MMLigner

Statistical inference of protein structural alignments using information and compression
Reference: J. H. Collier, L. Allison, A. M. Lesk, P. J. Stuckey, M. Garcia de la Banda & A. S. Konagurthu, Statistical inference of protein structural alignments using information and compression, Bioinformatics 33(7):1005-1013 2017. [DOI link] [BioRxiv preprint]

MMLigner Program

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Platform:GNU/LinuxWindowsOS/X 10.11.4
binary:1.0.2 (x86_64) 1.0.2 (x86_64) 1.0.2 (i686) 1.0.1 (x86_64)
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Instructions for running MMLigner
Synopsis:
mmligner FILE1[:CHAINID(S)] FILE2[:CHAINID(S)] [OPTION]...
Description:
Align two PDB (protein data bank format) FILEs (default operation).
A FILE is a Brookhaven protein data bank (PDB) column format data file.
CHAINID(S) is a string of single character chain identifiers.
--ivalue [ALIGNMENT_FILE]

Score ALIGNMENT_FILE (in fasta format) using I-value. Changes default operation: an alignment is not computed. Instead, ALIGNMENT_FILE (FASTA format) is scored using the I-value measure.


-o OUTPUT_PREFIX

Specify a prefix (OUTPUT_PREFIX) for the filenames on output files.


--superpose

Superimpose the input structures according to the computed alignments (which are given numeric identifiers sorted by compression).


Example command line inputs:
Generating an alignment using MMLigner:
Align chain A of the human haemoglobin protein with chain A of the sperm whale myoglobin protein and produce a transformed PDB file after alignment:
./mmligner 1HHO.pdb:A 1MBD.pdb:A --superpose
Scoring a given alignment using I-value
Score a given alignment of wwPDB:1HHO chain A against chain A of wwPDB:1MBD
./mmligner 1HHO.pdb:A 1MBD.pdb:A --ivalue alignment.fasta
Instructions for building MMLigner (v1.0.2)

Dependencies: GNUMake or equivalent. A modern C++ compiler. MMLigner is known to build with G++>=4.2 and clang 703.0.29 on LLVM 7.3.0. If these dependencies are met, follow these instructions:

  1. Download the source code from the link above.
  2. Extract the archive with: tar -xzf mmligner_1.0.2.tar.gz
  3. Type: cd mmligner_1.0.2/
  4. Build MMLigner with: make
  5. The built binary will appear in the bin/ subdirectory.
Copyright license
MMLigner is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
MMLigner is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with MMLigner. If not, see http://www.gnu.org/licenses/.
Bug reports
Please contact the following people for bug reports, web page errors, or questions:
  • Arun Konagurthu <arun DOT konagurthu AT monash DOT edu>
  • James Collier <james DOT collier412 AT gmail DOT com>

Supplementary Material

Supplementary animated movies of superpositions for alternative alignments generated by MMLigner
Click on the superposition thumbnails below to view the animated movies
Supplementary Movies S1: 1EID-A vs. 1CCW-A
(1EUD-A domain 1 vs 1CCW-A)
 (1EUD-A domain 2 vs 1CCW-A)
(a) (b)
Supplementary Movies S2: d2sasa_ vs. d1jfja_
(N-terminal vs N-terminal domains)
 (N-terminal vs C-terminal domains)
(a) (b)
(C-terminal vs N-terminal domains)
 (C-terminal vs C-terminal domains)
(c) (d)
SCOP dataset (PIVOT, FAMILY, SUPERFAMILY, FOLD, CLASS, DECOY)
scop_domains.txt
Results for the SCOP dataset using MMLigner
Score:CoverageRMSDDali z-scoreStructal scoreTM-ScoreGDT_TSLGA_S3SASGSASSIMII-value I(A)I-value compression
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Results for the SCOP data using other alignment programs
Score→
Aligner↓		CoverageRMSDDali z-scoreStructal scoreTM-ScoreGDT_TSLGA_S3SASGSASSIMII-value I(A)I-value compression
DALI plot
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TM-Align plot
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LGA plot
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CE plot
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FatCat plot
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MATLAB scripts

plotsGenerator.m

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