Thursday, February 21, 2008

NucProt Calculator Error in RNA Analysis

I was trying to use the program NucProt calculator for an RNA sequence of 7.4 kB. I always get an error message instead of an answer. What is the maximum length sequence allowed as input in the program.

It is actually a quite simple script. It only counts how many A, C, G, Us there are and uses the formula:
"Exact" calculation
volume (cubic Angstroms) = #A*315.45 + #C*291.285 + #G*323.028 + #U*291.285
mass (Daltons) = #A*329.2 + #C*305.2 + #G*345.2 + #U*306.2

For an RNA that size the average might just as good:
7.4kB * 304 A^3 ~= 2.25 million cubic Angstroms
7.4kB * 321.45 A^3 ~= 2.38 MD (MegaDaltons)
PSV is something like volume/mass*0.6022 ~= 0.57

Wednesday, February 13, 2008

How do I submit homology models to FlexOracle?

Does FlexOracle predict the hinge points in GPCR homology models? And has anyone done such a submission.

FlexOracle, as well as hNMb and stonehinge, assumes the protein is solvated -- this is less than ideal for you since GPCR is a membrane protein. FlexOracle works by splitting the protein into two fragments at every possible pair of points, and computing the stability of the fragments using the FoldX force field. However FoldX will not guess at the effect of lipids, it can only estimate the effect of a solvent environment. That having been said, I have had some luck with membrane proteins, if only because often people are interested in some cytosolic domain. This may be the case for you.

TLSMD, on the other hand, uses the crystallographic B-factors and so it will tell you how it flexes in the crystal, which is often similar to how it will flex in vivo. All of these analyses are done for you when you submit to the HingeMaster server on, as I encourage you to do. Bear in mind that the analysis will be done on one chain only. For particularly large proteins you may have to wait a couple of days. If you don't hear back from me when you get your results you are welcome to email me and I will help you interpret the results.

Threaded models have an additional strike against them in that the structure is almost certainly not properly equilibrated and thus is likely to be full of residual strains. This further limits the ability of FlexOracle to probe stability of fragments. hNMb is less sensitive to such details and so may be more useful, especially for the cytosolic domains. TLSMD will actually not return any results, since there will be no B-factors in a theoretical structure.

It still costs nothing to make a submission to our server, and despite these various issues you may still learn something.

Monday, February 11, 2008

How Do You Save or Download pdb file?

I need any pdb file like 119l or morph name: Small G-protein Arf6 with movie. I didn’t find an option to save or download and what software does it need to work on power point presentation to show protein motion.

A small movie is made on the old morph page. This is the easiest option but you can't control the perspective and have limited rendering options. More sophisticated movie making is available on our polyview3D page, administered by Alexey. Both are linked to from the top of the morph page.

Saturday, February 9, 2008

Resolving Conflicts in More than One Complex in the Same PFam Family

if there were two known complexes in the same pfam family, how did you use the combined information. And if homologs
were involved, did you just assign the aligned residues to the interface based on what interfacial residues were identified in the x-ray structure.

If we have known yeast complexes, this always takes precedent over any information in iPfam. If there is an interaction between two proteins known which share one Pfam domain _and_ the Pfam domain has been shown to bind itself in a crystal structure (i.e. in iPfam), we annotate that these two proteins will bind each other through the interface that is seen in that structure. In the
case of asymmetric binding between the same domain, the assignment is ad hoc. Ad II.) Yes, we use Pfam assignments as a form of homology mapping. We then assign the interface based on what is seen in the crystal structure.