CMASA Files

CMASA:contact matrix based local structure alignment version 1.0:

Please cite:
  Li GH, Huang JF CMASA: an accurate algorithm for detecting local protein 
  structural similarity and its application to enzyme catalytic site annotation. 
    BMC Bioinformatics. 2010 Aug 27;11(1):439.

Copyright Holder:
CMASA_pro_vs_site  Copyright (c) 2009-2010 Gong-Hua Li, Ph.D
                   State Key Laboratory of Genetic Resources and Evolution
                   Kunming Institute of Zoology
		   Chinese Academy of Sciences
CMASA_site_vs_pro  Copyright (c) 2009-2010 Gong-Hua Li
                   State Key Laboratory of Genetic Resources and Evolution
                   Kunming Institute of Zoology
		   Chinese Academy of Sciences


License: LGPL, GPL,GNU Lesser General Public License


Installation:

For windows:
       CMASA_pro_vs_site.c and CMASA_site_vs_pro.c have been compiled by GUN MingWin G++,
    the excuatable files are:
    
    CMASA_pro_vs_site.exe   and 
    CMASA_site_vs_pro.exe

    This two excuatable files have been tested in win32 for XP, window2003. 

For linux:
      CMASA_pro_vs_site.c and CMASA_site_vs_pro.c need GUN gsl(GNU Scientific Library,
    which is a free numerical library for C and C++ programmers) for compling.
    
    Gun gsl can be installed  by http://www.gnu.org/software/gsl/.

    If you are using ubuntu, it is luck!
    You can just type the following command to install GUN gsl:

      sudo apt-get install libgsl0-dev

    After the GNU gsl is installed, you can type the following command to compile:
    for CMASA_pro_vs_site.c  type:

      g++ CMASA_pro_vs_site.c -o CMASA_pro_vs_site /usr/lib/libgsl.a /usr/lib/libgslcblas.a 

    for CMASA_site_vs_pro.c type:

      g++ CMASA_site_vs_pro.c -o CMASA_site_vs_pro /usr/lib/libgsl.a /usr/lib/libgslcblas.a 

    There may be some warnings, it does not matter.

    If there are still some troubles for compling CMASA, you can try the pre compiled excuable files or
     you can e-mail to me: ligonghua_88@yahoo.com.cn



Aim of the CMASA:
    CMASA_site_vs_pro:   is to used when a active site search to a nrpdb database or nrscop database.
       This programm is to find the remote homologues or the functional convergence.
    
    CMASA_pro_vs_site:  is to predict the function of a protein by searching to a active site database,
       for example: csa database for predicting enzyme catalytic sites.
    

Database:
    CMASA use a specified database format. The database should contain the main file and the infor file.
    for example, the nrscop database should contain the two files "nrscop" and "nrscop.infor".
    In this downloadable version, two databases are specified.

    nrscop:  this database contains all of the specials level structures of scop1.75.
             Total 14519 structures.

    csa: this database is directly from CSA, you can visit:
        http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/CSA/CSA_Download.pl for more information.
	This csa database contains all of the sites of the version 2.2.11 and  just remove the multiple same chains
	in the same pdb file.
	Some csa sites are removed:
	1. number of residues of catalytic sites < 3
	2. 4 residues but 2 is "GLY".
        
	some catalytic sites >5, the most conserved 5 residues is selected.
	the conserve information are from Consurf database(http://consurf.tau.ac.il/)

	Total 15341 structures.


How to use:
     CMASA accept the following inputs:
     -i  query pdbfile, needed.
     -d  database name,needed.
     -o  output file  defult is stdout
     -t  output format
         F  text format
	 T  html format, defult
     -c  cmad cutoff value defult is 1.2
     -s  substitute file, defult is exact match.

     Please type the following comand to test CMASA:

        CMASA_pro_vs_site -i 1mctA.pdb -d csa -o 1mctA_csa.html

        CMASA_pro_vs_site -i 1mctA.pdb -d csa -o 1mctA_csa_blosum62.html -s blosum62.txt

        CMASA_site_vs_pro -i 1mct_site.pdb -d nrscop -o 1mct_site_nrscop.html

        CMASA_site_vs_pro -i 1mct_site.pdb -d nrscop -o 1mct_site_nrscop_blosum62.html -s blosum62.txt




How to define a substitute file:
   1. Create a file for example "mysub.txt"
   2. type the substitute amino types in a line,
      for example, "D" and "E", "R" and "K" can be substituted each other
      you just add the following two lines in the mysub.txt

      DE
      RK

   3. save file.


Can we use my own database?
    In this downloadable version, it is no.
    But in the next version(will be finished shortly), the "makedb" will be generated, 
    then you may create the own database to run CMASA.
    Let's expect the next version.