Rohan Gorantla

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

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

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!

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…

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

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:
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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...

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...

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!

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...

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/...

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.

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

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...

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!

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...

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.

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...

✏️🖥️ Drawing Tools

BioRender - www.biorender.com

BioGDP - biogdp.com

MolView - app.molview.com (Chemistry)

CDK Depict - www.simolecule.com/cdkdepict/de... (Molecules and Reactions)

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🎨📝Icon Libraries (Bio/Chem/Generic ones)

BioIcons - bioicons.com

SciDraw- scidraw.io

NIH’s BioArt - bioart.niaid.nih.gov

Flat Icon - www.flaticon.com

Noun Project - thenounproject.com

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🔍📚 Literature Search

Connected Papers - www.connectedpapers.com

Semantic Scholar - www.semanticscholar.org

OpenKnowledge Maps - openknowledgemaps.org

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👀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!

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#Science #AcademicSky #PhDSky

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

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/...

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.

Computational Biology pack - go.bsky.app/QVPoZXp by
@suinlee.bsky.social

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...

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

Covers of Science and Nature journals in the past 2 weeks denoting remarkable progress of life science with A.I. tools

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...

ML OSS & Open Source / Science enthusiasts - go.bsky.app/8MFcfXd by @yoshitomo-cs.bsky.social

🚀 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

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

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...

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

GitHub - IBM/materials: Foundation Model for Materials - FM4M Foundation Model for Materials - FM4M. Contribute to IBM/materials development by creating an account on GitHub.

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.

ML/AI Researchers - go.bsky.app/gPKeHz by @pelayoarbues.com