Vladas Oleinikovas
@oleinikovasv.bsky.social
Computational Chemist - CADD/TPD; PhD Chemistry at UCL; BA, MSci Natural Sciences, Chemistry (Cantab).
Reposted by Vladas Oleinikovas
This is the moment we've worked toward for a long time: First public disclosure of the @asapdiscovery.bsky.social pan-coronavirus antiviral aiming to help keep humanity safe from future pandemic threats like MERS-CoV and other bat coronaviruses.
📢Important announcement! Today, the @asapdiscovery.bsky.social consortium disclosed the structure of our preclinical candidate, ASAP-0017445, a promising broad-spectrum antiviral with potent activity against SARS-CoV2 and other viruses belonging to the same family. (1/10)
March 25, 2025 at 7:47 PM
This is the moment we've worked toward for a long time: First public disclosure of the @asapdiscovery.bsky.social pan-coronavirus antiviral aiming to help keep humanity safe from future pandemic threats like MERS-CoV and other bat coronaviruses.
Reposted by Vladas Oleinikovas
Check out this great BioEmu talk by @jjimenezluna.bsky.social and @yuxie.bsky.social in the VantAI lecture series. Thank you for hosting @mmbronstein.bsky.social @lucanaef.bsky.social
www.youtube.com/watch?v=8vsT...
www.youtube.com/watch?v=8vsT...
Emulation of protein equilibrium ensembles with generative deep learning | José Jiménez Luna, Yu Xie
YouTube video by VantAI
www.youtube.com
February 17, 2025 at 9:23 AM
Check out this great BioEmu talk by @jjimenezluna.bsky.social and @yuxie.bsky.social in the VantAI lecture series. Thank you for hosting @mmbronstein.bsky.social @lucanaef.bsky.social
www.youtube.com/watch?v=8vsT...
www.youtube.com/watch?v=8vsT...
Reposted by Vladas Oleinikovas
Basically, novelty is not defined by time in the PDB.
Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Have protein-ligand co-folding methods moved beyond memorisation?
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...
www.biorxiv.org
February 8, 2025 at 10:38 AM
Basically, novelty is not defined by time in the PDB.
Reposted by Vladas Oleinikovas
We’ve been benchmarking deep learning co-folding methods for protein-ligand complex prediction, leading to the creation of 🌹Runs N’ Poses🌹. Great effort by @peterskrinjar.bsky.social and @jeeberhardt.bsky.social putting this together so quickly. Please have a look, excited for community feedback!
Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Have protein-ligand co-folding methods moved beyond memorisation?
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...
www.biorxiv.org
February 8, 2025 at 10:30 AM
We’ve been benchmarking deep learning co-folding methods for protein-ligand complex prediction, leading to the creation of 🌹Runs N’ Poses🌹. Great effort by @peterskrinjar.bsky.social and @jeeberhardt.bsky.social putting this together so quickly. Please have a look, excited for community feedback!
Reposted by Vladas Oleinikovas
This is the kind of benchmarking work the field needs!
Here's a year-end update from #PLINDER. It's been really great working on this project and all the other projects that it has kickstarted - the gift that keeps on giving.
Happy holidays everyone!
www.plinder.sh/blog/updates
Happy holidays everyone!
www.plinder.sh/blog/updates
Updates
Updates
www.plinder.sh
December 24, 2024 at 4:06 PM
This is the kind of benchmarking work the field needs!
End of year notes from #PLINDER team!
It's been an incredible year for datasets and benchmarks for the #ML / #CompChem / #CompBio community.
Superbly grateful for the positive responses, constructive feedback and contributions!
It's just the start, lots more in 2️⃣0️⃣2️⃣5️⃣ 🎉
www.plinder.sh/blog/updates
It's been an incredible year for datasets and benchmarks for the #ML / #CompChem / #CompBio community.
Superbly grateful for the positive responses, constructive feedback and contributions!
It's just the start, lots more in 2️⃣0️⃣2️⃣5️⃣ 🎉
www.plinder.sh/blog/updates
Updates
Updates
www.plinder.sh
December 24, 2024 at 3:04 PM
End of year notes from #PLINDER team!
It's been an incredible year for datasets and benchmarks for the #ML / #CompChem / #CompBio community.
Superbly grateful for the positive responses, constructive feedback and contributions!
It's just the start, lots more in 2️⃣0️⃣2️⃣5️⃣ 🎉
www.plinder.sh/blog/updates
It's been an incredible year for datasets and benchmarks for the #ML / #CompChem / #CompBio community.
Superbly grateful for the positive responses, constructive feedback and contributions!
It's just the start, lots more in 2️⃣0️⃣2️⃣5️⃣ 🎉
www.plinder.sh/blog/updates
@asapdiscovery.bsky.social is accumulating a great resource for learning real world drug discovery, not obscured by corporate filters. Lots of good science and strategy decision making examples. 👏
This comes as a bonus, in addition to progressing pandemic preparedness data packs and molecules! 💊
This comes as a bonus, in addition to progressing pandemic preparedness data packs and molecules! 💊
Talking to clinicians last week I was reminded about the importance of TPPs and TCP in drug discovery. I'm a fan of these as the place where can meet and build a common language to get new treatments right. Here's a worked example from @asapdiscovery.bsky.social
www.youtube.com/watch?v=3frZ...
www.youtube.com/watch?v=3frZ...
Ed Griffen: Focusing projects with Target Product Profiles and Target Candidate Profiles
YouTube video by AViDD Open Science Forum
www.youtube.com
December 12, 2024 at 10:11 AM
@asapdiscovery.bsky.social is accumulating a great resource for learning real world drug discovery, not obscured by corporate filters. Lots of good science and strategy decision making examples. 👏
This comes as a bonus, in addition to progressing pandemic preparedness data packs and molecules! 💊
This comes as a bonus, in addition to progressing pandemic preparedness data packs and molecules! 💊
Reposted by Vladas Oleinikovas
Good news: You can post video on Bluesky now!
Bad news: Only up to 60s.
So here’s a clipped version of my latest video about a paper exploring the landscape of possible molecular glue degradation targets:
Bad news: Only up to 60s.
So here’s a clipped version of my latest video about a paper exploring the landscape of possible molecular glue degradation targets:
November 20, 2024 at 2:22 AM
Good news: You can post video on Bluesky now!
Bad news: Only up to 60s.
So here’s a clipped version of my latest video about a paper exploring the landscape of possible molecular glue degradation targets:
Bad news: Only up to 60s.
So here’s a clipped version of my latest video about a paper exploring the landscape of possible molecular glue degradation targets:
📢 Join us this Friday for a talk by @jeremywohlwend.bsky.social & @gcorso.bsky.social on their recent publication of #Boltz-1 - a new #opensource SOTA model for 3D biomolecular structure prediction.
🕰️: Fri, Dec 06 - 4p CET/10a ET
🔗: genaiindrugdiscovery.com
🕰️: Fri, Dec 06 - 4p CET/10a ET
🔗: genaiindrugdiscovery.com
December 3, 2024 at 2:00 PM
📢 Join us this Friday for a talk by @jeremywohlwend.bsky.social & @gcorso.bsky.social on their recent publication of #Boltz-1 - a new #opensource SOTA model for 3D biomolecular structure prediction.
🕰️: Fri, Dec 06 - 4p CET/10a ET
🔗: genaiindrugdiscovery.com
🕰️: Fri, Dec 06 - 4p CET/10a ET
🔗: genaiindrugdiscovery.com