Chain 1:   65 ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVST
Chain 2:   70 AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN

Chain 1:  135 VLTSKYR
Chain 2:  140 ALAHKYH

     X2 = ( 0.980144)*X1 + ( 0.023409)*Y1 + (-0.196902)*Z1 + (   -0.134999)
     Y2 = ( 0.023575)*X1 + (-0.999721)*Y1 + (-0.001503)*Z1 + (   -0.552679)
     Z2 = (-0.196883)*X1 + (-0.003169)*Y1 + (-0.980422)*Z1 + (    1.982153)

Alignment length - number of aligned positions;

Rmsd - root mean square deviation (in Angstroms) calculated for the best superposition;

Z-Score - z-score from CE statistical model. Typical values:

        >4.5    - family level similarity;

        4.0-4.5 - superfamily level similarities, strong 
                  function related similarities or strong
                  recurring fold;

        3.7-4.0 - twilight zone where some similarities
                  of biological significance can be seen;

        <3.7    - similarities of low significance, but still 
                  some biologically important similarities 
                  can be revealed, but interpretation normally
                  requires additional evidence.                 

Gaps - number of not aligned position within the alignment;

CPU - computation time in seconds;

Sequence identities - sequence identites for aligned positions;

Sequence alignment based on structure alignment is given followed by transformation matrix based on structure superposition calculated for this alignment.

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Reference:

Shindyalov I.N., Bourne P.E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engng, 1998, 9, 739-747.