SubAqua Server

About SubAqua

SubAqua^[1] (Suboptimal Alignment Based Quality Assessment) server can provide quality estimation of protein structural models in terms of the RMSD between the model and the unknown true structure. SubAqua algorithm combines suboptimal alignment stability score, SPAD^[2], and the sequence/structure compatibility score, Verify3D^[3] using linear and logistic regression. SubAqua score not only can be used to re-rank the different structural models for the same target but also can be used to estimate the absolute accuracy of the model and users can use this information to decide whether to use this model for further experimental design or computational study.

Model File

Only PDB format file with single chain should be uploaded. Amino acid sequence will be extracted from the PDB file for the subsequent SPAD score calculation.

Template File and BLAST Search

A template sequence is needed to calculate the suboptimal alignment score. User can enter the PDB ID and Chain ID of the template protein used for building the model. If template PDB ID is not provided, a PSI-BLAST search will be performed against the non-redundant PDB database to identify a template. In this case the template used to calculate the SubAqua score is not necessarily the same as the template the user used to build the model.

Reference

[1] (please cite this paper if prediction results are used for publication) Yifeng D. Yang, Preston Spratt, Hao Chen, Changsoon Park and Daisuke, Sub-AQUA: Real-Value Quality Assessment of Protein Structure Models, Protein Eng. Des. Sel. in press (2010) [Pubmed].

[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

Funding

IIS0915801

Contact Information

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