Here is a first setup for the main questions Bob stated.
>1. What is pharmacophore rendering?
The current definition of pharmacophores is
"a set of structural features in a molecule that is recognized at a receptor site and is responsible for that molecule's biological activity", (Peter Gund, 1977)
The article 3-D Pharmacophores in Drug Discovery gives an in-depth view of current pharmacophore use and also some useful references. Pharmacophores are mainly used to find similar molecules from databases.
>2. What objects are involved?
Pharmacophores are a set of up to 10 kinds of objects (plus possibly user-defined) that are the result of molecular structure. The objects are either spherical or ellipitic volumes, or vectors, or a combination of those (I think).For rendering, the objects need to be semi-transparant as they usually engulf the whole molecular structure. Selectively showing/hiding pharmacophores should also be possible, because only parts of the molecule may be functionally interesting.
The pharmacophore objects could be read from file, but could also be calculated (by Jmol). Different ways of calculations exist with different accuracies (2-, 3- and 4-centre). From what I've glanced, calculation techniques can be quite complex.
>3. What have others done in this area?
As pharmacophores are very interesting for drug companies many software packages exist. Most of them also provide database search tools, as that is generally the intended purpose of pharmacophores. So far I have found:
- Catalyst http://www.accelrys.com/products/catalyst/- THINK http://www.treweren.com/
- MOLOC http://www.msg.ucsf.edu/local/programs/moloc/home.html
- LigandScout http://www.inteligand.com/ligandscout/
- MOE http://www.chemcomp.com/software-ph4.htm
- GASP http://www.tripos.com/index.php?family=modules,SimplePage,sybyl_gasp
- DISCO http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=8097240&dopt=Abstract (best I could find)
I haven't tried any of them yet.
>4. What should we implement in Jmol?
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