How do I get data for the Bayesian Networks Paper?

I am a graduate student in University of Science and Technology of China majoring in bioinformatics. I am to perform some experiment concerning PPI network, and i found your article A Bayesian networks approach for predicting protein-protein interactions from genomic data very useful to my work, and need the variousdatasets preprocessed by your group. Will you send me a copy or tell me the site where i can download the data?


You could find the data from the supplementary website:http://networks.gersteinlab.org/intint/supplementary.htm

How to obtain Standalone version of Calc-surface?

I am wondering if I could get a stand-alone version of calc-surface programe, I cannot find it in the software page of Prof. Gerstein lab.

I don't release binaries, because I am not good enough at it, to make it compatible with most systems. I would be happy to compile it for you, but I need to know what type of system you have: Linux, Mac, 32bit, 64bit, G4, G5. I am sorry to say I can't do Windows. Please contact the lab

How do I modify source code of Calc-Surface?

I want to use calc-surface with a large probe of 14 Angstroms but calc-surface seg faults when the probe is larger than 3 to 4 Å. I would like to modify the code to handler larger probes, can you point me in the right direction as to where to edit the code? I am using version 2.3.1.


The code you should be editing is called calc-surface.main.c which is in:

libproteingeometry-2.3.1/src-prog

I would also be careful about some other scripts or sub-routines that this program calls. Most of the scripts are usually in the same dir. All the programs are in one of these three:
src-prog, src-pro2 and src-pro3.

We have a new integrin ectodomain structure with two molecules in the asymmetric unit. There is a small amount of breathing at what we call the headpiece-tailpiece interface when the two molecules are compared. This is very important to some molecular dynamic simulations that we are doing. The movement between the two molecules is small, a few degrees, but involves large units of the molecule. We would like to use the morph server to extrapolate, rather than interpolate, this motion. I have looked at your description of frodo lite and this seems a good approach. So, following up our meeting at Yale, we would appreciate some help with this.



By "extrapolate" I believe you mean that you want to predict an unknown conformation from one or two known ones. FRODA can in fact be run in "undirected" mode and this will sample the accessible phase space consistent with sterics and the hydrogen bonding pattern. However it does not pick out the desired conformer from the large number of generated conformers. Certain assumptions are also made about the hydrogen bonding pattern which may result in the desired conformation not being present at all in the generated ensemble.

Instead of FRODA, perhaps you want to try our soon to be announced motion prediction tool, the Conformation Explorer. It is specifically designed to predict the motion of domains. Domains are often too large and slow moving to be dynamically characterized by MD. Further complicating matters, the motions are stochastic and the MD force fields are far from perfect; therefore the motion may not be observed even when the trajectory has been computed for a period of time experimentally
known to be sufficient. We have been successful in predicting large scale domain hinge bending motions for five proteins, including biotin carboxylase, glutamine binding protein, and MurA.

We do need to know something about the conformation which is to be predicted, however, in order to pick the right conformer out of the ensemble. If it binds a small ligand, for instance, we can find the holo structure given the apo by computing stability, free energy of ligand binding, gyration radius, and other quantities. Your use of the word "extrapolate" suggests you may have some geometric information about the target conformer which we can use.

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

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 molmovdb.org, 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.

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.