Ab Initio Protein Structure Prediction Using a Size-dependent Tertiary Folding Potential

Summary

The chapter is organized as follows. Section II describes the new potential function, discussing its novel qualitative features and presenting an algorithm for optimization of parameters using a large training set derived from the Protein Data Bank (PDB). Section III briefly reviews the computational methodology used to carry out the tertiary folding simulations and then presents simulation results using native secondary structure and ideal secondary structure. As a test set in this section, the authors employ a subset of the proteins studied previously so that comparisons can be made with the results reported in that publication, and improvements in the potential functions quantified. In Section IV, the authors utilize predicted secondary structure lengths and positions and ideal secondary structure elements to carry out ab initio prediction experiments; they focus in this chapter on helical proteins, and include, in addition to proteins from the test set of Section IV, two targets from CASP3.