Biomedical Engineering Reference
In-Depth Information
In July 2007 a mailing list was created to work through details of challenges
related to the UsefulChem project [26]. This was done to capture discussions
taking place by e-mail. Collaborators outside of the core UsefulChem team
seemed to prefer e-mail over the wiki or blog to communicate and this was
done to keep the discussions public.
In April 2008 FriendFeed was fi rst investigated as a collaboration platform
for UsefulChem [27]. Its basic function is to aggregate all relevant feeds from
various social networking sites for a user to a single account. For example,
feeds for all blogs, SlideShare, LinkedIn, Google Reader, YouTube, SciVee,
and so on, can be aggregated to one uniform resource locator (URL) [28].
Whenever the user generates a new entry in any of the source accounts, a
FriendFeed post is automatically made and reported to all subscribers.
Discussions can then take place on FriendFeed itself instead of on the original
blog or other type of post. This is particularly convenient since extended
discussions on FriendFeed around a post can be referenced with a short URL.
Since the open-science community is well represented on FriendFeed, much
of the discussion and activity related to UsefulChem now takes place on this
platform. This was later detailed in an article in
Chemical and Engineering
News
[29] .
25.3.2 Medicinal Chemistry: Collaborations Between Synthetic Chemists,
Computational Chemists, and Biochemists
The UsefulChem project started with searches on Google Scholar and Scirus
in the chemistry category for phrases like “there is a pressing need for,”
“what is needed now,” and “needs to be synthesized.” A need for new antima-
larial compounds proved to be a recurrent theme [30, 31]. An example of early
collaboration spontaneously arose, with renowned blogger David Bradley
suggesting to vary the spelling of “synthesize” to the British version of “syn-
thesise ” [30] .
A deeper collaboration followed the identifi cation of Find - A - Drug as a
source of virtual libraries for HIV protease inhibitors [32] and malarial enoyl
reductase inhibitors [33]. Find-A-Drug provided a virtual library of diketopi-
perazines and three-dimensional (3D) docking information of a sample
member onto malarial enoyl reductase [34].
The Drexel group started to perform docking calculations using the THINK
software [35]. With the intention of adhering to the concept of ONS, the
docking runs were recorded using a similar format to wet laboratory experi-
ments so that other researchers would be able to reproduce the computational
results and conclusions based on the information provided in the notebook.
A response to an open request for docking collaborators changed the
course of the UsefulChem project [36]. A member of the bioinformatics group
at Nanyang Polytechnic in Singapore attempted to dock the Ugi product pre-
cursors to the diketopiperazine targets and determined that some of them
docked onto enoyl reductase. As a result, the problematic cyclization step (see
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