Multiple Structure Alignment

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  Now, it is no longer maintained and has become a legacy.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 ( 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 ( and a new link for MStA ( 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 No server I. Shindyalov 2000 Alive
BLOMAPS Conformation-based alphabet alignments nil server W-M. Zheng & S. Wang 2008 Dead
CAALIGN Cα Align nil site T.J. Oldfield 2007 Dead
MISTRAL Energy-based multiple structural alignment of proteins No server C. Micheletti & H. Orland 2009 Alive
EXPRESSO Fast Multiple Structural Alignment using T-Coffee and Sap nil site C. Notredame et al. 2007 Alive
MAMMOTH-mult MAMMOTH-based multiple structure alignment No server D. Lupyan 2005 Dead
Matt Multiple Alignment with Translations and Twists Yes server M. Menke 2008 Alive
POSA Partial Order Structure Alignment Yes server Y. Ye & A. Godzik 2005 Alive
ProFit Protein least-squares Fitting nil server ACR. Martin 1996 Alive, but not exactly what you are looking for
STAMP STructural Alignment of Multiple Proteins No server R. Russell & G. Barton 1992 Alive, pairwise alignment
STRAP STRucture based Alignment Program 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.


Further reading:

Chapter 16 from “Structural Bioinformatics”
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

  1. Ran said:

    How about using source code to perform local structural alignment? Let’s say you want to align 25 PDBs with respect to one used as a reference.

    Here is the source code of the program I use (RASH):

    I just copy the PDBs to a folder and execute in terminal:
    ls -l | awk ‘{print $8}’ | grep pdb > input

    I ran my program as:
    perl rash input

    The rotated PDBs appear as ****rot.pdb

    The problem is that I am not allowed to openly give my script due to lab regulations…

    I am looking for a PUBLIC local structural alignment source code program? Do you know where could I get one?

    • ragothamanyennamalli said:

      Thanks for the comment. I will try RASH. Seems like pretty handy. I used to use another source code to do the same. It was called PROCOR. Unfortunately, it worked only with SGI and had library issues too run on unix based OS.


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