Help
Tutorials
- Beginning Docking
- Constraints: Attraction and Repulsion
- Tails & Unstructured Resiudes
- Antibody Mode
- Dimer Mode
FAQ
- I keep getting errors that my file has unknown residues. What should I do?
- I see four different choices for my docking results, "Balanced", "Electrostatic-favored", and so on. Which one should I choose?
- What is Piper and what is ClusPro? How does this version differ from the previous ClusPro?
The problem is that some record in your pdb file is marked as ATOM, but is not one of the
20 standard amino acids or an RNA base. Some programs will place HETATMs in
ATOM records.
You can edit the file to remove these residues or change them to
HETATM records.
We provide many different options for docking because we believe good results go hand-in-hand with
experimental knowledge of the complex. If you don't have any prior knowledge of what forces dominate
in your complex, we recommend using the balanced coefficients. If your complex is antibody-antigen, we recommend
using our antibody mode.
Piper is the FFT-based rigid docking program developed in our lab. It provides 1000 low energy results to our clustering program, ClusPro to
attempt to find the native site under the assumption that it will have a wide free-energy attractor with the largest number of results.
The previous version of ClusPro used a smimilar clustering algorithm, but obtained 2000 results from other docking programs, not Piper.