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%% Program: AlignProteins                                       %%
%% Authors: Gaolin Zheng                                        %%
%%          Giri Narasimhan                                     %%
%%          Florida International University                    %%
%% E-mail:  giri@cs.fiu.edu                                     %%
%% Copyright: Giri Narasimhan, FIU.                             %%
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%% This ia MatLab program to align two proteins or protein 
%% fragments. As input, 2 protein files in pdb format are needed
%% along with the positions of the residues to be considered. 

%% Other files in the package: 
%% ReadProtein.m, for reading in the protein pdb file
%% MassCenter.m, for computing the center of mass of protein
%% RMSD.m, for computing the RMSD for the best alignment and
%% PlotMatrix.m, for displaying the result.

%% Matches two protein fragments given in PDB format and displays
%% the aligned protein fragments along with the RMSD value.
%% The proteins are displayed, one in red and one in blue.
%% Need to provide the start and end location of the fragment in
%% the two proteins. For e.g., at the MatLab prompt, if you type:
%% >> AlignProteins('1cro.pdb','1wrp.pdb',17,40,62,85)
%% you should get RMSD=3.8619 and the alignment between proteins
%% 1cro (positions 17-40) and 1wrp (positions 62-85)

