A number of post translational modifications can occur to a protein, including phosphorylation, methylation etc. I am aware that there are a number of servers and tools to predict positions for these modifications based on sequence and/or structural patterns or motifs. However, is there a tool (or server) available that can actually model them on a structure (or a model)?
Hi Fotis,
There were an old server called SWEET which modeled carbohydrate chains, but I have checked and seems to be down
http://link.springer.com/article/10.1007%2Fs008940050068#page-1
MOE has a carbohydrate monomer library and builder. I also recommend read the following file, sory fro the size of the address.
Good luck
Arturo
http://www.google.com.mx/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=0CIIBEBYwCQ&url=http%3A%2F%2Fpeople.cs.uct.ac.za%2F~ymao%2Fcarbloader_keiran_mao_nasser%2Fdownloads%2Fymao_report.pdf&ei=4DcWU4fQCqSU2QXNk4Bo&usg=AFQjCNF17h4NisJPgXsx675mPpWhKlc0Mw&sig2=KsBascvT-40WyAPylXJXyA&bvm=bv.62286460,d.b2I&cad=rja
Hey Fotis,
FoldX might be of some use to you. FoldX has the option to add on phosphorylation (STY but not DEH) and calculates changes in potential energy as a result of the addition.
However, you will probably need to use the buildModel function instead of the siteMutate. Reason for this is that the parameter to specify a THR to TPO is 'o' which unfortunately is the same as mutating to polar residues -> The polar option wins out in this case and TPO is never run. I'm not certain if this has been fixed yet but was still an issue when I last used it (January).
I have not done a whole lot with post-translational modifications, but there are a couple simple things you could try. First, Swiss PDB Viewer allows point mutations. You could load a PDB file to Swiss PDBV, cause your point mutation, and then save and transfer the new file to a program that can do MD simulations. You could perform energy minimization just on the mutated residue and residues in the vicinity. Alternatively, you could use ChemBio3D Ultra from PerkinElmer to manually input your modification (add a phosphate, for example). It has several intrinsic MD options, though the software works best with small molecules and shorter peptides. Depending on exactly what you are doing you could likely gain some useful information from it.
As per usual, be careful with the energy minimizations and the environment. Post-translational modifications catalyzed by an enzyme may stabilize certain important residues in your protein and make certain conformations more likely than what you might find just by doing your computations in a generic solution or in vacuo.
Best of luck!
Ben
I have a list of peptides with cysteine posttranslational modifications , i m looking for a way to find and count the occurence ot that modification with a rapid manner ?Any ideas to suggest please ?
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools