Download Multiple Protein Structure Alignment Program
This is a implementation of the multiple protein structure alignment program mTM-align algorithm in C/C++.
How to use
========================= How to install mTM-align ========================= To compile the program in your Linux computer, simply enter cd src && make && cd .. The execuable program mTM-align is then available under the src folder. ===================== How to use TM-align ===================== Usage: ./src/mTM-align -i <input_list> [Options] Options: -i input_list The input_list is an input file, listing the file names of the structures to be aligned. Each line represents the file name for one structure. Please note that each input structure should be a single-chain structure. -o filename The name of the file to save the superimposed structures. The default is 'result.pdb' When the number of input structures is >61, the superimposed structures will be separated by 'MODEL' Otherwise, the structures are speparated using the chain IDs: A,B,C,... -outdir The output directory to save the results (the default is './mTM_result') -v Print the version of mTM-align -h Print this help information Example usage: ./src/mTM-align -i example/input_list ./src/mTM-align -i example/input_list -o result.pdb ./src/mTM-align -i example/input_list -outdir mTM_result Output: result.fasta Multiple structure alignment in the fasta format. result.pdb Superimposed structures, which can be shown by RasMol, PyMOL, Chimera and other softare. cc.pdb Superimposed structures in common core region, which can be shown by RasMol, PyMOL, Chimera and other software. pairwise_TMscore.txt Pairwise TM-score of structures. pairwise_rmsd.txt Pairwise RMSD of structures. infile Distance matrix, which can be used to generate phylogenetic tree by PHYLIP package. *_pair.pdb Pairwise superimposed structures. ============================================ How to generate phylogenetic tree by PHYLIP ============================================ 1.Download PHYLIP package from http://evolution.genetics.washington.edu/phylip/executables.html and install it. 2.To construct the phylogenetic tree, simplely enter phylip neighbor 3.enter 'N' to choose UPGMA method, and then enter 'Y' to confirm. 4.The phologenetic tree is shown in the file "outfile".