Application scenario of pdbfixer

[wangjiawen2013]

Hi,

pdbfixer is a versatile tools to fix pdb files before they can be used in a molecular dynamics simulation, while it seems that it has many functions overlapping with other tools, For example:

1. Adding missing hydrogen atoms can be performed using pymol, scrub and reduce
2. Adding missing residues can be performed using modeller
3. Deleting unwanted chains and heterogens can be performed using pymol

So what's the pdbfixer's application scenario and when should we use pdbfixer when performing molecular docking and molecular dynamics simulation ? How pdbfixer cooperates with these tools ?
Besides, modeller uses homologous modelling to add missing residues to pdb file, what algorithm does pdbfixer use to build missing loops and add missing residues ?

[peastman]

I'm not sure what your question is. PDBFixer is a tool that performs certain functions. If it does a good job of doing what you need, then use it. If not, possibly there exists a different tool that's a better fit for your needs.

Cooperating with other tools shouldn't be a problem. It reads and writes standard file formats: PDB and PDBx/mmCIF. As long as the other tools also support those formats, they should be able to exchange information.

To add missing residues, PDBFixer first places them in a straight line or along an arc that is positioned to minimize clashes with other residues, but otherwise makes no attempt to be physically realistic. It then energy minimizes with a soft core force field to turn it into something more realistic. This works well for adding short loops, or long loops that are flexible and don't have any fixed "correct" structure. But it's not a structure predictor, and it doesn't attempt to figure out how long loops would actually fold.