Just like Multiple Sequence Alignment (MSA) tools there is a definite need for multiple structure alignment tools. For a long time, I was a big fan of Combinatorial Extension (CE)’s Multiple Structure Alignment (MStA) on their web server. Now, it is no longer maintained and has become a legacy. The good thing about it was you can do pairwise, database search, and MStA by either giving the PDB id or uploading a file.
For a brief period, the Univ. of Albany server hosted the MStA of CE, but now the link is dead (http://bioinformatics.albany.edu/~cemc). That lead to my quest of finding an alternate and equally easy web server that can do the same job. Fortunately, CE came under the care of RCSB and with a new website (http://source.rcsb.org/jfatcatserver/ceHome.jsp) and a new link for MStA (http://schubert.bio.uniroma1.it/CEMC/). A downside of this MStA server is that one cannot upload pdb files of our choice.
Those who use PyMOL know the two commands that does MStA (alignto and super). While alignto actually implements the CE algorithm, super does a dynamic programming based alignment. Alignto is an excellent addition to PyMOL and makes structure analysis much easier. This way better than align in PyMOL, when there is low sequence identity.
Still, how about a webserver where I can upload my own pdb files and do a MStA? The answer is yes, there are many webservers available to choose from. Of course, the algorithm and implementation are different than from CE. So, go ahead and pick one of the list below: (I haven’t personally tried each and every web server, still they are all worth a try for a quick result). The following list has been culled from the Wikipedia page “Structural Alignment Software” with the last column being my comments on the server.
|Name||Description||Class||Flexible||Link||Author||Year||Is the link dead or alive?|
|deconSTRUCT||Database search on substructural level and pairwise alignment.||SSE||No||server||ZH. Zhang et al.||2010||Alive, but not exactly what you are looking for|
|MASS||Multiple Alignment by Secondary Structure||SSE||nil||server||O. Dror & H. Wolfson||2003||Alive|
|PrISM||Protein Informatics Systems for Modeling||SSE||nil||server||B. Honig||2000||Dead|
|SSM||Secondary Structure Matching||SSE||nil||server||E. Krissinel||2003||Link directs to PDBeFold|
|SSAP||Sequential Structure Alignment Program||SSE||No||server||C. Orengo & W. Taylor||1989||Dead|
|SALIGN||Sequence-Structure Hybrid Method||Seq||No||site||M.S. Madhusudhan et al.||2007||Alive|
|SWAPSC||Sliding Window Analysis Procedure for detecting Selective Constraints for analysing genetic data structured for a family or phylogenetic tree using constraints in protein-coding sequence alignments.||Seq||yes||Server||Mario A. Fares||2004||Dead|
|C-BOP||Coordinate-Based Organization of Proteins||N/A||nil||server||E. Sandelin||2005||Alive, but not exactly what you are looking for|
|MultiProt||Multiple Alignment of Protein Structures||Geometry||Yes||server||M. Shatsky & H. Wolfson||2004||Alive|
|msTALI||multiple sTructure ALIgnment||Cα & Dihed & SSE & Surf||nil||server||P. Shealy & H. Valafar||2012||Alive and Needs registration|
|CE/CE-MC||Combinatorial Extension — Monte Carlo||Cα||No||server||I. Shindyalov||2000||Alive|
|BLOMAPS||Conformation-based alphabet alignments||Cα||nil||server||W-M. Zheng & S. Wang||2008||Dead|
|CAALIGN||Cα Align||Cα||nil||site||T.J. Oldfield||2007||Dead|
|MISTRAL||Energy-based multiple structural alignment of proteins||Cα||No||server||C. Micheletti & H. Orland||2009||Alive|
|EXPRESSO||Fast Multiple Structural Alignment using T-Coffee and Sap||Cα||nil||site||C. Notredame et al.||2007||Alive|
|MAMMOTH-mult||MAMMOTH-based multiple structure alignment||Cα||No||server||D. Lupyan||2005||Dead|
|Matt||Multiple Alignment with Translations and Twists||Cα||Yes||server||M. Menke||2008||Alive|
|POSA||Partial Order Structure Alignment||Cα||Yes||server||Y. Ye & A. Godzik||2005||Alive|
|ProFit||Protein least-squares Fitting||Cα||nil||server||ACR. Martin||1996||Alive, but not exactly what you are looking for|
|STAMP||STructural Alignment of Multiple Proteins||Cα||No||server||R. Russell & G. Barton||1992||Alive, pairwise alignment|
|STRAP||STRucture based Alignment Program||Cα||nil||server||C. Gille||2006||Java based, not a web server|
|Vorolign||Fast structure alignment using Voronoi contacts||C-Map||Yes||server||F. Birzele et al.||2007||Alive|
UPDATE: I realized that the Minimalist theme doesn’t gel well with the table above. So, in case you dont see the table properly. See the image attached below. Click on it to see the full-size image.
Chapter 16 from “Structural Bioinformatics” http://books.google.com/books?id=4H_ai7ivRIcC&lpg=PP1&pg=PA397#v=onepage&q&f=false
Marc A. Marti-Renom, Emidio Capriotti, Ilya N. Shindyalov, and Philip E. Bourne (2009). Structure Comparison and Alignment Structural Bioinformatics DOI: 10.1002/0471721204.ch16