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

From: Carlos Simmerling <>
Date: Tue, 23 Mar 2021 09:38:04 -0400

great idea Dave. I'd be happy to help (but not take it on alone).
But maybe we actually could do this as a review?

On Tue, Mar 23, 2021 at 9:34 AM David A Case <> wrote:

> 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
> bibliography.
> 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.
> ...thx..dac
> ----- Forwarded message from Carlos Simmerling <
>> -----
> 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 - 07:00:03 PDT
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