HingeAtlas (2007)

Q:
I am reading your Hinge Atlas (2007) paper.
I searched for your dataset to study the pdb structures you used and their
hinge residues, but I could not download it from the page:
http://molmovdb.org/cgi-bin/sets.cgi.
Could you please send a file if it is possible by email, or please check and
fix if there is a bug on the web page.

A:
Please try the Hinge Atlas Gold while we investigate the webpage. This may take time.

MolmovDB job ID b956969-31750

Q:
Could you please have a look at my submission from yesterday and tell me what I did wrong that they job does not finish?

http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b956969-31750

A:
The server is running fine. Please follow the tutorial vedio for input file preparations. We are not responsible for user’a input files that are not compatible with the original script of the server.

We do not run jobs for those users, given that the server runs fine as it is originally supposed to be. There’s FAQ and tutorial I made on the webpage that you should follow.

Inquiry about STRESS

Q:
I am writing this e-mail to inquire about STRESS software.

We have learned from your paper (Structure 2016,24:826-837)
that STRESS software can be used for identifying allosteric pockets.
We are interested in using the software for our drug discovery research.
We will perform evaluation of the software for a start.

Will you allow us to use STRESS software for the purpose of our
commercial drug discovery project free of charge?

As this is an urgent project, we would highly appreciate if you could
reply soon.

A:
see license at https://sites.gersteinlab.org/permissions/

Questions About MolmovDB Database

Q:
I am working with conformational change in protein structure. I would like to do some
research using your molmovdb (Domain motion) database, however I check
the website and it doesn’t work. How could I get access to the Molmov
database?

I mean when I tried to check the molecular movements database at this address

http://www.molmovdb.org/cgi-bin/browse.cgi

I got error msg when i opened morph button:

"Your request could not be processed. The following error was detected:
Morph va1cbuB-1c9kB not found in database.
Please email protmot if you think this message was caused by a server error.

Last year, we developed a probabilistic model for detecting rigid domains.

https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw442

We use Dyndom database for benchmarking which contain a lot of redundancies. I am looking for alternative database for benchmarking our methods.

A:
Would you mind sending me the PDB files you submitted, as well as you job ID, and we’ll investigate. In the meantime, we’ve compiled a list of related resources that may be of interest:

http://www2.molmovdb.org/wiki/info/index.php/Related_Resources

Also — what do you mean when you say it does not work?

it no longer sends out acknowledgement emails. However save the morph ID and come back later (sometimes as long as a day later) to check on it.

You can also use my macromoleculebuilder (MMB) software. It’s good if you have a very large complex undergoing a large scale conformational change.