NYAGIM
@nyagim.bsky.social
Posting new opportunities & breakthroughs in & around NYC.
https://www.meetup.com/new-york-area-group-for-informatics-and-modeling/
Managed by @markpolk.io.
https://www.meetup.com/new-york-area-group-for-informatics-and-modeling/
Managed by @markpolk.io.
Pinned
NYAGIM
@nyagim.bsky.social
· Feb 9
New York Area Group for Informatics and Modeling (NYAGIM) | Meetup
We are a growing community of greater New York City area scientists focused on the advances of in silico methods related to drug discovery, and how they increasingly impact and transform pharmaceutica...
www.meetup.com
We are a growing community of greater New York City area scientists focused on the advances of in silico methods related to drug discovery, and how they increasingly impact and transform pharmaceutical research.
Learn more: www.meetup.com/new-york-are...
Learn more: www.meetup.com/new-york-are...
Reposted by NYAGIM
My institution---the Sloan Kettering Institute, the basic science arm of the Memorial Sloan Kettering Cancer Center---is hiring new faculty this cycle! Applications close Nov 15.
www.mskcc.org/research/ski...
www.mskcc.org/research/ski...
Faculty Positions
The Sloan Kettering Institute is seeking innovative scientists to join our faculty.
www.mskcc.org
October 27, 2025 at 2:45 PM
My institution---the Sloan Kettering Institute, the basic science arm of the Memorial Sloan Kettering Cancer Center---is hiring new faculty this cycle! Applications close Nov 15.
www.mskcc.org/research/ski...
www.mskcc.org/research/ski...
Reposted by NYAGIM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Join us for the NYAGIM 2025 Q3 event, featuring Dan Sindhikara on recent advances and persistent challenges in the computational design of macrocyclic peptides. Sep. 16 at 6 PM. RSVP: www.meetup.com/new-york-are...
Computational Design of Macrocyclic Peptides Containing Non-Natural Amino Acids , Tue, Sep 16, 2025, 6:00 PM | Meetup
Join us for the NYAGIM 2025 Q3 event, supported by Cresset and the New York Academy of Sciences, featuring Dan Sindhikara on recent advances and persistent challenges in th
www.meetup.com
September 4, 2025 at 3:20 PM
Join us for the NYAGIM 2025 Q3 event, featuring Dan Sindhikara on recent advances and persistent challenges in the computational design of macrocyclic peptides. Sep. 16 at 6 PM. RSVP: www.meetup.com/new-york-are...
Reposted by NYAGIM
Summer 2025 #keedylab news round-up: come read about what we did on our summer vacation! keedylab.org/news/
Associated with this website update, I also embedded the lab's Bluesky feed on the website's news page -- thus creating an infinite cycle of delightful lab news links 🔁 💯
Associated with this website update, I also embedded the lab's Bluesky feed on the website's news page -- thus creating an infinite cycle of delightful lab news links 🔁 💯
News | Keedy Lab
keedylab.org
August 13, 2025 at 8:43 PM
Summer 2025 #keedylab news round-up: come read about what we did on our summer vacation! keedylab.org/news/
Associated with this website update, I also embedded the lab's Bluesky feed on the website's news page -- thus creating an infinite cycle of delightful lab news links 🔁 💯
Associated with this website update, I also embedded the lab's Bluesky feed on the website's news page -- thus creating an infinite cycle of delightful lab news links 🔁 💯
Reposted by NYAGIM
Shiny new probabilistic model, gruyere 🧀, for powering up rare variant associations w/ DL effect prediction! We find novel associations for Alzheimer's disease, e.g. nuclear pore protein NUP93 in microglia. Big thanks to NIH/NIA/ADSP and Anjali for the hard work! authors.elsevier.com/a/1ldzwgeXDzHj
authors.elsevier.com
August 20, 2025 at 10:06 PM
Shiny new probabilistic model, gruyere 🧀, for powering up rare variant associations w/ DL effect prediction! We find novel associations for Alzheimer's disease, e.g. nuclear pore protein NUP93 in microglia. Big thanks to NIH/NIA/ADSP and Anjali for the hard work! authors.elsevier.com/a/1ldzwgeXDzHj
Reposted by NYAGIM
Check out how OpenADMET is aiming to transform drug discovery! 🚀
Read more about OpenADMET initiatives in this blog post by @fraserlab.com, @jchodera.bsky.social and @srikosuri.bsky.social.
openadmet.ghost.io/what-is-open...
openadmet.ghost.io/what-is-open...
What is OpenADMET?
Small molecule therapies have always been and continue to be the dominant way we treat diseases worldwide. Small molecules have unique advantages such as cost, scalability, convenience, the ability to...
openadmet.ghost.io
August 23, 2025 at 8:01 PM
Check out how OpenADMET is aiming to transform drug discovery! 🚀
Reposted by NYAGIM
New @biorxiv-biophys.bsky.social preprint from the #keedylab! 👀
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
Mapping allosteric rewiring in related protein structures from collections of crystallographic multiconformer models
How do related proteins with a common fold perform diverse biological functions? Although the average structure may be similar, structural excursions from this average may differ, giving rise to allos...
www.biorxiv.org
May 27, 2025 at 7:23 PM
New @biorxiv-biophys.bsky.social preprint from the #keedylab! 👀
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
CORRECTION: The speaker is David J. Huggins. Please RSVP: www.meetup.com/new-york-are...
May 13, 2025 at 10:26 PM
CORRECTION: The speaker is David J. Huggins. Please RSVP: www.meetup.com/new-york-are...
May 22: Hear from Ayşegül Özen about a groundbreaking drug discovery effort recently published in Nature, showcasing the use of advanced CADD techniques to develop a novel antiviral targeting SARS-CoV-2. RSVP: www.meetup.com/new-york-are...
Computational Design of First-in-Class Inhibitors Targeting SARS-CoV-2 NSP14, Thu, May 22, 2025, 6:00 PM | Meetup
Join the NYAGIM 2025 Q2 event as we spotlight a groundbreaking drug discovery effort recently published in *Nature*, showcasing the use of advanced computer-aided drug desi
www.meetup.com
May 12, 2025 at 11:02 AM
May 22: Hear from Ayşegül Özen about a groundbreaking drug discovery effort recently published in Nature, showcasing the use of advanced CADD techniques to develop a novel antiviral targeting SARS-CoV-2. RSVP: www.meetup.com/new-york-are...
Reposted by NYAGIM
Check out our recent preprint 👇on counting particles to estimate populations in #cryoem: noise can bias the estimates; with Luke Evans & a great team.
Counting particles could give wrong probabilities in Cryo-Electron Microscopy https://www.biorxiv.org/content/10.1101/2025.03.27.644168v1
March 30, 2025 at 1:29 PM
Check out our recent preprint 👇on counting particles to estimate populations in #cryoem: noise can bias the estimates; with Luke Evans & a great team.
Reposted by NYAGIM
the longest journey begins with a single step. luckily for us, @arianaclerkin.bsky.social is writing hers down!
read the first PLUMB blab of many below, and follow along as Ariana builds an open comp.chem project from the ground up.
read the first PLUMB blab of many below, and follow along as Ariana builds an open comp.chem project from the ground up.
PLUMB blab #1: We need better benchmarks for computer-aided drug design
Written by: Ariana Brenner Clerkin, PhD
Welcome to a new series on the OMSF blog: PLUMB blab! This series will take you behind the scenes of PLUMB (Protein-Ligand Unified Metrics Benchmark), an open-...
omsf-blog.ghost.io
April 1, 2025 at 3:14 PM
the longest journey begins with a single step. luckily for us, @arianaclerkin.bsky.social is writing hers down!
read the first PLUMB blab of many below, and follow along as Ariana builds an open comp.chem project from the ground up.
read the first PLUMB blab of many below, and follow along as Ariana builds an open comp.chem project from the ground up.
Happening today with @sonyahanson.bsky.social!
Please join us for our next event on March 18, 2025, with Dr. Sonya Hanson: "Progress and Pitfalls in Free Energy Landscapes from Cryo-EM." Full details and RSVP: www.meetup.com/new-york-are....
March 18, 2025 at 6:11 PM
Happening today with @sonyahanson.bsky.social!
Reposted by NYAGIM
Excited to share this new preprint from our group, led by grad student Anne van Vlimmeren! We used TurboID proximity labeling to explore how mechanistically diverse mutations in the phosphatase SHP2 differentially alter protein-protein interactions and localization.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Proximity-labeling proteomics reveals remodeled interactomes and altered localization of pathogenic SHP2 variants
Missense mutations in PTPN11, the gene encoding the protein tyrosine phosphatase SHP2, are common in several developmental disorders and cancers. While many SHP2 mutations disrupt auto-inhibition and ...
www.biorxiv.org
March 3, 2025 at 5:16 PM
Excited to share this new preprint from our group, led by grad student Anne van Vlimmeren! We used TurboID proximity labeling to explore how mechanistically diverse mutations in the phosphatase SHP2 differentially alter protein-protein interactions and localization.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by NYAGIM
This work is now published in J Phys Chem B! Check out our work showing that simulations predict the impact of distal mutations on kinase-inhibitor binding, and our experimental NanoBRET dataset of 94 kinase mutations that provide a benchmark for future methods. Link:
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
March 10, 2025 at 6:19 PM
This work is now published in J Phys Chem B! Check out our work showing that simulations predict the impact of distal mutations on kinase-inhibitor binding, and our experimental NanoBRET dataset of 94 kinase mutations that provide a benchmark for future methods. Link:
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
Please join us for our next event on March 18, 2025, with Dr. Sonya Hanson: "Progress and Pitfalls in Free Energy Landscapes from Cryo-EM." Full details and RSVP: www.meetup.com/new-york-are....
March 6, 2025 at 4:51 PM
Please join us for our next event on March 18, 2025, with Dr. Sonya Hanson: "Progress and Pitfalls in Free Energy Landscapes from Cryo-EM." Full details and RSVP: www.meetup.com/new-york-are....
Reposted by NYAGIM
#MLCB2025 will be Sept 10-11 at @nygenome.org in NYC! Paper deadline June 1st & in-person registration will open in May. Please sign up for our mailing list groups.google.com/g/mlcb/ for future announcements. More details at mlcb.github.io. Please RP!
January 27, 2025 at 6:40 PM
#MLCB2025 will be Sept 10-11 at @nygenome.org in NYC! Paper deadline June 1st & in-person registration will open in May. Please sign up for our mailing list groups.google.com/g/mlcb/ for future announcements. More details at mlcb.github.io. Please RP!
Reposted by NYAGIM
Excited to share what I’ve been working on with @tkaraletsos.bsky.social to transform the field of drug discovery with atomistic foundation simulation models!
I could not be more thrilled to be working with this dream team.
achira.ai
I could not be more thrilled to be working with this dream team.
achira.ai
NEW: Achira has launched with a $33M seed round
I talked with CEO @jchodera.bsky.social about plans to combine AI- and physics-based methods for drug discovery and moving beyond 45 years of the same type of models behind molecular dynamics.
My latest @endpts.com:
endpts.com/achira-raise...
I talked with CEO @jchodera.bsky.social about plans to combine AI- and physics-based methods for drug discovery and moving beyond 45 years of the same type of models behind molecular dynamics.
My latest @endpts.com:
endpts.com/achira-raise...
February 21, 2025 at 2:15 PM
Excited to share what I’ve been working on with @tkaraletsos.bsky.social to transform the field of drug discovery with atomistic foundation simulation models!
I could not be more thrilled to be working with this dream team.
achira.ai
I could not be more thrilled to be working with this dream team.
achira.ai
Reposted by NYAGIM
Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.
February 24, 2025 at 12:23 PM
Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.
Reposted by NYAGIM
Registration is now open for the 2025 NYC CryoEM meeting, organized by Bill Rice (NYU) & @fravallese.bsky.social (CUNY/ASRC)
Always a great meeting with lots of new #cryoem work by rising stars in/around NYC
Max 140 people so register now (it’s free)!
Always a great meeting with lots of new #cryoem work by rising stars in/around NYC
Max 140 people so register now (it’s free)!
Fifth New York Area Cryo-EM Meeting | NYU Langone Health
Join the 2025 Cryo-EM & Cryo-ET Meeting at NYU Langone! Share unpublished work, discuss breakthroughs, and tackle challenges. June 25. Register now!
med.nyu.edu
February 12, 2025 at 12:33 AM
Registration is now open for the 2025 NYC CryoEM meeting, organized by Bill Rice (NYU) & @fravallese.bsky.social (CUNY/ASRC)
Always a great meeting with lots of new #cryoem work by rising stars in/around NYC
Max 140 people so register now (it’s free)!
Always a great meeting with lots of new #cryoem work by rising stars in/around NYC
Max 140 people so register now (it’s free)!
We are a growing community of greater New York City area scientists focused on the advances of in silico methods related to drug discovery, and how they increasingly impact and transform pharmaceutical research.
Learn more: www.meetup.com/new-york-are...
Learn more: www.meetup.com/new-york-are...
New York Area Group for Informatics and Modeling (NYAGIM) | Meetup
We are a growing community of greater New York City area scientists focused on the advances of in silico methods related to drug discovery, and how they increasingly impact and transform pharmaceutica...
www.meetup.com
February 9, 2025 at 7:09 PM
We are a growing community of greater New York City area scientists focused on the advances of in silico methods related to drug discovery, and how they increasingly impact and transform pharmaceutical research.
Learn more: www.meetup.com/new-york-are...
Learn more: www.meetup.com/new-york-are...