SubAqua (Suboptimal Alignment based Quality Assessment) Package 1.0

Installation

• Download SubAqua_package.tar.gz . Uncompress SubAqua_package.tar.gz and move it to your preferred directory
• Download and install following programs and packages:
  • Verfiy3D: go to webpage: http://nihserver.mbi.ucla.edu/Verify_3D/software.php to download verify3d and copy the verify3d to the subaqua folder and rename it to V3D_run.
  • blastpgp: download blastpgp from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ and copy the executable file(blastpgp) to the subaqua folder
  • databases: download pdb (pdbaa) and non-redundant (nr) database from ftp://ftp.ncbi.nih.gov/blast/db/. Move pdbaa and nr folders to the subaqua folder or make corresponding simbolic links.
  • Sable: download sable from ftp://ftp.chmcc.org/pdi/jmeller/sable/, copy the folder to the subaqua folder and rename it to sable_distr
  • dsspcmbi: download dsspcmbi from http://swift.cmbi.kun.nl/gv/dssp/ and copy it to the subaqua folder

Usage

SubAqua.pl [ -t template_file] [-o output_file] protein_structure_model.

template_file: should provide a template file in pdb format, template should only have one chain. When template file is not provided, psi-blast search will be performed to find a template.

output_file: specify the output file. Verify 3D score, SPAD score, predicted RMSD, predicted probability of being a good model (RMSD<6A) and predicted LGA will be printed to the output file.

protein_structure_model: should provide a pdb file with a single chain.

Example Output

Structure Model: abcd.pdb
Verify3D: 0.25
SPAD: 3.65
Predicted RMSD: 12.73
Predicted LGA:  31
Probability of being a good model (rmsd<6A): 1.41%

LE Data Set

SubAqua models are trained on LE data set which can be downloaded here.

Reference

[1] Yifeng D. Yang, Preston Spratt, Hao Chen, Changsoon Park and Daisuke, Real-Value Quality Assessment of Protein Structure Models, in review

[2]Chen H, Kihara D.,Estimating Quality of Template-Based Protein Models by Alignment Stability,Proteins, 2008 May 15;71(3):1255-74

[3]Luthy R, Bowie JU, Eisenberg D. Assessment of Protein Models with Three-Dimensional Profiles,Nature, 1992 Mar 5;356(6364):83-5

Contact Information

Daisuke Kihara (Principal Investigator)
Lilly Bld. B235
Department of Biological Sciences
Purdue University
West Lafayette, IN, 47906
Tel: 765-494-2744
Email:dkihara@purdue.edu

Yifeng Yang (Graduate Student)
Lilly Bld. B207
Department of Biological Sciences
Purdue University
West Lafayette, IN, 47906
Tel: 765-494-6766
Email:yang41@purdue.edu