[AMBER-Developers] Could we get a short, annotated, bibliography of amber TI calculations?

From: David A Case <david.case.rutgers.edu>
Date: Tue, 23 Mar 2021 09:34:10 -0400

Hi everyone:

Carlos's post (below) prompted me to think of the following:

Could we create (for the Amber 2021 Reference Manual), a short, annotated
bibliography of selected results for "modern" TI calculations in Amber?
I'm thinking of a list of recent papers, with 1 or 2 sentences about what
sorts of problems were addressed. We don't want to draw conclusions here
about "accuracy", just make it easier for users (including me!) to find
articles that show how Amber developers (or others) are applying the tools
we offer. This would not be a review, just an entry-path into the literature.

The obvious problem is that we may have more articles to put in this list
than makes good sense, but we can see who volunteers what.

Other application topics, besides TI, could also benefit from such a annotated

Some of this information is already scattered in various places in the
manual, but having such lists (say) as an introduction to various chapters,
might be helpful.

Putting this info on a web page might be another alternative.

Suggestions (and volunteers) are hereby solicted.


----- Forwarded message from Carlos Simmerling <carlos.simmerling.gmail.com> -----

Subject: Re: [AMBER] Pmemd to run TI on protein mutations

we've done calculations on protein-protein binding affinity for sets of
mutations using Amber pmemd TI on GPUs and found (in most cases) very good
accuracy vs experiment: ...

we also have a recent review that discusses accuracy of calculations, with
references to recent examples ....

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Received on Tue Mar 23 2021 - 07:00:02 PDT
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