Muhammad Radifar
@radifar.bsky.social
Software Engineer - Computational Chemist
https://github.com/radifar
https://github.com/radifar
Reposted by Muhammad Radifar
Introducing HMPV-GLUE: a comprehensive, open-source resource for human metapneumovirus (HMPV) research.
With the recent rise in HMPV cases in China, this tool offers timely support for the scientific community.
github.com/giffordlabcv...
With the recent rise in HMPV cases in China, this tool offers timely support for the scientific community.
github.com/giffordlabcv...
January 9, 2025 at 1:57 PM
Introducing HMPV-GLUE: a comprehensive, open-source resource for human metapneumovirus (HMPV) research.
With the recent rise in HMPV cases in China, this tool offers timely support for the scientific community.
github.com/giffordlabcv...
With the recent rise in HMPV cases in China, this tool offers timely support for the scientific community.
github.com/giffordlabcv...
Reposted by Muhammad Radifar
Happy New Year to all the BioExcel community! 🎇
Our first #webinar of the year will feature Attilio Vargiu who will talk about how to account for protein and ligand flexibility in molecular docking
🗓️ 28 January 2025, 15:00 CET
➡️ bit.ly/40q3gKG
#moleculardocking #virtualscreening #compchem
Our first #webinar of the year will feature Attilio Vargiu who will talk about how to account for protein and ligand flexibility in molecular docking
🗓️ 28 January 2025, 15:00 CET
➡️ bit.ly/40q3gKG
#moleculardocking #virtualscreening #compchem
January 8, 2025 at 12:40 PM
Happy New Year to all the BioExcel community! 🎇
Our first #webinar of the year will feature Attilio Vargiu who will talk about how to account for protein and ligand flexibility in molecular docking
🗓️ 28 January 2025, 15:00 CET
➡️ bit.ly/40q3gKG
#moleculardocking #virtualscreening #compchem
Our first #webinar of the year will feature Attilio Vargiu who will talk about how to account for protein and ligand flexibility in molecular docking
🗓️ 28 January 2025, 15:00 CET
➡️ bit.ly/40q3gKG
#moleculardocking #virtualscreening #compchem
Reposted by Muhammad Radifar
Rigorous first-principles methods are slow for big biomolecules. PM6 is faster but has gaps in complex interactions. Nováček et al. propose PM6-ML (integrated into MOPAC --Molecular Orbital PACkage) achieving near-DFT accuracy for large-scale simulations. pubs.acs.org/doi/full/10....
PM6-ML: The Synergy of Semiempirical Quantum Chemistry and Machine Learning Transformed into a Practical Computational Method
Machine learning (ML) methods offer a promising route to the construction of universal molecular potentials with high accuracy and low computational cost. It is becoming evident that integrating physi...
pubs.acs.org
January 6, 2025 at 2:35 PM
Rigorous first-principles methods are slow for big biomolecules. PM6 is faster but has gaps in complex interactions. Nováček et al. propose PM6-ML (integrated into MOPAC --Molecular Orbital PACkage) achieving near-DFT accuracy for large-scale simulations. pubs.acs.org/doi/full/10....
Reposted by Muhammad Radifar
This is what I have added to my .bashrc file
alias untar="tar xvf"
alias untgz="tar xvzf"
alias untargz="tar xvzf"
alias unbz2="tar xvjf"
#Linux #Bash #bioinformatics
alias untar="tar xvf"
alias untgz="tar xvzf"
alias untargz="tar xvzf"
alias unbz2="tar xvjf"
#Linux #Bash #bioinformatics
December 30, 2024 at 12:41 AM
This is what I have added to my .bashrc file
alias untar="tar xvf"
alias untgz="tar xvzf"
alias untargz="tar xvzf"
alias unbz2="tar xvjf"
#Linux #Bash #bioinformatics
alias untar="tar xvf"
alias untgz="tar xvzf"
alias untargz="tar xvzf"
alias unbz2="tar xvjf"
#Linux #Bash #bioinformatics
Reposted by Muhammad Radifar
Hi Bluesky community! 👋
Are you looking forward to 2025 as much as we are? 👀
We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look!
➡️ s.embl.org/poster-bl
#EMBLEvents #molecularbiology #lifesciencetraining
Are you looking forward to 2025 as much as we are? 👀
We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look!
➡️ s.embl.org/poster-bl
#EMBLEvents #molecularbiology #lifesciencetraining
December 13, 2024 at 9:06 AM
Hi Bluesky community! 👋
Are you looking forward to 2025 as much as we are? 👀
We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look!
➡️ s.embl.org/poster-bl
#EMBLEvents #molecularbiology #lifesciencetraining
Are you looking forward to 2025 as much as we are? 👀
We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look!
➡️ s.embl.org/poster-bl
#EMBLEvents #molecularbiology #lifesciencetraining
Reposted by Muhammad Radifar
Online Symposium on Molecular Machine Learning on January 16th, organized by the Glorius Group at @unimuenster.bsky.social - with @fjduarte.bsky.social, @kulikgroup.bsky.social, Bingqing Cheng, Matthew Sigman: www.uni-muenster.de/Chemie.oc/gl.... Registration is free and highly recommended!
December 17, 2024 at 3:48 PM
Online Symposium on Molecular Machine Learning on January 16th, organized by the Glorius Group at @unimuenster.bsky.social - with @fjduarte.bsky.social, @kulikgroup.bsky.social, Bingqing Cheng, Matthew Sigman: www.uni-muenster.de/Chemie.oc/gl.... Registration is free and highly recommended!
Reposted by Muhammad Radifar
We're excited to announce a generous $3.3M grant from the Bill & Melinda Gates Foundation. This support reinforces our mission to inspire new transformative open science models and pioneer a shift away from traditional publishing models and APCs. Read more on The Official PLOS Blog. plos.io/4iynqsD
PLOS receives $3.3M grant to support Open Access publishing & business model transformation - The Official PLOS Blog
Note: PLOS issued the following press release on Tuesday, December 10. PLOS has been awarded a $3.3million grant from the Bill &…
theplosblog.plos.org
December 18, 2024 at 7:07 PM
We're excited to announce a generous $3.3M grant from the Bill & Melinda Gates Foundation. This support reinforces our mission to inspire new transformative open science models and pioneer a shift away from traditional publishing models and APCs. Read more on The Official PLOS Blog. plos.io/4iynqsD
Reposted by Muhammad Radifar
Finally!
Microsoft just released a tool that lets you convert Office files to Markdown. Never thought I'd see the day.
Google also added Markdown export to Google Docs a few months ago.
github.com/microsoft/markitdown
Google also added Markdown export to Google Docs a few months ago.
github.com/microsoft/markitdown
GitHub - microsoft/markitdown: Python tool for converting files and office documents to Markdown.
Python tool for converting files and office documents to Markdown. - microsoft/markitdown
github.com
December 14, 2024 at 12:00 AM
Finally!
Reposted by Muhammad Radifar
For those following the @prof-ajay-jain.bsky.social /Cleaves/ @wpwalters.bsky.social preprint re: DiffDock @gcorso.bsky.social
I have read some of the back-&-forth between the author groups
As a practitioner in the field for > 20 yrs (academic side), here is my take: 🧵
I have read some of the back-&-forth between the author groups
As a practitioner in the field for > 20 yrs (academic side), here is my take: 🧵
@dereklowe.bsky.social honing in on the same bottom line message from @wpwalters.bsky.social @prof-ajay-jain.bsky.social
it's so true and hits so hard:
it's so true and hits so hard:
December 9, 2024 at 3:46 AM
For those following the @prof-ajay-jain.bsky.social /Cleaves/ @wpwalters.bsky.social preprint re: DiffDock @gcorso.bsky.social
I have read some of the back-&-forth between the author groups
As a practitioner in the field for > 20 yrs (academic side), here is my take: 🧵
I have read some of the back-&-forth between the author groups
As a practitioner in the field for > 20 yrs (academic side), here is my take: 🧵
Reposted by Muhammad Radifar
I was taught in grad school that scientists should have 3 versions of talks about their work ready: a 30 second “elevator pitch,” a 12 minute conference length talk, and a 40 minute seminar length talk.
I think we should also have a short version aimed at non-scientists.
I think we should also have a short version aimed at non-scientists.
December 8, 2024 at 4:22 PM
I was taught in grad school that scientists should have 3 versions of talks about their work ready: a 30 second “elevator pitch,” a 12 minute conference length talk, and a 40 minute seminar length talk.
I think we should also have a short version aimed at non-scientists.
I think we should also have a short version aimed at non-scientists.
Reposted by Muhammad Radifar
H5N1 , we are one mutation away from Human-to-human transmission. I hope that lessons from the Covid pandemic have been learned .
A single mutation in bovine influenza H5N1 hemagglutinin switches specificity to human receptors
In 2024, several human infections with highly pathogenic clade 2.3.4.4b bovine influenza H5N1 viruses in the United States raised concerns about their capability for bovine-to-human or even human-to-h...
www.science.org
December 7, 2024 at 8:54 AM
H5N1 , we are one mutation away from Human-to-human transmission. I hope that lessons from the Covid pandemic have been learned .
Reposted by Muhammad Radifar
@dereklowe.bsky.social honing in on the same bottom line message from @wpwalters.bsky.social @prof-ajay-jain.bsky.social
it's so true and hits so hard:
it's so true and hits so hard:
December 6, 2024 at 8:57 PM
@dereklowe.bsky.social honing in on the same bottom line message from @wpwalters.bsky.social @prof-ajay-jain.bsky.social
it's so true and hits so hard:
it's so true and hits so hard:
Reposted by Muhammad Radifar
We're excited to work with @omsf.io OpenADMET and @polarishub.io to bring you this blind predictive modeling community challenge!
If you're developing predictive models for drug discovery---potency or ADMET---here's your chance to test them prospectively on real discovery data from ASAP!
If you're developing predictive models for drug discovery---potency or ADMET---here's your chance to test them prospectively on real discovery data from ASAP!
🦠 We’re excited to announce our first competition in partnership with @asapdiscovery.bsky.social and @omsf.io!
Test your skills across three sub-challenges revolving around SARS-CoV-2 and MERS-CoV Mpro🧵
Full details: polarishub.io/competitions
Blog: polarishub.io/blog/antivir...
Test your skills across three sub-challenges revolving around SARS-CoV-2 and MERS-CoV Mpro🧵
Full details: polarishub.io/competitions
Blog: polarishub.io/blog/antivir...
December 3, 2024 at 4:46 PM
We're excited to work with @omsf.io OpenADMET and @polarishub.io to bring you this blind predictive modeling community challenge!
If you're developing predictive models for drug discovery---potency or ADMET---here's your chance to test them prospectively on real discovery data from ASAP!
If you're developing predictive models for drug discovery---potency or ADMET---here's your chance to test them prospectively on real discovery data from ASAP!
Reposted by Muhammad Radifar
Hey 👋 I'm new here and I did my best to compile some starter packs to help other new people in the same community!
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
December 5, 2024 at 8:27 PM
Hey 👋 I'm new here and I did my best to compile some starter packs to help other new people in the same community!
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
Reposted by Muhammad Radifar
Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research.
A Place of Joy.
A Place of Joy.
December 3, 2024 at 2:10 PM
Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
Reposted by Muhammad Radifar
🚨Our Machine Learning Force Field Mattersim is now available! 🚨
Check it out here 👇
msft.it/6013oBZLt
The force field is designed to be used on a vast range of temperatures and pressures, try it yourself :)
Feedback and suggestions are very welcome!
Check it out here 👇
msft.it/6013oBZLt
The force field is designed to be used on a vast range of temperatures and pressures, try it yourself :)
Feedback and suggestions are very welcome!
GitHub - microsoft/mattersim: MatterSim: A deep learning atomistic model across elements, temperatures and pressures.
MatterSim: A deep learning atomistic model across elements, temperatures and pressures. - microsoft/mattersim
msft.it
December 3, 2024 at 5:11 PM
🚨Our Machine Learning Force Field Mattersim is now available! 🚨
Check it out here 👇
msft.it/6013oBZLt
The force field is designed to be used on a vast range of temperatures and pressures, try it yourself :)
Feedback and suggestions are very welcome!
Check it out here 👇
msft.it/6013oBZLt
The force field is designed to be used on a vast range of temperatures and pressures, try it yourself :)
Feedback and suggestions are very welcome!
Reposted by Muhammad Radifar
There’s a new Practical Cheminformatics post, “Some Thoughts on Dataset Splitting,” (with code and a robot cartoon) at practicalcheminformatics.blogspot.com/2024/11/some... .
November 18, 2024 at 1:34 PM
There’s a new Practical Cheminformatics post, “Some Thoughts on Dataset Splitting,” (with code and a robot cartoon) at practicalcheminformatics.blogspot.com/2024/11/some... .
Reposted by Muhammad Radifar
I didn’t know I could REPL Python in a notebookesque way like this. TIL!
Oh yeah I saw— that's what my reply was to lol 😆
I no joke think about these two videos periodically which surprisingly standup even 4-5 years later
But personally I cheat & do both by mostly writing .py files in VS Code but using Jupyter code cells within it
code.visualstudio.com/docs/python/...
I no joke think about these two videos periodically which surprisingly standup even 4-5 years later
But personally I cheat & do both by mostly writing .py files in VS Code but using Jupyter code cells within it
code.visualstudio.com/docs/python/...
Working with Jupyter code cells in the Python Interactive window
Working with Jupyter code cells in the Python Interactive window
code.visualstudio.com
December 1, 2024 at 2:36 PM
I didn’t know I could REPL Python in a notebookesque way like this. TIL!
Reposted by Muhammad Radifar
Doing good science is 90% finding a science buddy to constantly talk to about the project.
November 9, 2024 at 10:53 PM
Doing good science is 90% finding a science buddy to constantly talk to about the project.