Greetings!

Could you please inform wether CHARMM will be used in this project at least in beta-applications, or should I help to improve it participating in Docking@Home project?

Thanx in advance!

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From Siberia with love!

The wikipedia shows CHARMm in several varients for a varitety of interactions:

CHARMM19 - united-atom (sometimes called "extended atom").
CHARMM22 and its dihedral potential corrected variant CHARMM22/CMAP - all-atom.
CHARMM22 for the TIP3P explicit water model.
CHARMM22/CMAP for use with implicit solvent GBSW.
CHARMM27 for DNA, RNA, and lipids.

And it shows two BOINC projects that use CHARMm simulations in their applications: Docking@Home, and the World Community Grid Clean Energy Project

The clean energy project is clearly aimed at studying solar cell materials. And so while the work may bring us cheap, clean electricity some day, it is not oriented towards improving CHARMm itself.

The wikpedia for Docking@Home says it's ultimate aim is the development of new pharmaceutical drugs, particularly those related to HIV. Wikipedia is certainly not a definitive source of information, but I did not readily find the issue addressed on the Docking homepage. The statement would seem to imply they are studying HIV more then CHARMm. It is unclear if they are pouring resources back in to the development of CHARMm, or simply utilizing it to study HIV.

With Rosetta@home, you are helping the inventors of the program to further refine and develop it so that it produces more accurate models of a variety of proteins and interactions. This is often what makes it difficult to explain what R@h is. R@h isn't specifically studying HIV, and yet is always doing some study of HIV. R@h isn't specifically studying protein-protein docking and drug design, and yet is always doing some study of each.

You see R@h is sort of the showcase for an entire community of researchers called RosettaCommons. As you can see in the link, this is made up of researchers throughout the world.

The program used has various protocols that are designed to study specific situations. Everything from a single protein, to protein-protein docking, protein-DNA interaction, small molecule-protein docking, and a number of design protocols. Read more here: http://www.rosettacommons.org/software/

And so, similar to how some BOINC projects are using CHARMm to conduct their research, other projects are using Rosetta to do so. Learning more about which yields better models for various situations is part of the ongoing research. At this point I wish I was keeping a list of all the BOINC projects that use Rosetta in their research. Perhaps someone else has one and can post it here.

So, no, if you believe CHARMm is the way to go and you are wishing to support CHARMm, R@h doesn't give you that, and is unlikely to ever do so. If you believe that HIV research is the way to go, and you are wishing to support it, then Docking sounds like it is more directly focused on that. If you believe in fundamental research for expanding our understanding of proteins and protein interactions, then I would say R@h is the way to best achieve that.

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Rosetta Moderator: Mod.Sense

And it shows two BOINC projects that use CHARMm simulations in their applications: Docking@Home, and the World Community Grid Clean Energy Project

The clean energy project is clearly aimed at studying solar cell materials. And so while the work may bring us cheap, clean electricity some day, it is not oriented towards improving CHARMm itself.

The World Community Grid Clean Energy Project is also essentially shut down for now. There may be a phase 2 later.

{The wikpedia for Docking@Home says it's ultimate aim is the development of new pharmaceutical drugs, particularly those related to HIV. Wikipedia is certainly not a definitive source of information, but I did not readily find the issue addressed on the Docking homepage. The statement would seem to imply they are studying HIV more then CHARMm. It is unclear if they are pouring resources back in to the development of CHARMm, or simply utilizing it to study HIV.

The best I can tell, they are currently primarily working on a wrapper to make CHARMM (at least the academic version) BOINC compatible, and doing most of their work so far on just 3 proteins, one of which is HIV1 protease; a second one is the trypsin involved in digestion, and the third is P38alpha. They seem to be chosen mainly to get a range of protein flexibilities, to help develop the software. They're currently using CHARMM mainly to find assorted compounds (not just proteins) that will dock to these three proteins, both with the aim of helping HIV research and to develop their software. They plan to use their software later to look for compounds that will dock to a wider range of proteins, to help pharmaceutical research.

I can't tell if they're also working on developing CHARMM, even after reading most of what's in their forums.

There's a thread Message boards: Docking@Home Science: What is the main goal of Docking@home? that gives more details, but hasn't been updated lately.