Ameya Harmalkar
@ameyaharmalkar.bsky.social
PhD w/ Jeff Gray on protein docking/design @JHU ChemBE | Tweaking generative models for protein design @Generate Biomedicines | Runner | (chaotic) Protein geek (he/him/his)
Reposted by Ameya Harmalkar
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ameya Harmalkar
🚀 Excited to release BoltzDesign1!
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
June 3, 2025 at 1:31 AM
🚀 Excited to release BoltzDesign1!
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
Love to see entropy getting the attention it deserves ha! Great read to start Monday morning.
A Perspective by @stephanieaw.bsky.social and @fraserlab.com discusses ways macromolecules use conformational entropy to control binding, catalysis, and allostery
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Advances in uncovering the mechanisms of macromolecular conformational entropy - Nature Chemical Biology
Protein conformational entropy plays a vital role in functions like binding and catalysis. This Perspective discusses three ways macromolecules use conformational entropy: prepaying entropic costs, re...
www.nature.com
April 28, 2025 at 12:05 PM
Love to see entropy getting the attention it deserves ha! Great read to start Monday morning.
Cool work from Profluent on scaling up protein language models ft. ProGen-3!
What does pushing the boundaries of model capacity and data scale do for generative protein language models? I’m super excited to share our latest work at Profluent Bio where we begin to explore and test some of our hypotheses!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Scaling unlocks broader generation and deeper functional understanding of proteins
Generative protein language models (PLMs) are powerful tools for designing proteins purpose-built to solve problems in medicine, agriculture, and industrial processes. Recent work has trained ever lar...
www.biorxiv.org
April 18, 2025 at 10:30 AM
Cool work from Profluent on scaling up protein language models ft. ProGen-3!
Reposted by Ameya Harmalkar
If anyone has any tips for fellowships or grants or giftfunds our group can apply for (in the US), please send our way.
So far, we've not had much luck in raising funds... 💰 In this relatively popular area, so I feel like I'm doing something wrong 😅
So far, we've not had much luck in raising funds... 💰 In this relatively popular area, so I feel like I'm doing something wrong 😅
April 9, 2025 at 12:30 PM
If anyone has any tips for fellowships or grants or giftfunds our group can apply for (in the US), please send our way.
So far, we've not had much luck in raising funds... 💰 In this relatively popular area, so I feel like I'm doing something wrong 😅
So far, we've not had much luck in raising funds... 💰 In this relatively popular area, so I feel like I'm doing something wrong 😅
Reposted by Ameya Harmalkar
Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
April 8, 2025 at 12:17 PM
Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
Woke up to have #BoltzDesign1 on the top of my reading list. Was excited since I heard about it from Sergey in Keystone!
Work by @yehlincho.bsky.social et al.
www.biorxiv.org/content/10.1...
Work by @yehlincho.bsky.social et al.
www.biorxiv.org/content/10.1...
BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design
Deep learning in structure prediction has revolutionized protein research, enabling large-scale screening, novel hypothesis generation, and accelerated experimental design across biological domains. R...
www.biorxiv.org
April 7, 2025 at 11:55 AM
Woke up to have #BoltzDesign1 on the top of my reading list. Was excited since I heard about it from Sergey in Keystone!
Work by @yehlincho.bsky.social et al.
www.biorxiv.org/content/10.1...
Work by @yehlincho.bsky.social et al.
www.biorxiv.org/content/10.1...
Reposted by Ameya Harmalkar
A single python package for calculation of quality metrics like DockQ, LDDT, RMSD, & others
peppr.vant.ai
peppr.vant.ai
April 4, 2025 at 6:32 AM
A single python package for calculation of quality metrics like DockQ, LDDT, RMSD, & others
peppr.vant.ai
peppr.vant.ai
Just wrapped the @keystonesymposia.bsky.social conference last night – still buzzing from all the spicy talks and incredible science! 🌶️✨
Here’s a quick thread of my personal favorites from the cutting edge of protein ML, dynamics, and design:
Here’s a quick thread of my personal favorites from the cutting edge of protein ML, dynamics, and design:
March 27, 2025 at 6:58 PM
Just wrapped the @keystonesymposia.bsky.social conference last night – still buzzing from all the spicy talks and incredible science! 🌶️✨
Here’s a quick thread of my personal favorites from the cutting edge of protein ML, dynamics, and design:
Here’s a quick thread of my personal favorites from the cutting edge of protein ML, dynamics, and design:
Just arrived in Keystone,CO for the @keystonesymposia.bsky.social conference on ML Applied to Macromolecular Structure and Function! Super excited to nerd out on all things proteins + ML.
If you’re around, hit me up — would love to catch up with familiar faces and meet new ones! #KSMLStructure25
If you’re around, hit me up — would love to catch up with familiar faces and meet new ones! #KSMLStructure25
March 23, 2025 at 11:57 PM
Just arrived in Keystone,CO for the @keystonesymposia.bsky.social conference on ML Applied to Macromolecular Structure and Function! Super excited to nerd out on all things proteins + ML.
If you’re around, hit me up — would love to catch up with familiar faces and meet new ones! #KSMLStructure25
If you’re around, hit me up — would love to catch up with familiar faces and meet new ones! #KSMLStructure25