Does anyone know what's the probability that Remdesivir is indeed a solution against Coronavirus?
We Made One Gram Of Remdesivir
131–140 of 236 posts
Re: We Made One Gram Of Remdesivir
#132Earlier quoted context omitted.
As someone who spent 4 years working on a PhD (wireless/RF technology) and then quit, your points 2 and 3 ring a lot of bells. I think "journal of failed experiments" is a wonderful idea.
Anyone can put a paper on arXiv. The bigger problem is that most journal editors will be skeptical of citing arXiv. If you're collaborating with more traditional academics it can be a challenge to even submit a paper with such citations. I've had to push my colleagues to cite a number of non-traditional sources: arXiv, github, and zenodo for example. Fortunately most of them agree that citations are cheap and that gi…
I think that's less true than it used to be: a lot of papers now cite bioarxiv or arxiv preprints. I've never gotten any pushback and most journals explicitly allow it.
Science: "We do allow citations to papers posted at arXiv or bioRxiv." https://www.sciencemag.org/authors/instructions-preparing-in...
Nature (and other NPG journals): "Preprints may be cited in the reference list of articles under consideration at Nature Research journals...." https://www.nature.com/nature-research/editorial-policies/pr...
Cell (and other Cell Press journals, including Neuron and Current Biology): "Posted preprints may also be included in the References list with appropriate identification information...." https://www.cell.com/cell/authors
PNAS: "Preprints are cited as follows with a DOI or preprint ID number, and the date of posting...."https://www.cell.com/cell/authors
Re: We Made One Gram Of Remdesivir
#133In my former life I was a graduate organic chemist, but I “quit” with a Masters. I loved Synthetic Chemistry as an undergrad and thought I wanted a PhD in. There were three lousy things (for me) about the career that made me bail. 1). So many syntheses have horrible yields just like this one. You’d start with grams of material to end up with micrograms. I loved solving these problems as an undergrad in books, but rea…
That's kind of my experience with research, but in physics. Already have three projects under my belt w/ no publishable results. All of them involved much more work than the other grad. students in my lab including building like three different instruments from scratch, but the other students have published. Their projects were much more "safe" than mine and their papers are pretty small, but at least they have paper…
Why would the results not be publishable?
Re: We Made One Gram Of Remdesivir
#134I was able to create several small molecule candidates which achieved docking scores of almost -18 but they still need to be assessed for their synthetic feasibility. (Docking scores of leading existing drugs (HIV inhibitors) are around -10 to -11 (the more negative the score the better), Remdesivir drug is around -13 which already entered clinical testing.
I know that binding affinity has been shown not to be the best indicator of efficacy always, but I want to know if it's feasible, if someone can help
Re: We Made One Gram Of Remdesivir
#135In my former life I was a graduate organic chemist, but I “quit” with a Masters. I loved Synthetic Chemistry as an undergrad and thought I wanted a PhD in. There were three lousy things (for me) about the career that made me bail. 1). So many syntheses have horrible yields just like this one. You’d start with grams of material to end up with micrograms. I loved solving these problems as an undergrad in books, but rea…
> They need a journal of failed chemistry because only the working stuff gets published.
I think there's theoretical value in this, and many have tried, but the incentives/disincentives for doing so isn't favorable. Here's some reasons why I think it's difficult to motivate people to publish negative results:
1) Negative results, while important in advancing science, don't get you grants.
2) Negative results need to be peer-reviewed -- there are "good" negative results (good protocol, failed result) and "bad" negative results due to bad data collection, wrong conclusions (bad protocol, failed result).
3) Given that it's so much easier to get a negative result than a positive one (as in anything there are only few ways to be right, tons of ways to be wrong), the volume of papers to review is orders of magnitude higher. Reviewers have to really sift to find the needle in the haystack. Between teaching classes, sitting on mindless committees, writing grants, mentoring grad students, etc. academics don't have that kind of time.
4) It would incentivize poor/mediocre labs to publish a lot of negative results to get their pub count up (these are the ones that currently publish unsubstantiated positive results in fly-by-night journals).
5) Bad faith authors may publish fake negative results to throw others off a promising line of inquiry.
(Note: some of these disincentives also apply to positive results in journals today)
The current method I know for exchanging "good" negative results is word-of-mouth, usually during post-conference drinks at the bar. (works for tech too!) I'm not sure if it's possible to arrange incentives in such a way as to make publishing "good" negative results worthwhile.
EDIT: there are exceptions. If the space of solutions is known a priori and bounded (say only n ways to do something), then publishing n results if even all n are failures is worthwhile. This situation doesn't come up all the time (the solution space is often open), but when it does, it's worth publishing all n results.
Re: We Made One Gram Of Remdesivir
#136This article really reinforces my choice to drop ochem in college. It's funny how deciphering assembly code seems downright mundane compared to this jargon. Like, I get how given the process you could recreate things, or you could devise possible reactions based on electron shells and bonding tendencies, but how do researchers even figure out how to make these reactions happen? Especially when they require -100C, or…
Isn’t there analytical chemistry software?
You must utilize the software beyond the vendors' design goals before you can be as effective as you could before there was software.
Re: We Made One Gram Of Remdesivir
#137[deleted]
Re: We Made One Gram Of Remdesivir
#138I was able to create several small molecule candidates which achieved docking scores of almost -18 but they still need to be assessed for their synthetic feasibility. (Docking scores of leading existing drugs (HIV inhibitors) are around -10 to -11 (the more negative the score the better), Remdesivir drug is around -13 which already entered clinical testing. I know that binding affinity has been shown not to be the be…
Are you a chemist?
Re: We Made One Gram Of Remdesivir
#139Earlier quoted context omitted.
Isn’t there analytical chemistry software?
Yes, but good luck interpreting the output if you aren't an accomplished synthetic organic chemist.
Analysts can benefit tremendously from better knowledge of research, synthesis or process work, and vice versa.
But great professionalism can also be developed without as much cross-functionality between subdisciplines.
Like many things, detailed efforts unique to the subprofession can be the most essential.
Re: We Made One Gram Of Remdesivir
#140In my former life I was a graduate organic chemist, but I “quit” with a Masters. I loved Synthetic Chemistry as an undergrad and thought I wanted a PhD in. There were three lousy things (for me) about the career that made me bail. 1). So many syntheses have horrible yields just like this one. You’d start with grams of material to end up with micrograms. I loved solving these problems as an undergrad in books, but rea…
As an IT guy, I am wondering why this is still a mostly manual and rather dangerous process. Surely programmable machines can be built to process reagents in a safe and flexible way?
Chemistry uses a very large set of "primitive steps" (from reactants and catalyzers to reactors and reaction conditions), so any such machine will have a narrow set of reactions it can produce. Unless of course, your automation machine has the capacity of assembling and dissembling equipment.
Besides, cleaning everything is very machine unfriendly.