Rohan Gorantla
@rohangorantla.bsky.social
Developing ML methods for Drug Discovery @ Novartis 🧬💻 | prev: PhD student @ University of Edinburgh with Toni Mey
Pinned
Rohan Gorantla
@rohangorantla.bsky.social
· Nov 20
Hi Bluesky! 👋
I'm a PhD student working on ML methods for Drug Discovery at Edinburgh with @ppxasjsm.bsky.social. Looking forward to connecting with fellow ML, CompChem, Bio and Drug Discovery folks!🧬💊💻
Sharing starter packs in 🧵 below that I found helpful in finding people working in the domain.
I'm a PhD student working on ML methods for Drug Discovery at Edinburgh with @ppxasjsm.bsky.social. Looking forward to connecting with fellow ML, CompChem, Bio and Drug Discovery folks!🧬💊💻
Sharing starter packs in 🧵 below that I found helpful in finding people working in the domain.
Interested in doing PhD at the intersection of ML and Drug Discovery🧬💊? Great opportunity to work with an amazing supervisor @ppxasjsm.bsky.social and apply ML to optimize fragment-to-lead decision-making.
🔗 www.findaphd.com/phds/project...
#PhD #MachineLearning #DrugDiscovery
🔗 www.findaphd.com/phds/project...
#PhD #MachineLearning #DrugDiscovery
Active Learning for Optimising Fragment-to-Lead Decision-Making in High-Throughput Experiments at University of Edinburgh on FindAPhD.com
PhD Project - Active Learning for Optimising Fragment-to-Lead Decision-Making in High-Throughput Experiments at University of Edinburgh, listed on FindAPhD.com
www.findaphd.com
February 27, 2025 at 1:42 PM
Interested in doing PhD at the intersection of ML and Drug Discovery🧬💊? Great opportunity to work with an amazing supervisor @ppxasjsm.bsky.social and apply ML to optimize fragment-to-lead decision-making.
🔗 www.findaphd.com/phds/project...
#PhD #MachineLearning #DrugDiscovery
🔗 www.findaphd.com/phds/project...
#PhD #MachineLearning #DrugDiscovery
Reposted by Rohan Gorantla
Congratulations to Dr @rohangorantla.bsky.social for passing his PhD viva today marking the first official Mey group Dr. Thank you to Andrea Volkamer and Chris Wood for conducting the viva and all the best on your future scientific adventures Rohan!
January 23, 2025 at 7:06 PM
Congratulations to Dr @rohangorantla.bsky.social for passing his PhD viva today marking the first official Mey group Dr. Thank you to Andrea Volkamer and Chris Wood for conducting the viva and all the best on your future scientific adventures Rohan!
Reposted by Rohan Gorantla
I'm co-hosting the first Builders in Biology meetup with Samarth Jajoo in Hyderabad on Jan 7 at the @popvax.com lab. It's an informal gathering to discuss research ideas people are excited about. Please feel free to register here if you're interested: lu.ma/po606g0h
HYD: builders in biology · Luma
Casual evening of discussing ideas on the frontier of biology — come chat about whatever research you're excited to do. Snacks provided!
Organized by Silver…
lu.ma
January 2, 2025 at 11:34 AM
I'm co-hosting the first Builders in Biology meetup with Samarth Jajoo in Hyderabad on Jan 7 at the @popvax.com lab. It's an informal gathering to discuss research ideas people are excited about. Please feel free to register here if you're interested: lu.ma/po606g0h
Reposted by Rohan Gorantla
2025 will be the year of AI for science
Leveraging all the things we've recently learned training AI models for 1000x impact in science
and this will need data!
More details: huggingface.co/blog/lemater...
Thread:
...
Leveraging all the things we've recently learned training AI models for 1000x impact in science
and this will need data!
More details: huggingface.co/blog/lemater...
Thread:
...
December 14, 2024 at 10:22 AM
2025 will be the year of AI for science
Leveraging all the things we've recently learned training AI models for 1000x impact in science
and this will need data!
More details: huggingface.co/blog/lemater...
Thread:
...
Leveraging all the things we've recently learned training AI models for 1000x impact in science
and this will need data!
More details: huggingface.co/blog/lemater...
Thread:
...
Reposted by Rohan Gorantla
How can we build an Al virtual cell that simulates all functions and interactions of a cell? How will it transform research and drive breakthroughs in programmable biology, drug discovery and personalized medicine?
Take a look at our paper in @cellpress.bsky.social!
www.cell.com/cell/fulltex...
Take a look at our paper in @cellpress.bsky.social!
www.cell.com/cell/fulltex...
December 12, 2024 at 8:09 PM
How can we build an Al virtual cell that simulates all functions and interactions of a cell? How will it transform research and drive breakthroughs in programmable biology, drug discovery and personalized medicine?
Take a look at our paper in @cellpress.bsky.social!
www.cell.com/cell/fulltex...
Take a look at our paper in @cellpress.bsky.social!
www.cell.com/cell/fulltex...
Reposted by Rohan Gorantla
We’re thrilled to share our Nature Methods review on #CellPainting — your go-to resource for mastering Cell Painting! From MOA and toxicity prediction to contributing to candidate drugs in clinical trials, we’ve distilled 10 years of insights!
Cell Painting: a decade of discovery and innovation in cellular imaging - Nature Methods
This Review synthesizes the literature from over 10 years of Cell Painting for image-based profiling and highlights how advances in this technology enable new biological discovery of cellular phenotyp...
www.nature.com
December 5, 2024 at 5:35 PM
We’re thrilled to share our Nature Methods review on #CellPainting — your go-to resource for mastering Cell Painting! From MOA and toxicity prediction to contributing to candidate drugs in clinical trials, we’ve distilled 10 years of insights!
Reposted by Rohan Gorantla
Excellent new paper (with code) by my former colleagues Steven Kearnes and Patrick Riley describing a procedure for associating confidence levels with regression model predictions in drug discovery. pubs.acs.org/doi/10.1021/...
Ordinal Confidence Level Assignments for Regression Model Predictions
We present a simple method for assigning accurate confidence levels to molecular property predictions from regression models. These confidence levels are easy to interpret and useful for making decisi...
pubs.acs.org
December 10, 2024 at 1:02 PM
Excellent new paper (with code) by my former colleagues Steven Kearnes and Patrick Riley describing a procedure for associating confidence levels with regression model predictions in drug discovery. pubs.acs.org/doi/10.1021/...
Reposted by Rohan Gorantla
Entropy is one of those formulas that many of us learn, swallow whole, and even use regularly without really understanding.
(E.g., where does that “log” come from? Are there other possible formulas?)
Yet there's an intuitive & almost inevitable way to arrive at this expression.
(E.g., where does that “log” come from? Are there other possible formulas?)
Yet there's an intuitive & almost inevitable way to arrive at this expression.
December 9, 2024 at 10:44 PM
Entropy is one of those formulas that many of us learn, swallow whole, and even use regularly without really understanding.
(E.g., where does that “log” come from? Are there other possible formulas?)
Yet there's an intuitive & almost inevitable way to arrive at this expression.
(E.g., where does that “log” come from? Are there other possible formulas?)
Yet there's an intuitive & almost inevitable way to arrive at this expression.
Reposted by Rohan Gorantla
After two years, our paper on generative models for structure-based drug design is finally out in @natcomputsci.bsky.social
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Structure-based drug design with equivariant diffusion models - Nature Computational Science
This work applies diffusion models to conditional molecule generation and shows how they can be used to tackle various structure-based drug design problems
www.nature.com
December 9, 2024 at 2:00 PM
After two years, our paper on generative models for structure-based drug design is finally out in @natcomputsci.bsky.social
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Reposted by Rohan Gorantla
We trained a model to co-generate protein sequence and structure by working in the ESMFold latent space, which encodes both. PLAID only requires sequences for training but generates all-atom structures!
Really proud of @amyxlu.bsky.social 's effort leading this project end-to-end!
Really proud of @amyxlu.bsky.social 's effort leading this project end-to-end!
December 9, 2024 at 2:58 PM
We trained a model to co-generate protein sequence and structure by working in the ESMFold latent space, which encodes both. PLAID only requires sequences for training but generates all-atom structures!
Really proud of @amyxlu.bsky.social 's effort leading this project end-to-end!
Really proud of @amyxlu.bsky.social 's effort leading this project end-to-end!
Reposted by Rohan Gorantla
Can we do alchemistry with zinc? That’s the question we set out to answer in our paper tinyurl.com/j88h4n73. where we calculated binding free energies (RBFE) of known inhibitors with cross-class inhibition against serine- and metallo-β-lactamases, using open-source RBFE methods and metal models.
Protocols for Metallo- and Serine-β-Lactamase Free Energy Predictions: Insights from Cross-Class Inhibitors
While relative binding free energy (RBFE) calculations using alchemical methods are routinely carried out for many pharmaceutically relevant protein targets, challenges remain. For example, open-sourc...
tinyurl.com
December 6, 2024 at 3:01 PM
Can we do alchemistry with zinc? That’s the question we set out to answer in our paper tinyurl.com/j88h4n73. where we calculated binding free energies (RBFE) of known inhibitors with cross-class inhibition against serine- and metallo-β-lactamases, using open-source RBFE methods and metal models.
Reposted by Rohan Gorantla
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 6, 2024 at 8:39 AM
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
👀What tools are you all using for finding literature and creating scientific figures? 📚🎨
Here's what I found useful - would love to hear your favourites!
🧵1/4
#Science #AcademicSky #PhDSky
Here's what I found useful - would love to hear your favourites!
🧵1/4
#Science #AcademicSky #PhDSky
December 4, 2024 at 12:58 PM
👀What tools are you all using for finding literature and creating scientific figures? 📚🎨
Here's what I found useful - would love to hear your favourites!
🧵1/4
#Science #AcademicSky #PhDSky
Here's what I found useful - would love to hear your favourites!
🧵1/4
#Science #AcademicSky #PhDSky
Reposted by Rohan Gorantla
Releasing SmolVLM, a small 2 billion parameters Vision+Language Model (VLM) built for on-device/in-browser inference with images/videos.
Outperforms all models at similar GPU RAM usage and tokens throughputs
Blog post: huggingface.co/blog/smolvlm
Outperforms all models at similar GPU RAM usage and tokens throughputs
Blog post: huggingface.co/blog/smolvlm
November 26, 2024 at 4:58 PM
Releasing SmolVLM, a small 2 billion parameters Vision+Language Model (VLM) built for on-device/in-browser inference with images/videos.
Outperforms all models at similar GPU RAM usage and tokens throughputs
Blog post: huggingface.co/blog/smolvlm
Outperforms all models at similar GPU RAM usage and tokens throughputs
Blog post: huggingface.co/blog/smolvlm
Reposted by Rohan Gorantla
Exciting opportunity to intern with me 🙋♀️ & the entire research unit lead by @jhartford.bsky.social 🧠 on single-cell representation challenges 🦠 in gene perturbation imaging data 🧬 Come join Valence Labs London office 🇬🇧 powered by @recursionpharma.bsky.social: job-boards.greenhouse.io/valencelabs/...
November 25, 2024 at 11:00 AM
Exciting opportunity to intern with me 🙋♀️ & the entire research unit lead by @jhartford.bsky.social 🧠 on single-cell representation challenges 🦠 in gene perturbation imaging data 🧬 Come join Valence Labs London office 🇬🇧 powered by @recursionpharma.bsky.social: job-boards.greenhouse.io/valencelabs/...
Reposted by Rohan Gorantla
Hi Bluesky! 👋
I'm a PhD student working on ML methods for Drug Discovery at Edinburgh with @ppxasjsm.bsky.social. Looking forward to connecting with fellow ML, CompChem, Bio and Drug Discovery folks!🧬💊💻
Sharing starter packs in 🧵 below that I found helpful in finding people working in the domain.
I'm a PhD student working on ML methods for Drug Discovery at Edinburgh with @ppxasjsm.bsky.social. Looking forward to connecting with fellow ML, CompChem, Bio and Drug Discovery folks!🧬💊💻
Sharing starter packs in 🧵 below that I found helpful in finding people working in the domain.
November 20, 2024 at 2:14 PM
Hi Bluesky! 👋
I'm a PhD student working on ML methods for Drug Discovery at Edinburgh with @ppxasjsm.bsky.social. Looking forward to connecting with fellow ML, CompChem, Bio and Drug Discovery folks!🧬💊💻
Sharing starter packs in 🧵 below that I found helpful in finding people working in the domain.
I'm a PhD student working on ML methods for Drug Discovery at Edinburgh with @ppxasjsm.bsky.social. Looking forward to connecting with fellow ML, CompChem, Bio and Drug Discovery folks!🧬💊💻
Sharing starter packs in 🧵 below that I found helpful in finding people working in the domain.
Reposted by Rohan Gorantla
Together with @Novartis and the @theNCI using a fragment-based approach, we discovered novel hits which bound in the KRas "Switch I/II Pocket" and optimised these via a macrocyclization strategy. It was great fun.
chemrxiv.org/engage/chemr...
#computationalchemistry #medchem #compchem
chemrxiv.org/engage/chemr...
#computationalchemistry #medchem #compchem
Reversible Small Molecule pan-Ras Inhibitors Display Tunable Affinity for the Active and Inactive forms of Ras.
Activating mutations of Ras are one of the most prevalent drivers of cancer and are often associated with poor clinical outcomes. Despite FDA approval for two irreversible inhibitors that target the i...
chemrxiv.org
November 22, 2024 at 9:42 AM
Together with @Novartis and the @theNCI using a fragment-based approach, we discovered novel hits which bound in the KRas "Switch I/II Pocket" and optimised these via a macrocyclization strategy. It was great fun.
chemrxiv.org/engage/chemr...
#computationalchemistry #medchem #compchem
chemrxiv.org/engage/chemr...
#computationalchemistry #medchem #compchem
Reposted by Rohan Gorantla
A vertical takeoff of life science with #AI LLLMs.
Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks!
Unprecedented progress, reviewed in the new Ground Truths
erictopol.substack.com/p/learning-t...
Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks!
Unprecedented progress, reviewed in the new Ground Truths
erictopol.substack.com/p/learning-t...
November 24, 2024 at 6:12 PM
A vertical takeoff of life science with #AI LLLMs.
Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks!
Unprecedented progress, reviewed in the new Ground Truths
erictopol.substack.com/p/learning-t...
Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks!
Unprecedented progress, reviewed in the new Ground Truths
erictopol.substack.com/p/learning-t...
Reposted by Rohan Gorantla
🚀 P2Rank 2.5 now offers #ChimeraX visualizations of ligand-binding site predictions (alongside #PyMOL ones)! Huge thanks to @javierutges.bsky.social and ChimeraX team for inspiration and help.
Release Details: github.com/rdk/p2rank/r...
💡 Feedback welcome!
#Bioinformatics #DrugDiscovery
Release Details: github.com/rdk/p2rank/r...
💡 Feedback welcome!
#Bioinformatics #DrugDiscovery
November 16, 2024 at 7:15 PM
🚀 P2Rank 2.5 now offers #ChimeraX visualizations of ligand-binding site predictions (alongside #PyMOL ones)! Huge thanks to @javierutges.bsky.social and ChimeraX team for inspiration and help.
Release Details: github.com/rdk/p2rank/r...
💡 Feedback welcome!
#Bioinformatics #DrugDiscovery
Release Details: github.com/rdk/p2rank/r...
💡 Feedback welcome!
#Bioinformatics #DrugDiscovery
Reposted by Rohan Gorantla
Your body has 20-30 TRILLION red blood cells, but modeling them all isn’t feasible. To understand cancer spread, we developed a method (Adaptive Physics Refinement) to model cancer cells interacting with blood using just one AWS node.
#cancerresearch #bloodflowmodel #HPC #bioengineering
#cancerresearch #bloodflowmodel #HPC #bioengineering
November 17, 2024 at 8:53 PM
Your body has 20-30 TRILLION red blood cells, but modeling them all isn’t feasible. To understand cancer spread, we developed a method (Adaptive Physics Refinement) to model cancer cells interacting with blood using just one AWS node.
#cancerresearch #bloodflowmodel #HPC #bioengineering
#cancerresearch #bloodflowmodel #HPC #bioengineering
Reposted by Rohan Gorantla
Now I can share external links without the posts being down regulated - I thought it would share this again!:)
I have compiled a list of now 100+ companies in the 'TechBio' space into a fully open database for the community.
Find here and please share if you like
open.substack.com/pub/harrisbi...
I have compiled a list of now 100+ companies in the 'TechBio' space into a fully open database for the community.
Find here and please share if you like
open.substack.com/pub/harrisbi...
November 21, 2024 at 8:53 AM
Now I can share external links without the posts being down regulated - I thought it would share this again!:)
I have compiled a list of now 100+ companies in the 'TechBio' space into a fully open database for the community.
Find here and please share if you like
open.substack.com/pub/harrisbi...
I have compiled a list of now 100+ companies in the 'TechBio' space into a fully open database for the community.
Find here and please share if you like
open.substack.com/pub/harrisbi...
Reposted by Rohan Gorantla
Today’s #JournalClub from @chemwedding.bsky.social discusses (questions?) the value of #equivalence in #neural_network architectures, feat. Works by @mmbronstein.bsky.social, Tess Smidt, Michele Ceriotti, and others. www.grynova-ccc.org/journal-club... #chemsky #ML
November 21, 2024 at 1:32 PM
Today’s #JournalClub from @chemwedding.bsky.social discusses (questions?) the value of #equivalence in #neural_network architectures, feat. Works by @mmbronstein.bsky.social, Tess Smidt, Michele Ceriotti, and others. www.grynova-ccc.org/journal-club... #chemsky #ML
Reposted by Rohan Gorantla
If you're interested in foundation models for materials and molecules, check out our repo: github.com/IBM/materials
We have three models released based on SMILES, SELFIES and molecular graphs.
More to come shortly - we aim to have a unified collection of state-of art models across all modalities.
We have three models released based on SMILES, SELFIES and molecular graphs.
More to come shortly - we aim to have a unified collection of state-of art models across all modalities.
GitHub - IBM/materials: Foundation Model for Materials - FM4M
Foundation Model for Materials - FM4M. Contribute to IBM/materials development by creating an account on GitHub.
github.com
November 7, 2024 at 5:14 PM
If you're interested in foundation models for materials and molecules, check out our repo: github.com/IBM/materials
We have three models released based on SMILES, SELFIES and molecular graphs.
More to come shortly - we aim to have a unified collection of state-of art models across all modalities.
We have three models released based on SMILES, SELFIES and molecular graphs.
More to come shortly - we aim to have a unified collection of state-of art models across all modalities.
Curious about how the Discover feed algorithm works on @bsky.app. Mine is mostly galaxy and nature photos - beautiful, but is that the norm? any ideas on how to improve my feed to find more content of interest? what are people seeing? 🤔
November 20, 2024 at 5:38 PM
Curious about how the Discover feed algorithm works on @bsky.app. Mine is mostly galaxy and nature photos - beautiful, but is that the norm? any ideas on how to improve my feed to find more content of interest? what are people seeing? 🤔