Sushil Mishra

Assistant Professor of Biomedical Engineering @OleMiss | PhD @muni_cz Former Fellow @MSCActions & @jsps_sns | Glycoscience, Molecular Simulations, ML.

[Gabriele Corso @GabriCorso]

Big news from Boltz - our biggest update yet! 🚀
Today we’re releasing two new state-of-the-art models for protein and small molecule design with extensive wet lab validation and a new API to run all of our models on scalable GPUs wherever you (or your agents) work! 🔥

[AMBER md @ambermdprog]

Amber26 and AmberTools26 have now been released!
Full info is at https://t.co/quQSVY2j5E

[JCIM & JCTC Journals @JCIM_JCTC]

LigandExplorer: An Automated Tool for Ligand Extraction from PDB Structures
https://t.co/RjzOmaFfsF
#JCIM Vol66 Issue6 #MachineLearning #DeepLearning

[Corey Howe @design_proteins]

New SOTA de novo enzyme design model, outperforming RFD3 + LigMPNN

"de novo enzymes generated by the fine-tuned EnzyGen2 model exhibit catalytic efficiencies comparable to, or exceeding, those of their natural counterparts, despite sharing sequence identities as low as 51.6%"

[Alex Rives @alexrives]

Sequence is all you need. Protein language models set a new state of the art for predicting the clinical effect of genetic variations.

https://t.co/RxNRgZrNgL

[Machine Learning for Protein Engineering Seminar @ml4proteins]

Next Tues (3/24) at 4PM ET, @DidiKieran
and Danny Reisenbach will present "Proteina-Complexa: Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute"

Papers: https://t.co/OpKn9nH9g7

Sign up on our website for zoom links!

[Arash Vahdat @ArashVahdat]

🚨 We’re Hiring in Generative AI for Biomolecular Design! 🧬🤖

We’re looking for Research Scientists working on biomolecular design, including small molecules, proteins, RNA, and molecular dynamics.

Join us to help shape the next generation of AI-driven discovery, expanding our frameworks (e.g., Proteina-Complexa, La-Proteina, ReaSyn, and GenMol) to new domains and problems.

If you’re excited about pushing the frontier of generative AI for biology and chemistry, we’d love to hear from you.

🔗 Apply: https://t.co/D43PKbcJt5
🌐 Group page: https://t.co/MUAt4mcewx

[澪乃ゆい@バイオインフォVTuber🧪🖥💊 @mionoyui]

タンパク質・リガンド設計ツール30種以上を統合したPythonフレームワークBioPipelinesが公開されました
RFdiffusion・ProteinMPNN・Boltz2等を数行コードで連携することが可能で、JupyterからSlurmまで同一スクリプトで動作するため、運用がしやすくなりそうです
ソースはリプ🔽

[Tominaga K. (tomiken) @pacyc1841]

AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2 | Nature Methods https://t.co/vFUV7rgpb2

[Mohammed AlQuraishi @MoAlQuraishi]

New OpenFold3 preview out! (OF3p2)

It closes the gap to AlphaFold3 for most modalities.

Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9

[Sushil Mishra @glycodynamics]

Postdoc Opportunity | Protein Design

My lab is looking for a suitable postdoctoral candidate for a project on glycan-binding protein/antibody design using MD simulation, AI/ML.

If interested, submit an expression of interest:

https://t.co/7wXcoaxRHR

#md #glycotime #ML #DL

[Ole Miss @OleMiss]

We are grateful for the generosity our community has shown. That support is making an immediate impact but the needs remain urgent and requests for help continue. Support the Rebel Relief Disaster Fund today.

Give Now: https://t.co/ld5wYW1BHE

[Ole Miss @OleMiss]

Winter Storm Fern Response, Weekend Reminders

•The Student Union is a warming center, with overnight access.
•The Rebel Market is serving food daily, 10 a.m.–5 p.m., regardless of whether you have a meal plan.
•Turner Center open to students and employees for showers from noon–4 p.m today through Monday, Feb. 2.
•Pharmacy Health Services will be open for students and employees Monday through Friday, Noon–2 p.m. If you are an established patient in need of a prescription refill, please text [phone] in advance.
•The South Campus Rail Trails remain closed to allow debris removal crews to work safely and efficiently. We appreciate everyone’s patience as this cleanup continues.

Calendar items:
◦We have received a number of questions about Spring Break. We do not want to and do not anticipate needing to use Spring Break or extending the semester to make up any class days. We are seeking the necessary approvals.
◦The 2026-2027 Returner Housing Application will NOT open on Feb. 2 and Feb. 3, as previously scheduled. Updated information will be posted on the Student Housing website once the university reopens.
◦The Parker McCollum show at the SJB Pavilion has been rescheduled for April 9.
•Oxford Community Market is sharing Winter Storm Fern local community resources.

[Ole Miss @OleMiss]

REBALERT: The Oxford campus at the University of Mississippi will be closed through Sunday, Feb. 8, due to the extreme impact and ongoing recovery efforts from the recent ice storm and severe winter weather.

This includes the cancellation of all classes, events and activities. The university will continue to evaluate conditions and will notify the campus community of any further necessary adjustments to operations.

The university, city and county have experienced significant impacts from the ice storm including downed trees and power lines, power outages, falling ice and hazardous road conditions.
• For those currently in the area who decide to travel: Please check weather and road conditions along your route and make travel decisions accordingly. Some roads in the region are currently shut down. The Mississippi Department of Transportation has free resources related to road conditions, weather and more.
• For those not on campus or not in the local area: Do not return at this time in order to provide our first responders and university teams the ability to safely undertake recovery efforts.
Work continues to reinstate basic services such as power and water, clear roads and walkways, remove trees and debris, and assess and address ongoing impacts to buildings and campus infrastructure.

All classes and academic activities are cancelled until the university reopens. Once reopened, faculty and instructors will communicate directly with students regarding adjustments to coursework, academic activities, assignments, exams and deadlines. Additional details and information will be shared by the Office of the Provost.

The Student Union continues to serve as a warming center for students and employees, with overnight access. The Rebel Market continues to serve as our food service location for this event.

OUT buses have resumed limited operations with service from the majority of the Master Lease locations to the Student Union and to Walmart, 8 a.m.–3:30 p.m. on a continuous loop. Follow @outransit on Twitter and Instagram for schedule updates.
Regional campuses make decisions about changing operating hours in conjunction with their host campuses. Check regional campus websites for any changes or updates to operating schedules.

[Ole Miss @OleMiss]

The safety and well-being of our students, faculty, and staff remain our highest priority as winter weather continues to impact our campus and community. Please see the following updates:

The GCF Student Union has power and is open as a warming shelter for University of Mississippi students and employees. Please note that we don’t have the ability or staff to provide food at the Student Union at this time. The water bottle dispensers on every level are working.

The Rebel Market has been our food service location for this event. Monday hours: 10 a.m.– 5 p.m.

Power has been restored to several residence halls, and crews continue working around the clock, in close coordination with local utility providers and emergency partners, to restore power to remaining residence halls as safely and quickly as conditions allow.

The university has established a Call Center for non-emergency university updates, 662-915-7211. Call Center hours: 8 a.m.– 8 p.m.

We appreciate your patience and care for one another during these challenging conditions. Additional updates will be shared as new information becomes available.

[Lafayette County EMA @LafayetteEMA]

🚨 Winter Storm Update for Lafayette County 🚨

Confidence has increased that Lafayette County could see significant impacts from ICE with this weekend’s winter storm. 🧊🌨️

[Sushil Mishra @glycodynamics]

My lab has published its first paper in collaboration with colleagues from Japan! We show how a single amino acid can alter the enzymatic activity of GnTs.

Enzymatic basis of branching and extension of O-Man glycans for keratan sulfate biosynthesis
https://t.co/eD2133PQsQ

[CHARMM-GUI @CharmmGui]

[Jobs and Events] Ph.D. positions in bimolecular simulation and free-energy calculation, The laboratory of Dr. Sushil Mishra, University of Mississippi, Oxford, MS, USA:
https://t.co/haRXQvYinf

[Sushil Mishra @glycodynamics]

#glycotime

[Nikki Reinemann @OleMiss_MBELab]

Applications for the #NSF-funded Ole Miss Nanoengineering Summer REU Program are open!

More information and application: https://t.co/JTUKWai4df

Application deadline: February 15, 2025

Please share!

#nanoREU #nano #REU #nanoengineering

[The Nobel Prize @NobelPrize]

BREAKING NEWS
The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Chemistry with one half to David Baker “for computational protein design” and the other half jointly to Demis Hassabis and John M. Jumper “for protein structure prediction.”