印度昌迪加尔市微生物技术研究所生物信息学课件sec_pred.pptVIP

Protein Secondary Structure Prediction G P S Raghava Protein Structure Prediction Importance CASP Competition What is secondary structure Assignment of secondary structure (SS) Type of SS prediction methods Description of various methods Role of multiple sequence alignment/profiles How to use Importance of secondary structure prediction Classification of protein structures Definition of loops/core Use in fold recognition methods Improvements of alignments Definition of domain boundaries CASP changed the landscape Critical Assessment of Structure Prediction competition. Even numbered years since 1994 Solved, but unpublished structures are posted in May, predictions due in September Various categories Relation to existing structures, ab initio, homology, fold, etc. Partial vs. Fully automated approaches Produces lots of information about what aspects of the problems are hard, and ends arguments about test sets. Results showing steady improvement, and the value of integrative approaches. CASP Experiment Experimentalists are solicited to provide information about structures expected to be soon solved Predictors retrieve the sequence from prediction center () Deposit predictions throughout the season Meeting held to assess results Assignment of Secondary Structure Program DSSP (Sander Group) Stride (Argos Group) Pcurve DSSP 3 helix states (I=3,4,5 ) 2 Sheets (isolated and extended) Irregular Regions dssp The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format Usage: dssp [-na] [-v] pdb_file [dssp_file] Output : Automatic assignment programs DSSP ( http://www.cmbi.kun.nl/gv/dssp/ ) STRIDE ( http://www.hgmp.mrc.ac.uk/Registered/Option/stride.html ) Secondary Structure Types Secondary Structure Prediction What to predict? All 8 types or pool types into groups Type of Secondary Structure Prediction Information based classification Property based methods (Manual / Subjectiv