Saturday, June 23, 2007

Program for calculating number of waters inside protein

Concerning your paper entiled Packing at the protein-water interface (PNAS
93), do you have an algorithm available for distribution (or know of one)
that can calculate the number of waters inside a protein ?

Only programs are available at which calculate packing density but position waters best done by other programs.

Monday, June 18, 2007

Adding Original Genes with Gene Names to Pseudogenes Website

On the Pseudogenes website, only a few(~300) of the 16K pseudogene hits could be linked to a gene in the RefSeq gene list file. Would it be possible to add a list off all the original genes with their genome location on your website.

Most of the original genes are listed by Ensembl ID. You can look up their information at

Sunday, June 17, 2007

Deciding which Fragment is Flexible or not on MolmovDB

We want to know which fragment is flexible or not according to the information from “the molmovdb” database.

If your protein has been crystallized in two conformations you can submit a job to our "morph server." Visual inspection may then give you the information you seek. If you have only one structure, you can submit it to our HingeMaster server, and several different flexibility analysis programs will be used to find the hinge location. Note that this is designed for use with domain hinge bending proteins. It will not be very helpful if your protein moves by shear or order-disorder transition mechanisms.

We also have a motion prediction program, the Conformation Explorer, which predicts conformational change for hinge bending proteins, either induced by ligand or otherwise. It's still under development, and use would require further discussion.

Tuesday, June 12, 2007

MolMovDB Data Dump

You offer to provide the MolMovDB as a complete data set upon request. Where can we get a copy of it, preferably as a MySQL database?

The Hinge Atlas dataset, described in our recently accepted BMC Bioinformatics paper, is available for download here:

Just scroll down to the Hinge Atlas section. You probably want the coordinate set data, more than the mysql dump. The rest of the database is not yet available for download.

Monday, June 11, 2007

How to Create a Movie of Motions if there's DNA Lesion

We would like to create a movie of these motions for our publication and would not like to use the public morphing server if possible. The morphing of our structures might not possible at all, due to the cisplatin containing DNA lesion. We could send you also the CNS parameter and topology files we used for refinements.

If you submit the protein and DNA separately this should work. You would then have the problem, though, of putting the two back together. What I would suggest is submitting the two jobs and emailing me when they are done. I would then remove them from the public part of the database, but you could still download the structural interpolations. I would suggest using a small number of interpolated frames, at least for a first try, to minimize compute time.

Tuesday, June 5, 2007

Pseudogene Sequence Data Download

We know there is a way to download the pseugogenes of each organism, the file that is downloaded comes with the name of the pseudogene, the start and end position etc. But we wanted to download the sequences of each pseudogene of each organism directly, and we didn't find a way to do that in the database. Is it possible to download the sequence? Or do we have to make a program that, given the genome of the organism and the start/end positions of each peseudogene, extract the correspondent sequence?

None of the flatfiles contain the raw sequence information. On an individual pseudogene basis, however you can query the system for either the amino acid or nucleotide sequence. Simply search for the pseudogene you're looking for and on the results page click either the red or yellow button.

(Example results page: )

To get the sequence information for a large set of pseudogenes, however, it would probably be best to write the program you suggested.