Proposal to remove "targeted" from TargetDB and PepcDD
Feb 23, 2005

Dear ISGO members,

At ICSG2004 the suggestion was made that the status of "Targeted" in
TargetDB was not a useful designation because it just signalled intent in a
vague way. This has now been discussed thoroughly by the ISGO executive
committee, advisory panel, and the RCSB and the following proposal has been
prepared for your approval.

Could you possibly consider this proposal and let me know of any objections
to it (if you agree, no action is needed!)

Thanks very much,

-Tom Terwilliger

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A Proposal for Modification of Status Codes in TargetDB and PepcDB

TargetDB has played a major role in structural genomics and structural
biology by providing a concise and relatively uniform set of data on the
success rates at steps in protein structure determination, and by providing
a means for individual structural genomics centers to abandon targets
similar to those that have been or are about to be determined by
others. The designed scope of TargetDB has been limited to high-level
information. In response to user needs, a more comprehensive database of
protein production and crystallization called PepcDB is being
developed. In anticipation of the production phase PepcDB, we propose some
refinement of the definitions in TargetDB and PepcDB.

In many analyses of throughput, the number of "Selected" structures is used
as the denominator against which all progress is measured. However,
"Selected" often means "intent to work on this target", but in analyses it
is often used as "started work on this target". As cloning is a highly
efficient process, a much better measure of "started work" is
"Cloned". The proposal is to start the pipeline statistics with "cloned"
so that a more reasonable measure of progress in the structure
determination pipeline can be assessed.
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: terwilliger@LANL.gov
Fax: 505-665-3024   SOLVE web site: http://solve.lanl.gov
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB