AutomatedModel-BuildingwithTEXTAL：同类型的自动模式建设.pptVIP

Ioerger Lab – Bioinformatics Research Pattern recognition/machine learning issues of representation effect of feature extraction, weighting, and interaction on performance of induction algorithm Applications in Structural Biology molecular basis of biology: protein structures predicting structures tools for solving structures (X-ray crystallography, NMR) stability, folding, packing, motions drug design (small-molecule inhibitors) large datasets exist – exploit them – find the patterns TEXTAL - Automated Crystallographic Protein Structure Determination Using Pattern Recognition Principal Investigators: Thomas Ioerger (Dept. Computer Science) James Sacchettini (Dept. Biochem/Biophys) Other contributors: Tod D. Romo, Kreshna Gopal, Erik McKee, Lalji Kanbi, Reetal Pai Jacob Smith Funding: National Institutes of Health Texas AM University X-ray crystallography Most widely used method for protein modeling Steps: Grow crystal Collect diffraction data Generate electron density map (Fourier transform) Interpret map i.e. infer atomic coordinates Refine structure Model-building Currently: crystallographers Challenges: noise, resolution Goal: automation X-ray crystallography Most widely used method for protein modeling Steps: Grow crystal Collect diffraction data Generate electron density map (Fourier transform) Interpret map i.e. infer atomic coordinates Refine structure Model-building Currently: crystallographers Challenges: noise, resolution Goal: automation Overview of TEXTAL Automated model-building program Can we automate the kind of visual processing of patterns that crystallographers use? Intelligent methods to interpret density, despite noise Exploit knowledge about typical protein structure Focus on medium-resolution maps optimized for 2.8A (actually, 2.6-3.2A is fine) typical for MAD data (useful for high-throughput) other programs exist for higher-res data (ARP/wARP) Examples of Numeric Density Features Quality of TEXTAL models Typi