QCS: Quality Control Score

For Quality Assessment of Protein Structure Prediction

Quality Control Score (QCS) is a new method to evaluate the quality of structure predictions, especially for template free structure prediction. It was developed to mimic visual inspction by human expert and it captures both global and local structural features, with emphasis on global topology.

Specifically, the following features are measured and scored:
(1) the correct prediction of Secondary Structure Elements (SSE) measured by the length of SSEs;
(2) the relative position of pairs of SSEs measured by the distances between representative points on the SSEs;
(3) the relative angle between SSEs pairs;
(4) the distances between the C alpha atoms in the key contacts between SSEs;
(5) the handedness of SSE triplets;
(6) the all C-alpha Contact Score (used in CASP5 and CASP9).

We applied this method to all FM targets from CASP9, and overall the results showed the best agreement with Manual Inspection Scores among automatic prediction assessment methods previously applied in CASPs, such as Global Distance Test Total Score (GDT_TS) and Contact Score (CS). As one of the important components to guide our assessment of CASP9 FM category predictions, this method correlates well with other scoring methods and yet is able to reveal good-quality models that are missed by GDT_TS.

Source codes are available here.
Short Tutorial how to use QCS is available here.
Details of QCS are described in our paper here.

Reference: Cong Q, Kinch LN, Pei J, Shi S, Grishin VN, Li W, Grishin NV. An automatic method for CASP9 free modeling structure prediction assessment. Bioinformatics. 2011 Dec 15;27(24):3371-8. Epub 2011 Oct 12.

For questions and suggestions, please send email to:
qian.cong@utsouthwestern.edu or grishin@chop.swmed.edu