From Protein Structure to Function with Bioinformatics.pdf

ContentsSection I Generating and Inferring Structures1 Ab Initio Protein Structure Prediction ................................................... 3Jooyoung Lee, Sitao Wu, and Yang Zhang1.1 Introduction ....................................................................................... 31.2 Energy Functions .............................................................................. 51.2.1 Physics-Based Energy Functions .......................................... 51.2.2 Knowledge-Based Energy Function Combinedwith Fragments ..................................................................... 91.3 Conformational Search Methods ...................................................... 131.3.1 Monte Carlo Simulations ...................................................... 141.3.2 Molecular Dynamics ............................................................. 151.3.3 Genetic Algorithm ................................................................ 151.3.4 Mathematical Optimization .................................................. 161.4 Model Selection ................................................................................ 161.4.1 Physics-Based Energy Function ........................................... 171.4.2 Knowledge-Based Energy Function ..................................... 171.4.3 Sequence-Structure Compatibility Function ......................... 181.4.4 Clustering of Decoy Structures ............................................. 191.5 Remarks and Discussions ................................................................. 192 Fold Recognition ...................................................................................... 27Lawrence A. Kelley2.1 Introduction ....................................................................................... 272.1.1 The Importance of Blind Trials:The CASP Competition ........................................................ 282.1.2 Ab Initio Structure Prediction VersusHomology Modelling ............................................................ 282.1.3 The Limits of Fold Space ...................................................... 302.1.4 A Note on Terminology: ‘Threading’and ‘Fold Recognition’ ......................................................... 312.2 Threading .......................................................................................... 31ix