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Rohan Gorantla

@rohangorantla.bsky.social
3.7K followers 299 following 20 posts

Developing ML methods for Drug Discovery @ Novartis 🧬💻 | prev: PhD student @ University of Edinburgh with Toni Mey

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Reposted by Rohan Gorantla
Toni Mey @ppxasjsm.bsky.social · 08/03/2026
We have a funded PhD position in my group at Edinburgh Uni. Learning design rules for substrate affinity in metalloenzymes. The project combines computational chemistry and enzyme design to understand and engineer metalloenzyme–substrate interactions: shorturl.at/cikuU
shorturl.at
Learning design rules for substrate affinity in metalloenzymes at University of Edinburgh on FindAPhD.com
PhD Project - Learning design rules for substrate affinity in metalloenzymes at University of Edinburgh, listed on FindAPhD.com
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Rohan Gorantla @rohangorantla.bsky.social · 27/02/2025
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
findaphd.com
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
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Toni Mey @ppxasjsm.bsky.social · 23/01/2025
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!
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Soham Sankaran @soh.am · 02/01/2025
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
lu.ma
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…
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Thomas Wolf @thomwolf.bsky.social · 14/12/2024
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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Charlotte Bunne @bunnech.bsky.social · 12/12/2024
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...
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Srijit Seal 🇺🇸🇬🇧🇩🇪🇯🇵🇮🇳 @srijitseal.com · 05/12/2024
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!
nature.com
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...
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Pat Walters @wpwalters.bsky.social · 10/12/2024
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/...
pubs.acs.org
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...
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Keenan Crane @keenancrane.bsky.social · 09/12/2024
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.
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Michael Bronstein @mmbronstein.bsky.social · 09/12/2024
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...
nature.com
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
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 09/12/2024
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!
generations from PLAIDThe PLAID model architectureConditional generations from PLAID
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J. Jasmin Güven @jjguven.bsky.social · 06/12/2024
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.
tinyurl.com
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...
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Frank Noe @franknoe.bsky.social · 06/12/2024
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...
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Rohan Gorantla @rohangorantla.bsky.social · 04/12/2024
👀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
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Thomas Wolf @thomwolf.bsky.social · 26/11/2024
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
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Kristina Ulicna @kristinaulicna.bsky.social · 25/11/2024
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/...
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Rohan Gorantla @rohangorantla.bsky.social · 20/11/2024
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.
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Angelo Pugliese @angelo-rules.bsky.social · 22/11/2024
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
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...
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Eric Topol @erictopol.bsky.social · 24/11/2024
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...
Covers of Science and Nature journals in the past 2 weeks denoting remarkable progress of life science with A.I. tools
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Radoslav Krivak @rdkbio.bsky.social · 16/11/2024
🚀 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
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Amanda Randles 🧪⚛️ 👩‍🔬 @profamandarandles.bsky.social · 17/11/2024
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
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Charlie Harris @harrisbio.bsky.social · 21/11/2024
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...
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Ganna (Anya) Gryn’ova 🇺🇦 @grynova.bsky.social · 21/11/2024
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
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Flaviu Cipcigan @flaviucipcigan.bsky.social · 07/11/2024
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.
github.com
GitHub - IBM/materials: Foundation Model for Materials - FM4M
Foundation Model for Materials - FM4M. Contribute to IBM/materials development by creating an account on GitHub.
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Rohan Gorantla @rohangorantla.bsky.social · 20/11/2024
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? 🤔
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Ian Simpson @tisimpson.bsky.social · 20/11/2024
Absolutely delighted to be partnering with SIDB; combining AI and Autism Research to improve our understanding of ASDs. We have a very exciting collection of PhD projects open for applications - www.ai4biomed.io/research/pro... closing 8th January.
ai4biomed.io
Projects for 2025 entry – UKRI AI CDT in Biomedical Innovation
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Sukrit Singh @sukritsingh92.bsky.social · 19/11/2024
New preprint! We prospectively evaluate structure-based methods and measure how well they classify clinical kinase mutations as inhibitor–resistant or –sensitizing when compared against our NanoBRET assay. Alchemical methods are well-suited to modeling distal mutants! Link: doi.org/10.1101/2024...
doi.org
Prospective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor binding
Small molecule kinase inhibitors are critical in the modern treatment of cancers, evidenced by the existence of over 80 FDA-approved small-molecule kinase inhibitors. Unfortunately, intrinsic or acqui...
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John Chodera @jchodera.bsky.social · 20/11/2024
This is happening in 30 min!
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Rohan Gorantla @rohangorantla.bsky.social · 20/11/2024
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.
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