Week 9

Sybyl is a frustrating piece of software, made even more annoying by the fact that I lack knowledge about biochemistry to know what I really should be doing to find the partial charges. With some help from David and Miguel we figured out that the the charges and hydrogens on the protein were mostly right except in some special cases like disulfide bonds. This should be ok as long as the special cases aren't near the active site. However, the ligand is another problem.

Sybyl seems to have trouble detecting the correct atom type for the ligand. The atom type is important because it's how Sybyl calculates the hydrogens and partial charges. So to get the correct hydrogens and charges you have to go through the ligand by hand and correct the wrong atom types. I don't really understand how to determine the atom types, so David figured them out. He also gave me some general guidelines to help me figure them out myself. So I started working through the different examples. I found that sometimes Sybyl does find the correct atom types, which is nice. But more often than not at least a few of the types are wrong. On most the examples Autodock works great. Next I need to try out our program on the examples.

Week: 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10