Hi,
I’d be interested in helping out and JCIM would love to see this best practices/review. Kennie
> On Mar 23, 2021, at 9:38 AM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> 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?
> carlos
>
> On Tue, Mar 23, 2021 at 9:34 AM David A Case <david.case.rutgers.edu> 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 <
>> 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 ....
>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber-developers__;!!HXCxUKc!ntAFdoQb5qqeQ9QXiKeASEMDe0lFZrghrVXVjjiC9FA8nnbgQGN82pbfqB2j-NvxDQdL$
>>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber-developers__;!!HXCxUKc!ntAFdoQb5qqeQ9QXiKeASEMDe0lFZrghrVXVjjiC9FA8nnbgQGN82pbfqB2j-NvxDQdL$
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Tue Mar 23 2021 - 07:00:03 PDT
