Analysis of CASP8 targets and predictions

These web pages present the analysis of CASP8 targets and predictions by the Grishin lab. Only 3D models (TS: Tertiary structure prediction) were used here, other types of predictions, such as high-resolution, disorder, or function, were not considered. Predictions were evaluated using LGA GDT-TS scores and several other methods. Targets were analyzed individually for their sequence-structure properties and prediction quality. PDB structures of targets were modified to match target sequences, and evolutionary domains were deduced from structures. Evaluation of predictions was performed on both domains and whole chains of targets, and the effects of domain parsing on the evaluation were examined. NMR structures were processed for evaluation, poorly structured regions being removed. Expert evolutionary classification was done for all targets, including most intricate cases: e.g. T0465, a very distant version of the FYSH domain; and T0460, a modified NADH-quinone oxidoreductase chain 5 (Nqo5) domain, but a singleton sequence. Server models superimposed with target structures can be downloaded and visualized as PyMOL scripts. Structure images (mostly animated GIFs) on target pages were prepared in PyMOL.

Reference: Shuoyong Shi, Jimin Pei, Ruslan I. Sadreyev, Lisa N. Kinch, Indraneel Majumdar, Jing Tong, Hua Cheng, Bong-Hyun Kim, Nick V. Grishin. Analysis of CASP8 targets, predictions and assessment methods. Database: The Journal of Biological Database and Curation (2009).

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Domain parse of targets

Target category definition

Scores used in evaluation

Random model and random score

Changing PDBs to match targets

Target structures modified to match target sequences

Human/Server targets

X-ray targets

Server only targets

NMR targets

Discussion of whole chain vs. domain evaluations

Preparation of NMR structures