Posts by Jim1348

1) Message boards : Science : Target 20: corona_DHODH_v1 (Message 1717)
Posted 24 Aug 2022 by Jim1348
This seems to be an interesting target.

Do you have plans to test it in the lab?
2) Message boards : Science : COVID-19 news (Message 1712)
Posted 22 Aug 2022 by Jim1348
A new study published in Nature Communications has homed in on a part of the SARS-CoV-2 spike protein that seems to be shared across all known variants. The research also reveals an antibody fragment that can hypothetically block the virus from entering human cells, paving the way for future therapies to neutralize all COVID-19 variants.
3) Questions and Answers : Windows : Will not queue more than about 4 work units per core despite set for 10 days of work (Message 1704)
Posted 17 Aug 2022 by Jim1348
i have noticed that for say an 8th gen Intel box, 6 core, it won't queue more than about 24 work units at a time despite having my queue settings maxxed out in BOINC at 10 days in both fields.

There is a limit, based on the number of cores you have. I am not quite sure what it is, but I have never gotten more than a day's work either on any of my machines (currently a Ryzen 5950X).
4) Message boards : Number crunching : Target 17: corona_Eprot_v2; Target 18: corona_Eprot_v3 (Message 1672)
Posted 21 Jul 2022 by Jim1348
I see new Coronavirus targets. Very good.
Is that due to new targets for the new variants, or are the original targets still good for them?
5) Message boards : Science : COVID-19 news (Message 1484)
Posted 28 Jan 2022 by Jim1348
New MERS-related virus NeoCoV may be more lethal, transmissible - study

A new lethal virus known as NeoCoV has been discovered, and it may be more transmissible - with one mutation - according to a new study by Chinese scientists from Wuhan, though some experts are cautioning that further study is needed. It has not yet made the leap to humans.
This is not COVID-19, but too close for comfort.
6) Message boards : Cafe : Comparison to other projects? (Message 1470)
Posted 22 Jan 2022 by Jim1348
I have done all of those projects to some considerable degree, and they are all backed by very capable scientists.
To make a long story short, at the moment I am doing SiDock. I like their considered choice of targets, which is a large part of the puzzle.

And the other reason is a bit negative. After many years of crunching on various docking projects, I have really not seen any of them yield a useful treatment. Since SiDock is new to the distributed computing world, I think they should be given a chance to see what they can do. The best of luck to them.
7) Message boards : Number crunching : Problems accessing the project and web site (Message 1445)
Posted 10 Jan 2022 by Jim1348
Me too. I think their server is at the limit due to the short work units.
8) Message boards : Science : COVID-19 news (Message 1391)
Posted 15 Dec 2021 by Jim1348
Omicron is a wake-up call for COVID-19 vaccine developers

Arrival of the highly-mutated Omicron variant is a wake-up call to develop vaccines less susceptible to the rapid changes of the coronavirus, leading virologists and immunologists told Reuters.
Most first-generation COVID-19 vaccines target the spike protein on the outer surface of the SARS-CoV-2 virus used to infect human cells. Omicron has prompted alarm among scientists because it has far more mutations than earlier variants, including more than 30 on its spike. Research to determine the extent to which Omicron evades immunity from existing vaccines or prior infection is underway.

New data on the Pfizer /BioNTech vaccine show some degree of reduced protection with the two-shot regimen. Even if current shots remain effective for now, the dramatic evolution of the virus highlights the need for vaccines targeting parts of the virus less prone to mutate. "One thing that is clear from Omicron is that the virus... is not going to go away," said Dr. Larry Corey, a virologist at Seattle's Fred Hutchinson Cancer Center who is overseeing U.S. government-backed COVID-19 vaccine trials. "There's a need for better vaccines."
9) Message boards : Number crunching : w/u run time (Message 1388)
Posted 12 Dec 2021 by Jim1348
Mine are running almost 6 hours on a Ryzen 3950X (Ubuntu 20.04.3).
The last batch was only about 30 minutes.
10) Message boards : Science : COVID-19 news (Message 1384)
Posted 10 Dec 2021 by Jim1348
Two doses of a Covid vaccine are not enough to stop you catching the Omicron variant, UK scientists have warned.
Early analysis of UK Omicron and Delta cases showed the vaccines were less effective at stopping the new variant.

However, a third booster dose significantly increased protection to around 75%.
11) Message boards : Science : COVID-19 news (Message 1372)
Posted 25 Nov 2021 by Jim1348
Covid: New heavily mutated variant B.1.1.529 in South Africa raises concern
We're back in familiar territory - growing concern about a new variant of coronavirus. The latest is the most heavily mutated version discovered so far - and it has such a long list of mutations that it was described by one scientist as "horrific", while another told me it was the worst variant they'd seen.
12) Message boards : Science : What is the Nipah virus and why is it more deadly than COVID-19? (Message 1140)
Posted 9 Sep 2021 by Jim1348
we should do HTVS also for NIPAH. Do you have an idea which protein to target?
Thanks, but you credit me with too much knowledge. That part is beyond me.
I just think that as a cruncher, the sooner we can start on them the better. They usually get worse.
13) Message boards : Science : What is the Nipah virus and why is it more deadly than COVID-19? (Message 1137)
Posted 8 Sep 2021 by Jim1348
This one is not related to COVID-19, so any vaccine or treatment will probably have to start from the beginning.
14) Message boards : News : Targets six, seven, eight (Message 1118)
Posted 29 Aug 2021 by Jim1348
Are those targets solved by AlphaFold already? How to compare Sidock to AlphaDock ?

Where do you see that "AlphaDock" exists? AlphaFold is for protein folding, not docking.
15) Message boards : News : Targets six, seven, eight (Message 1116)
Posted 28 Aug 2021 by Jim1348
I am glad that you are able to switch to more promising targets when they appear. This is no doubt still a rapidly-developing field, and everything is evolving rapidly (including the virus).
16) Message boards : Science : COVID-19 news (Message 1108)
Posted 12 Aug 2021 by Jim1348
A New Covid Variant On The Loose: B.1.621
A group of seven residents in a Belgian nursing home died after infection with a new variant, all of whom were fully vaccinated according to virologists on the scene. Though the vaccine used in these residents was not made public, it was likely either AstraZeneca or an mRNA vaccine such as Pfizer and Moderna, among those most frequently used in the country.

The new variant, B.1.621, has yet to receive a greek letter designation from the World Health Organization. The variant already accounts for around 2% of coronavirus infections in the United States, and as much as 10% in Miami, according to Carlos Migoya, CEO of Jackson Health System. The variant can be traced back to identification in samples from Colombia in March 2021 and according to the GISAID coronavirus database, the variant has been identified in as many as 28 countries, but potentially more.

Despite not having the official label of Variant of Interest or Concern, it should be noted that B.1.621 has certain characteristics that suggest it may be worth watching, as it could become a variant of interest or concern in the near future. Here we analyze those mutations and summarize what we know about their likely effects on transmissibility, virulence, vaccine evasion, and pathogenesis.

Looks interesting.
17) Message boards : Science : Other uses of docking than viruses? (Message 1106)
Posted 11 Aug 2021 by Jim1348
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.
18) Questions and Answers : Web site : COVID-19 news (Message 1100)
Posted 6 Aug 2021 by Jim1348
Licensed drug could reduce SARS-CoV-2 infection by up to 70 per cent, reveals study

That is quite interesting, but would probably be seen by more people in the other thread.
19) Message boards : Number crunching : Self reporting. (Message 1037)
Posted 13 Jun 2021 by Jim1348
You can use an app_config.xml:

20) Message boards : Number crunching : Deadline is too short (Message 907)
Posted 11 May 2021 by Jim1348
The default buffer of 0.1 + 0.5 days works for me. I have no SD High Priorities, and it works for practically all of my projects.
But if you load up on too many projects, BOINC sometimes has a problem handling all of them in time also.

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