Re: [AMBER] accuracy of FEW free energy calculation

From: Albert <>
Date: Sat, 20 Jun 2015 21:07:42 +0200

Well, well, well. Actually people from Schrodinger work together with me
very closely these days and they also would like to make it work.
Unfortunately, after trying additional 2 months, nothing significant
happen towards the accuracy for my system.

I only believe my own seeing, no matter what kind of paper work was
published. I am always concerned about any results in any paper.

As far as I learn from my friends from industrial area, 60% of nowadays
published scientific work are not repeatable! Considering Schrodinger
would like to make big money from other people, I won't be surprised
that they even risk to treat JACS paper. For instance, all the compounds
activity data are already published before their calculation and they
can definitely specify them in their initial input file. All the so
called FEP Mapper to do is somehow use some function to MAKE the finial
results correlate to original input values. This is definitely NOT
prediction, but post-prediction.

What's more is that few days ago Schordinger organized a online Webex
concering FEP+ and they also give a benchemark on the Glide docking
results, as well as MMGBSA in Schrodinger, correlate with experimental
data. They also show some promising pictures. According to my own
several years experiences with various project, Glide docking score and
the MMGBSA never, ever have any acceptable correlation with experimental
data at all. Several of my friends from both academy and pharmaceutical
industry share the same experience.

You see, how bad it is when people would like to make money. They can
promise you anything that you want. But what's the reality?

More interesting, in the Schrodinger FEP+ Webex days ago: in one slide
they show that the correlation for HSP90 is only 0.2, but on other slide
in the same presentation, they show the R^2 was high as 0.70!!! How
could this possible?

Expensive things is not always the good thing, neither popularity.



On 06/20/2015 06:29 PM, Jason Swails wrote:
> ​I think this is a little pessimistic. If you are having trouble
> correlating your results in the same way that Schrodinger did in their
> paper, you should contact them for help. They wouldn't stay in business if
> their methods were based on cheating and could only achieve good results on
> hand-tuned retrospective studies. I haven't read the paper yet, and it's
> entirely possible that the method doesn't work as well as the paper would
> suggest, but I know and respect a lot of the scientists that work at
> Schrodinger. Your accusations are at odds with my experience with them.
> So I would suggest trying to reconcile why your simulations are not
> yielding similar results to theirs rather than simply chalking it up to
> scientific dishonesty and corporate deceit.
> Another comment I'll make is that papers are subject to peer review which,
> while not a perfect system, has been quite effective at pushing forward
> good science and filtering out the bad (at least eventually). By contrast,
> none of our emails in which we answer questions here are subject to peer
> review, so I would suggest treating our responses with at least as much
> (and usually more) skepticism than, for instance, JACS papers. This isn't
> to say you should blindly accept anything people publish in JACS, but you
> shouldn't consider what we say here to be any more reliable (treat them as
> tips to help give you a fuller picture and/or get you pointed in the right
> direction).
> ​Good luck,
> Jason

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Received on Sat Jun 20 2015 - 12:30:02 PDT
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