Dear Ergon,
Thanks!
I posted a question on the ChemAxon site today asking if they could
specify the algorithm they use and to provide a literature reference. I
will let you know if I get any further information on this.
Best regards,
Rudy
----------------------------------------------------
Rudy J. Richardson, ScD, DABT
Dow Professor of Toxicology
Associate Professor of Neurology
The University of Michigan
1415 Washington Heights
Room M6065 SPH-II 2029
Ann Arbor, MI 48109-2029 USA
Tel: (734) 936-0769
Fax: (734) 763-8095
Email: [email protected]
----------------------------------------------------
On Tue, 7 Jun 2011, Egon Willighagen wrote:
Dear Rudy,
On Tue, Jun 7, 2011 at 3:56 PM, Rudy J. Richardson <[email protected]> wrote:
I do not have a specific algorithm at hand for calculating the van der Waals
molecular volume. However, there is a calculator plugin for ChemAxon Marvin
Sketch that calculates this descriptor.
I implemented that algorithm proposed in this 2003 paper:
Zhao, Y. H., Abraham, M. H., Zissimos, A. M., Sep. 2003. Fast
calculation of van der waals volume as a sum of atomic and bond
contributions and its application to drug compounds. The Journal of
Organic Chemistry 68 (19), 7368-7373.
URL http://dx.doi.org/10.1021/jo034808o
The code is available here:
https://github.com/egonw/cdk/commits/288-14x-volumeDescriptor
(Six commits...)
But I have not wrapped it as a descriptor yet... I will also try to
port of to the CDK version used by Bioclipse 2.5... but all that not
before this weekend.
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
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