Other uses of docking than viruses?

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Jim1348

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Message 761 - Posted: 1 Apr 2021, 12:10:11 UTC

I have only heard of docking (such as Autodock and VINA) being used against viruses.
But can docking be used for other types of diseases as well?
I don't know what they would be, but maybe you could give some idea.

Thanks.
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Falconet

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Message 762 - Posted: 1 Apr 2021, 12:48:40 UTC - in response to Message 761.  

The Help Fight Childhood Cancer at WCG used AutoDock and the Smash Childhood Cancer project uses AutoDock Vina.
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Jim1348

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Message 763 - Posted: 1 Apr 2021, 13:28:46 UTC - in response to Message 762.  

Thanks. I had not seen that.
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Falconet

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Message 765 - Posted: 2 Apr 2021, 12:28:21 UTC - in response to Message 763.  

You are welcome, Jim.
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Crtomir
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Message 766 - Posted: 3 Apr 2021, 11:32:31 UTC - in response to Message 761.  

Dear Jim,

molecular docking is method of structure based drug design, and is not limited only for screening for antiviral compounds. Docking is useful for all problems where we know high resolution structure of the target (usually proten, but could be also dna or rna). We will explore in the future also other targets than for corona; that would be not neccessarly connected with viruses. In future we will search also for antimalarics and other tropical neglected diseases, therapeutics against dementia, obesity, etc.

All the best,

Crtomir
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Jim1348

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Message 767 - Posted: 3 Apr 2021, 15:12:17 UTC - in response to Message 766.  

We will explore in the future also other targets than for corona; that would be not neccessarly connected with viruses.

Excellent. That is what I was hoping for.

And if you get a good GPU development volunteer, maybe you can get the remarkable (100x) speedup that Autodock is getting on WCG/OPNG.
They can tackle anything now I think.
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Crtomir
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Message 768 - Posted: 3 Apr 2021, 17:07:03 UTC - in response to Message 767.  

Dear Jim,

we are currently working on development of the GPU version of CMDock.

We are pretty sure, that with GPU version we will accelerate our research.

All the best,

Crtomir
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bozz4science

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Message 1103 - Posted: 8 Aug 2021, 10:03:18 UTC - in response to Message 768.  
Last modified: 8 Aug 2021, 10:03:53 UTC

Just wanted to check on the development progress of the GPU client. As Scripps which is the institute that developed the GPU client of AutoDock also took several months, I was wondering if you are making good progress with the development effort of your docking software. Looking forward to your feedback
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Jim1348

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Message 1106 - Posted: 11 Aug 2021, 14:14:36 UTC - in response to Message 1103.  

I am wondering too, but they may want to finish up the current work on CPUs for scientific consistency before jumping to GPUs.
And it will be interesting to see if they go entirely to GPUs, or whether they reserve some work for CPUs. I expect we will know more toward the end of the current batch.
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Crtomir
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Message 1107 - Posted: 12 Aug 2021, 8:18:37 UTC - in response to Message 1106.  

Dear all,

we are developing the GPU version of CMDOCK together with colleagues from the Faculty of Computer Science, University of Ljubljana. It is not so easy to convert the CPU version to GPU. Basically, colleagues from the Faculty of Computer Science have to rewrite the most important parts of the software. We expect a fully functional version of GPU CMDOCK at the end of this year or the beginning of next year. The GPU version will use OPENCL and run on NVIDIA and AMD graphics cards. All CPU (Win, Linux, macOS and Android) versions will be kept in the project. We will see how all versions will work together and serve the project.

Crtomir
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bozz4science

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Message 1109 - Posted: 16 Aug 2021, 16:34:44 UTC

Thanks for the update! Will you open a test channel to allow beta testing as a separate app here on Sidock@H or will you run tests exclusively internally?
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Mad_Max

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Message 1941 - Posted: 24 Jan 2023, 7:57:12 UTC - in response to Message 1107.  


We expect a fully functional version of GPU CMDOCK at the end of this year or the beginning of next year. The GPU version will use OPENCL and run on NVIDIA and AMD graphics cards.
Crtomir


Oops! The next year has not only begun, but has even already ended (it was the past 2022 - 1.5 year already passed ).
But not only is there no new GPU docking application released, a year after the originally planned deadline, but even no any news / updates about the progress of its development.

What happened to this project, where did it silently and without a trace go?
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Profile Natalia
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Message 1943 - Posted: 24 Jan 2023, 9:54:36 UTC - in response to Message 1941.  

Hello! GPU version of CmDock is under development. The latest CPU version is CmDock v0.2.0, December 2022.
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Mad_Max

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Message 1946 - Posted: 25 Jan 2023, 18:15:04 UTC - in response to Message 1943.  

I know that the CPU version is in active development.
But up to this point, I had heard nothing at all about the development of the GPU version. And I was VERY surprised to read in the old (you can say archival!) topic of the forum is that it turns out(according to the old plans) it should have already been ready about a year ago.

And no updates since then - why have the deadlines shifted a lot or plans changed or was it canceled completely? If not canceled, then at what stage it now and when at least approximately can we wait now first beta versions to test?
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Mad_Max

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Message 1947 - Posted: 25 Jan 2023, 18:33:18 UTC

I don't understand why so little time and attention is paid to GPU development in general (not only in your particular project).
I know it is not an easy and simple task...

But according to my personal and many other active volunteers opinion, for those tasks where it is generally applicable (and molecular dynamics is definitely one of such areas), the development/porting of the GPU version should be generally the number one priority.

Because the work that the project has been doing for a year in this case can be done in just a few weeks. I'm not overestimating or exaggerating. This is not only because GPU computing is much more productive/fast, but also because in the field of voluntary computing there is a great demand for projects that perform important meaningful scientific work in the field of biomedical research. Because most of the existing BOINC projects for GPU (especially for AMD/Intel = OpenCL, for NV/CUDA choice is somewhat larger) are devoted to pure, far-from-life theory - such as solving abstract mathematical problems or astrophysics. And when a new project appears that solves more applied and significant tasks, we can expect a large influx of new participants and computing power in additions to more efficient GPU computing by itself.

This was perfectly demonstrated at least twice with medical projects within WCG (Help Conquer Cancer - few years ago and Open Pandemic - last year) - as soon as it was possible to develop and launch a well-functioning GPU application - the overall calculation speed of the project increased not even by several times, but by more than an order of magnitude and from that moment on, the problem of the available amount of computing power ceased to stand at all - and the overall performance/throughput of the project was limited only by the available server resources for database operation and download servers for generation and processing of huge quantities of WUs for the computers of volunteers standing in line and waiting for when they can get some more work to process.
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Speedy51

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Message 2110 - Posted: 31 Aug 2023, 4:46:33 UTC - in response to Message 1943.  

How is the GPU application progressing?
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Message 2111 - Posted: 31 Aug 2023, 5:36:44 UTC - in response to Message 2110.  

Dear colleagues,

I am glad to inform, you that we did some trials with our version of the GPU (OpenCL) application. The scoring function for the GPU version is currently different from that of the CPU version,
and currently we are cleaning the code and are searching for bugs. We will very soon start with beta testing, ... In the near future, we will do some work on the entry page, maybe some visualisation
of the results would be beneficial for supporting this Open science project. Also, new targets, less computationally problematic than the last two, will appear soon.

All the best,

Crtomir
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Message 2112 - Posted: 31 Aug 2023, 7:43:33 UTC - in response to Message 2111.  

Thank you for the update much appreciated. Neat to hear their are some new targets that are less computationally problematic coming
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Mad_Max

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Message 2236 - Posted: 8 Apr 2024, 16:10:02 UTC - in response to Message 2111.  
Last modified: 8 Apr 2024, 16:10:13 UTC

Dear colleagues,

I am glad to inform, you that we did some trials with our version of the GPU (OpenCL) application. The scoring function for the GPU version is currently different from that of the CPU version,
and currently we are cleaning the code and are searching for bugs. We will very soon start with beta testing, ...

And more than half a year has passed again. Apparently, "very soon" in some scientific circles can stretch indefinitely... lol
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