Frequently Asked Questions
Q. What is this server all about?
A: This Server is dedidicated to predict protein function site using sequence alignment information as well as rosetta protein design and rosetta free energy calculation.
Q. What is the science behind this server
A: The science is to dissect the functional important residue from structural important residue in the sequence conservation information using Rosetta. For details, please read our paper.
Q. What if I have any question
A: If you have simple technical question, please contact the webmaster. If you have questions beyond that, please contact the corresponding author of the paper.
Q. What is the referece if I want to cite you?
A: The paper is Improvement in protein functional site predicting by distinguishing structural and functional constraints on protein family evolution using computational design by Gong Cheng, Bin Qian, Ram Samudrala, David Baker
Q. What is the restriction of PDB I submited?
A: There are 2 restriction, one is chain number, the other is the size of the PDB. First of all the PDB file should contain one chain, only one chain because the version of rosetta is working under single chain mode. The other restriction is the size of the PDB, ideally it shouldn't be bigger than 300 residues.
Q. What if I have no results?
The most common problem is that the pdb you submit has mutliple chains, if that is not the case please feel free to contact the webmaster .
Q. What software do you use to generate those beautiful pictures
A: I use pymol which is under control of a small perl script