January | 2013 | Getting to know Structural Bioinformatics

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 Now, it is no longer maintained and has become a legacy.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
CURVE	NA	Geometry	No	site	D. Zhi	2006	Dead
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.

—Getting to know Structural Bioinformatics

for the curious one

Archive

Monthly Archives: January 2013

Multiple Structure Alignment