Modeling Proteins (top) Details of the steps necessary for modeling proteins. Topics addressed: Installing MOPAC, PDB files, hydrogenation, salt bridges, making changes, transition states.
Accuracy of results (top) A survey of proteins is presented, this allows a comparison of the predicted and reported structures. Faults in the PM6 method are described and a simple fault detected in the 3CLpro enzyme PDB 4MDS is reported.
Modeling the Chymotrypsin catalytic mechanism (top) A detailed description of the steps involved in modeling the hydrolysis cycle are given.
Improving the accuracy of ligand - protein binding energies (top) Steps to improve the accuracy of the binding energy of a ligand non-covalently bound to a protein are described.
Tools for working with proteins (top) Utilities within MOPAC that are useful in working with proteins and in understanding details of their structure are described. These include hydrogenation, resequencing, "freezing" an interatomic distance, and different ways of referring to atoms.