Wednesday, November 15, 2006

Wanted: Docking Collaborator

As pointed out by Peter and Joerg, the chemical blogosphere is getting more and more populated. This represents a great opportunity for collaboration. Indeed, there have been some examples of chemists asking for information and getting advice on blogs. Chemistry forums and mailing lists have served this purpose as well for some time.

In general it has been difficult for people to ask for a lot of information because of the fear of disclosing too much, I assume for patent and journal publication issues. Even with those concerns, the extent of the aura of secrecy is surprising to me. For example many chemistry bloggers still use pseudonyms, even though their content is high in quality and very uncontroversial.

In our research on the synthesis of new anti-malarial agents, we started with a list of 218 compounds that were predicted to dock with the parasite's enoyl reductase enzyme. Treweren, the company that ran the not-for-profit Find-A-Drug initiative, was kind enough to provide us with that list and the THINK software they used for the docking calculations.

As we are moving forward with the synthesis, we are finding that some analogues not in the original list but more accessible synthetically are worth investigating. Keeping with our Open Notebook Science philosophy, we are reporting these docking trials in wet experiment format with sections for Procedure, Results, Discussion, etc. For example, Sean reports on his investigation of certain THINK variables and the resulting docking energies.

The problem is that our expertise is in synthetic organic chemistry, not docking. This makes it very difficult to interpret our results with a great deal of confidence to decide if it is worth investing laboratory time and resources. What would be extremely helpful is feedback on how the calculations were done and how to interpret the results in a meaningful way. Or even better have some help with docking the molecules with a different program.

Basically I am asking for a collaborator who is interested in this malaria project and is willing to work openly. Any takers?

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