Dylan N. (They/Them)
@kpmanstheorem.bsky.social
Postdoc in Filizola Lab @ ISMMS | Voelz lab + Folding@home alum | Muay Thai
Reposted by Dylan N. (They/Them)
It’s official: ChatGPT can't draw a GPCR, but you’ll master them in the Filizola Lab
😜 Join Us! (send your CV and the names of at least two references to my institutional email) #Postdoc #scientist #research
😜 Join Us! (send your CV and the names of at least two references to my institutional email) #Postdoc #scientist #research
October 17, 2025 at 4:50 AM
It’s official: ChatGPT can't draw a GPCR, but you’ll master them in the Filizola Lab
😜 Join Us! (send your CV and the names of at least two references to my institutional email) #Postdoc #scientist #research
😜 Join Us! (send your CV and the names of at least two references to my institutional email) #Postdoc #scientist #research
Reposted by Dylan N. (They/Them)
Reposted by Dylan N. (They/Them)
How many crystal structures do you need to trust your docking results? https://www.biorxiv.org/content/10.1101/2025.09.19.677428v1
September 25, 2025 at 2:48 AM
How many crystal structures do you need to trust your docking results? https://www.biorxiv.org/content/10.1101/2025.09.19.677428v1
Reposted by Dylan N. (They/Them)
Our first protein design paper out in Protein Science
onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com/doi/10.1002/...
September 24, 2025 at 2:54 PM
Our first protein design paper out in Protein Science
onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Dylan N. (They/Them)
Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia:
doi.org/10.5281/zeno...
We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
1/n
doi.org/10.5281/zeno...
We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
1/n
September 6, 2025 at 8:13 AM
Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia:
doi.org/10.5281/zeno...
We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
1/n
doi.org/10.5281/zeno...
We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
1/n
I actually love this!
arxiv.org/abs/2508.20863
The destruction of peer review.
We need experts to be trusted, and editors to be involved in the process. The act of peer review is meaningless if editors don't assess the work themselves. Any paper sneaking prompts in is likely drivel, no AI needed to learn that. 😮💨
The destruction of peer review.
We need experts to be trusted, and editors to be involved in the process. The act of peer review is meaningless if editors don't assess the work themselves. Any paper sneaking prompts in is likely drivel, no AI needed to learn that. 😮💨
Publish to Perish: Prompt Injection Attacks on LLM-Assisted Peer Review
Large Language Models (LLMs) are increasingly being integrated into the scientific peer-review process, raising new questions about their reliability and resilience to manipulation. In this work, we i...
arxiv.org
August 30, 2025 at 2:31 PM
I actually love this!
Reposted by Dylan N. (They/Them)
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...
Excited to share the final paper from my PhD in @voelzlab.bsky.social , out now in #JCTC @acs.org ! We ran ~43k expanded ensemble free energy calculations on @foldingathome.org to do in silico site saturation mutagenesis on designed hemagglutinin minibinder proteins.
🔗 doi.org/10.1021/acs....
🔗 doi.org/10.1021/acs....
Massively Parallel Free Energy Calculations for In Silico Affinity Maturation of Designed Miniproteins
Computational protein design efforts continue to make remarkable advances, yet the discovery of high-affinity binders typically requires large-scale experimental screening of site-saturated mutant (SS...
doi.org
August 19, 2025 at 3:57 PM
Excited to share the final paper from my PhD in @voelzlab.bsky.social , out now in #JCTC @acs.org ! We ran ~43k expanded ensemble free energy calculations on @foldingathome.org to do in silico site saturation mutagenesis on designed hemagglutinin minibinder proteins.
🔗 doi.org/10.1021/acs....
🔗 doi.org/10.1021/acs....
Reposted by Dylan N. (They/Them)
The Trump administration effectively created a de facto bathroom ban at Brown University and none of the major media is covering it, and if they do, they character it as about sports. This is how the trans visa ban was enacted and characterized.
www.advocate.com/news/transge...
www.advocate.com/news/transge...
Brown University is ‘functionally inaccessible’ to transgender students after Trump settlement
“Everyone I talked to thought it only applied to sports. But it applies to everything," one transgender student told The Advocate.
www.advocate.com
August 6, 2025 at 3:55 AM
The Trump administration effectively created a de facto bathroom ban at Brown University and none of the major media is covering it, and if they do, they character it as about sports. This is how the trans visa ban was enacted and characterized.
www.advocate.com/news/transge...
www.advocate.com/news/transge...
Reposted by Dylan N. (They/Them)
For your summer reading, check out the latest from our lab: www.biorxiv.org/content/10.1...
BOLD-GPCRs: A Transformer-Powered App for Predicting Ligand Bioactivity and Mutational Effects Across Class A GPCRs
G protein-coupled receptors (GPCRs) are important targets for drug discovery owing to their ability to respond to a broad range of stimuli and their involvement in numerous pathologies. Although tradi...
www.biorxiv.org
August 6, 2025 at 11:25 AM
For your summer reading, check out the latest from our lab: www.biorxiv.org/content/10.1...
Reposted by Dylan N. (They/Them)
CASP is the main reason the protein structure prediction technology and research field advanced over the last 30 years. And the main reason AI based methods have been accepted and widely applied in biology. So shortsighted of NIH to postpone or even halt funding. John Moult is a scientific hero.
Exclusive: An international scientific competition widely credited with spurring the development of artificial intelligence for biology appears to be on its deathbed. scim.ag/44ukS90
Exclusive: Famed protein structure competition nears end as NIH grant money runs out
Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold
scim.ag
July 2, 2025 at 10:36 PM
CASP is the main reason the protein structure prediction technology and research field advanced over the last 30 years. And the main reason AI based methods have been accepted and widely applied in biology. So shortsighted of NIH to postpone or even halt funding. John Moult is a scientific hero.
Reposted by Dylan N. (They/Them)
Excited to share our BICePs manuscript now out in #JCTC @acs.org – congrats Rob Raddi!
doi.org/10.1021/acs....
doi.org/10.1021/acs....
Model Selection Using Replica Averaging with Bayesian Inference of Conformational Populations
Bayesian Inference of Conformational Populations (BICePs) is a reweighting algorithm that reconciles simulated ensembles with sparse and/or noisy observables by sampling the full posterior distributio...
doi.org
June 29, 2025 at 3:46 PM
Excited to share our BICePs manuscript now out in #JCTC @acs.org – congrats Rob Raddi!
doi.org/10.1021/acs....
doi.org/10.1021/acs....
Very funny in the saddest and scariest way that people who are apparently in love with western civilization don't know that trans is a latin word that has an actually meaning and are willing to dismantle science in the u.s. using ctrl-f over their hatred of trans people. Very cool place 😎
Duke appears to have lost NIH grants because they used the prefix "trans" in reference to disease transmission, transgenic genetic material, translational studies, or signal transduction www.dukechronicle.com/article/2025...
June 27, 2025 at 2:43 PM
Very funny in the saddest and scariest way that people who are apparently in love with western civilization don't know that trans is a latin word that has an actually meaning and are willing to dismantle science in the u.s. using ctrl-f over their hatred of trans people. Very cool place 😎
Reposted by Dylan N. (They/Them)
Excited to share about new experimental structures of the coronavirus spike protein that confirm predictions we made early during the COVID-19 pandemic! Congrats to former student Max Zimmerman and the rest of the team at Generate Bio
foldingathome.org/2025/06/26/e...
foldingathome.org/2025/06/26/e...
June 26, 2025 at 3:01 PM
Excited to share about new experimental structures of the coronavirus spike protein that confirm predictions we made early during the COVID-19 pandemic! Congrats to former student Max Zimmerman and the rest of the team at Generate Bio
foldingathome.org/2025/06/26/e...
foldingathome.org/2025/06/26/e...
Reposted by Dylan N. (They/Them)
Excited to share work now out in #JCIM @acs.org !
doi.org/10.1021/acs....
Alchemical free energy calculations are indispensable in computational drug design. We present an improved approach for optimizing the schedule of alchemical intermediates by minimizing thermodynamic length.
1/7
doi.org/10.1021/acs....
Alchemical free energy calculations are indispensable in computational drug design. We present an improved approach for optimizing the schedule of alchemical intermediates by minimizing thermodynamic length.
1/7
Simple Method to Optimize the Spacing and Number of Alchemical Intermediates in Expanded Ensemble Free Energy Calculations
Alchemical free energy calculations are essential to modern structure-based drug design. Such calculations are usually performed at a series of discrete intermediates along a nonphysical thermodynamic...
doi.org
June 23, 2025 at 4:10 PM
Excited to share work now out in #JCIM @acs.org !
doi.org/10.1021/acs....
Alchemical free energy calculations are indispensable in computational drug design. We present an improved approach for optimizing the schedule of alchemical intermediates by minimizing thermodynamic length.
1/7
doi.org/10.1021/acs....
Alchemical free energy calculations are indispensable in computational drug design. We present an improved approach for optimizing the schedule of alchemical intermediates by minimizing thermodynamic length.
1/7
Reposted by Dylan N. (They/Them)
Science has published a letter I helped write, as part of Advancing Queer & Trans Equity in Science (AQTES), about why it's important for universities & other institutions to protect trans and gender-nonconforming scientists, and some practical things they can do.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Protect transgender scientists
Transgender and gender nonconforming (TGnC) people are a primary target of the Trump administration. Multiple executive orders seek to erase TGnC protections; mandate denial of gender identity; and ba...
www.science.org
June 19, 2025 at 6:42 PM
Science has published a letter I helped write, as part of Advancing Queer & Trans Equity in Science (AQTES), about why it's important for universities & other institutions to protect trans and gender-nonconforming scientists, and some practical things they can do.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Dylan N. (They/Them)
June 6, 2025 at 3:01 PM
Reposted by Dylan N. (They/Them)
Opinion | The Science I Would Be Doing if I Weren’t in ICE Detention
www.nytimes.com
May 13, 2025 at 12:56 PM
This is just DEI for bad ideas.
The Trump administration's war on higher education has already been very high-stakes, but this is a genuine escalation even from what we've already seen: trying to force accreditors to impose ideological quotas on faculty.
www.whitehouse.gov/presidential...
www.whitehouse.gov/presidential...
April 24, 2025 at 4:15 PM
This is just DEI for bad ideas.
Reposted by Dylan N. (They/Them)
We're disappointed to see Ben Barres's powerful book "The Autobiography of a Transgender Scientist" among the ~400 titles removed from the Naval Academy Library. Needless to say, we're proud to have published his book and will keep it — and his memory — alive.
The Coming Out of a Transgender Scientist
"I know that I am making the right decision because whenever I think about changing my gender role, I am flooded with feelings of relief."
thereader.mitpress.mit.edu
April 8, 2025 at 8:24 PM
We're disappointed to see Ben Barres's powerful book "The Autobiography of a Transgender Scientist" among the ~400 titles removed from the Naval Academy Library. Needless to say, we're proud to have published his book and will keep it — and his memory — alive.
Very true...years of computational chemistry has transgendered me.
April 8, 2025 at 4:45 PM
Very true...years of computational chemistry has transgendered me.
Let's fill in these funding gaps baybee!
The "empty space in plots could be used for advertisements" April Fools paper got me to literally laugh out loud 🔭🧪
arxiv.org/pdf/2503.24254
arxiv.org/pdf/2503.24254
April 1, 2025 at 3:17 PM
Let's fill in these funding gaps baybee!
tru
We polled Nature readers to ask if they were thinking of leaving the US for jobs abroad. Three-quarters of them (who said they were US-based scientists) said yes. 🧪
www.nature.com/articles/d41...
www.nature.com/articles/d41...
75% of US scientists who answered Nature poll consider leaving
More than 1,600 readers answered our poll; many said they were looking for jobs in Europe and Canada.
www.nature.com
March 27, 2025 at 3:04 PM
tru