At 15:17 19/12/2006, [EMAIL PROTECTED] wrote:
On 19 Dec, peter murray-rust wrote:
> What is meant by csd? If this is the Cambridge Database then this
> primarily only relevant if the alternative sources contains
> crystallographic data.
For our purposes I disagree, because a chemical crystallographic
structure is not necessary. In practice, an idealized chemical
structure can be fitted within a new protein crystal structure just as
well.
If what you meant is "can we have an open database of 3D structures,
the answer is a qualified 'yes'" - without taking them from CSD.
There are two main methods:
* extract them from non-copyright crystal structures (there are a lot
of these and we are collating them - watch this space.
* create them from connection tables. There are various levels of
"accuracy" including forcefields and theochem methods. We have done
this for 200,000 molecules - see
http://www.dspace.cam.ac.uk/handle/1810/724 If you are happy with
PM3, then use these
P.
Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road, Cambridge CB2 1EW, UK
+44-1223-763069
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