protein sequences co-evolution software

Q:

I’m writing to you in connection with your research on the computational tools for the study of residue co-evolution in protein sequences, described in Bioinformatics (2008), http://coevolution.gersteinlab.org

We have a summer internship opportunity here at Dupont Industrial Biosciences (IB) in Palo Alto and the proposed project would involve evaluating different methods for identifying co-evolving residues, so that the suitable method or methods could be applied to proteins and protein families of interest to the company. If this approach is successful, it could help guide future protein engineering efforts here at Dupont IB.

If you happen to know a candidate who would be interested in this internship opportunity, I would welcome your recommendations. I’m in the process of interviewing a few people, but would be glad to talk to additional qualified candidates.

This internship is somewhat unusual because it is not part of a bioinformatics group, so the intern would need to make independent judgments regarding the merits and drawbacks of different approaches and regarding the technical implementation of the project.

My second question is whether there are any terms or conditions associated with using the co-evolution computational tools from your lab? Are the terms different if we were to run these programs on a local computer here within the company (rather than submitting our sequences to the remote server)? I didn’t see any indications to that effect on the coevolution.gersteinlab.org page or in the publication, but it is an important aspect to clarify before using external software within the company, so I hope you can let me know what the rules are or suggest the person I should contact.

A:
I’ll look for an intern. There’s no conditions on the use of this software — it’s open source. Just cite us as described on the permissions page.

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