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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

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June 22, 2010

Free Software

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Posted by Derek

The folks at Cresset sent me a note about a free download of some software that they've developed for molecular fields (an approach you can read more about here). Fieldview is a free tool for trying this out yourself, and can be had here. Worth a look for the computationally curious, especially at the price. . .

Comments (11) + TrackBacks (0) | Category: In Silico


COMMENTS

1. DLIB on June 22, 2010 1:36 PM writes...

Nativis is going to have a "field" day with this :-)

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2. Evorich on June 22, 2010 2:04 PM writes...

I'd say this is a slightly more impartial paper on the area:

http://dx.doi.org/10.1016/j.jmgm.2009.01.003

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3. Cassius on June 22, 2010 2:55 PM writes...

But can this wonderful freeware calculate PHOTON fields?

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4. Anonymous on June 23, 2010 7:06 AM writes...

I just downloaded it- nice to make educational pictures..

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5. me on June 23, 2010 8:23 AM writes...

A number of faintly sarcastic comments about this - but this approach is a really nice way of visualising molecules and possible interactions overlaid in 3D. I've used it with some success on a few projects for lead hopping.

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6. Cassius on June 23, 2010 8:37 AM writes...

My comment was intended for Nativis, not the software. I have the download link and will try it out. I am currently working on a modeling project and welcome other algorithms to sort out our virtual screening data. Thanks for the link, Derek. More information, and no money out of the grant budget.

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7. Anonymous on June 23, 2010 9:43 AM writes...

Anything to make chemists look at structures in anthing other than flat ISIS/Chemdraw notation is a good thing.

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8. David formerly known as a chemist on June 23, 2010 2:41 PM writes...

Looks like a decent tool, especially for the price. It's useful for measuring interatomic distances in 3D sstructures at the desktop, which is helpful. I like the field visualization as well. Thanks for posting the link, Derek, I suspect this will get a lot of use.

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9. Anonymous on June 24, 2010 1:24 AM writes...

Cressets science is really strong, it is one of the very few molecular modeling companies that has understood that electrostatics isn't described properly with only atomic point charges.

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10. Anonymous on June 24, 2010 2:58 AM writes...

I have now tried this tool from Cresset on several SDFiles and compared its outcome with some 2D-->3D generators. I seriously doubt the geometric relevance of 3D structures it converts and then displays a few "text-book" style interactions in form of pretty pictures. It is not trivial to show one lousy 3D conformation and by-pass the whole effort of conformational analysis. Also the physical properties (including electrostatics) and eventually the "field" will change depending on the conformation of the small molecule.

One Last thing- Tripos is the pioneer in this work- read CoMFA. Also remember how CoMFA models depend on alignment (alignment is a child of conformation by the way).

I wonder why should I use this tool when my eyes can be more open (read ROCS, OMEGA,...) :)

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11. Comp Chemist on June 24, 2010 9:50 PM writes...

We've used their software for a few years now, with good virtual screening success on multiple (but not all) projects. I'm a fan.

The thing Cresset does better is their force field: unlike CoMFA and OpenEye they use off-centered charges which more accurately represent delocalization and polarization. If these features are important to your virtual screening template--i.e., it's not just a greasy ball fitting into a slot--it can make a real difference.

In response to the previous comment: the new FieldView is nifty, and you can use 3D input to it, but the paid versions of their software use a more sophisticated conformational generator and templating engine.

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