Martin Vögele
@Blendenfleck
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Computational biophysicist at Schrödinger, prev. @Stanford & @MPIBP | amateur photographer | history+language nerd | ö=oe | 🇩🇪 🇪🇺 🏳️🌈 | all views my own
New York, NY
Joined July 2014
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Now online in
@JCIM_JCTC
:
“Is the Functional Response of a Receptor Determined by the Thermodynamics of Ligand Binding?”
Our answer: Yes, it is!
And we can use it to predict ligand efficacy.
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Exciting times ahead:
In two weeks, I am going to move to New York City to join
@Schrodinger
as a senior scientist in the life science software team.
👨💻
This is a dream coming true and I am deeply grateful for everyone who has been supporting me on the way there.
🙏
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I ran molecular dynamics simulations for my doctoral thesis. Can I call myself MD-PhD? 🙃🙂
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Force fields are like sausages. If you like them, it is best not to see them being made.
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Herpes viruses evade the immune system using "fake" receptors, binding to the proteins that orchestrate immune cells.
Complementing structures and assays, our MD simulations help to better understand how the human herpes virus HCMV achieves this.
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After a long period of uncertainty, my visa status change was approved — switching from J-1 (research scholar) to O-1A (individual with extraordinary ability in the sciences, education, business, or athletics).
🍾🇺🇸🎉
Major life update coming soon. 😉
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I started writing a little python library + workflow for exploratory analysis and comparison of protein simulations.
This project, called PENSA, is now on Github, including tutorial.
Here's what it can do so far (thread):
[1/4]
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AlphaFold2 usually only predicts single protein structures. Now, del Alamo et al. present an approach to use it for sampling alternative conformations, demonstrating it on transporters and receptors.
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My amazing colleague Joe demonstrates that one can substantially improve ligand poses and affinity predictions using data about completely different molecules that bind to the same target — without requiring any target-bound structures of these molecules.
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I have been working with molecular simulations for ten years now. Yet still I seem to think sometimes that they run faster if I check them every five minutes.
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New preprint about PENSA, our software package for comprehensive and thorough analysis of biomolecular conformational ensembles:
On three examples, we show how it helps understand an enzyme mechanism, DNA forcefields, and signaling in an opioid receptor.
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My first preprint about work at Schrödinger:
We predict ligand efficacy via absolute binding free energy perturbation on different receptor conformations, confirming the thermodynamic link between ligand binding and the receptor's functional response.
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Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation
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I found an app, Termius, that provides me a terminal on my phone and lets me log into our computing cluster from anywhere.
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It took less time to develop a Covid vaccine than to fix a Conda environement.
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I have always been fascinated by how medicinal chemists have such a good intuition for spotting good ligand binding modes. Finally some of them reveal their secrets.
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German word of the day: Morgenmuffel
Meaning: a person who is grumpy in the mornings and does not like to wake up early.
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Finally visiting my hometown in Germany again.
It has been almost three years due to COVID-19 and US visa regulations.
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'The firing will have “significant implications” for the 39 people who worked in the Sabatini lab.'
😟
This fatal dependency is one of the reasons why it often takes ages until someone speaks up.
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Remember the "year 2000 problem"? 🗓️
In computational biophysics, the infamous "atom 100,000 problem" is still a thing. 🙄
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Pro tip for junior academics: If a professor has given two students or postdocs the same research project to see who does it faster, run and stay away from them. Competition is tough enough between labs; you don't need it within.
#AcademicTwitter
#AcademicChatter
#ScienceTwitter
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This was definitely the most pleasant surprise of the year: Walter Greiner Award for best physics PhD thesis 2019/20 at
@goetheuni
. 🥳
(+ Corona-delayed remote ceremony)
Many thanks to the
@MPIbp
Theor. Biophysics group for the opportunity and the support - and the amazing time!
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First day at my first full-time industry job tomorrow. 😳
Dear professionals out there, any important advice that you would like to have had when you started?
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Successfully defended my thesis! 🎉
Many many thanks to everyone who made this possible!
My doctoral cap is a giant lipid membrane. 🎓👍
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After four months trying to explain some "surprisingly good results", I found the bug in the code.
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Arrived in Philadelphia for the
@BiophysicalSoc
Annual Meeting, my first in-person conference after almost four years.
#BPS2024
Come visit me at my poster (2643-Pos) on Wednesday 10:30 am in Exhibit Hall AB, B35.
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"We have now reached a stage where the full complexity of real cell membranes is being captured."
Marrink et al. look back on three decades of membrane simulations and ask "what stage comes next?"
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“If so many people who are in a certain field would come together in a room and forget their names, their egos, their titles, and just think, they would come up with so many solutions for so many things, but all these titles and whatever get in the way.”
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Sign at the railway station:
"Trespassers will be cited."
Me, an academic:
*runs back and forth across the tracks*
#AcademicTwitter
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Best paper award for ATOM3D!
🎉 ⚛ 🍾
Many thanks and congratulations to
@raphaeljlt
,
@PatriciaSuriana
,
@awfderry
and everyone who contributed! It has been a blast to be part of this project and I am looking forward to
#NeurIPS2021
.
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New PENSA release: Main addition in version 0.2.8 is functionality to estimate uncertainty via block analysis. Thanks to
@njthomson_
for taking the lead on implementing this!
Update it via: pip install pensa==0.2.8
Feedback is always welcome!
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I contributed to
@500QueerSci
, a visibility campaign for LGBTQ+ people and their allies working in STEM and STEM-supporting jobs. 🏳️🌈
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Everyone talks about how Instagram with its emphasis on promoting ideal and unrealistic lifestyles is bad for mental health.
But nobody talks about Google Scholar. 🙃
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UPCOMING WEBINAR | Accurate modeling of receptor functional response: GPCRs and beyond
Date/Time:
February 28th, 2024
11:00 AM ET / 5:00 PM CET
Speakers:
Lingle Wang, Martin Vögele
View the full abstract and register here:
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Membranes crumple in MD simulations with a semi-isotropic barostat if neighbor list cutoffs are too small and updates too infrequent. 🤯
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Pneumococci attack host cells by perforating their membranes with large pores. We used atomistic and coarse-grained MD simulations of the pore-forming toxin pneumolysin together with an elastic membrane model to show how these pores are formed: . (1/8)
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C arrays vs. FORTRAN arrays
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#autumn
#sunset
behind the
#library
of the Max Planck Institute of Biophysics in
#frankfurt
.
@maxplanckpress
@Stadt_FFM
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Life update: My appointment at
@Stanford
has been extended beyond the end of my fellowship and I found a new room. 🥳
Being cautiously optimistic, I'm going to move closer to campus – to beautiful Menlo Park. 🙂
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I am happy to join the pool of early-career reviewers for
@eLife
and looking forward to be part of the
@eLifeCommunity
in "structural biology and molecular biophysics."
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Interesting new method to sample conformational space of proteins. The authors claim to discover the full landscape of the β2 adrenergic receptor.
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What people think my meetings look like when I tell them I work with protein models.
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This was my most popular tweet of 2021. 🤪
Shout-out to everyone who is working on making it less true.
🙏
And a happy 2022 to everyone! 🎆
Force fields are like sausages. If you like them, it is best not to see them being made.
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When you've spent a lot of time helping someone with their project and then, by accident, you see the paper which does not even acknowledge that anywhere.
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In molecular dynamics we don't say "I hate you" we say "I wouldn't be sure that your simulation has converged" and that's just cruel.
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We have updated our preprint about ligand efficacy prediction with FEP+.
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Trying to switch to a Central European sleep rhythm so I can virtually attend
#EMBOBioSim
.
I have a poster on PENSA tomorrow (P87).
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After 3.5 years in crisis mode and while again being in work-visa limbo, I'm seriously questioning all my life choices.
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Just submitted my poster for the
@BiophysicalSoc
annual meeting.
Meet me there on Wednesday, February 24, 2021 to ask whether we've already managed to release some of the "coming soon" functionality. 🤞
#BPS2021
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Bug of the day:
import numpy as pd
import pandas as np
🤦♂️
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The last chapter of my PhD thesis is published! 🎉
Inspired by 2D membrane protein crystallization, we simulate how carbon nanotube porins can self-assemble in lipid membranes to form efficient nanofiltration devices.
🧵👇
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Just a bunch of proteins, vibin' in the membrane.
(background: )
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Men will literally buy themselves a social media platform instead of going to therapy.
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Me: "Make sure we cite all relevant literature."
Raphael: "Everything?"
Me: "Yes, everything."
Raphael:
Unhappy your work hasn't been cited? 😡 Finding it tricky to get credit attribution right? 🧐 We present a definitive solution: simply cite everything!
11M citations, 200K pages, 1.8 GB PDF.
Enabled by the great
@opencitations
resource.
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Finally ported my code for the membrane diffusion corrections to Python 3.
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Had a great read catching up with coarse-grained simulations in materials science. A lot has happened in the last few years:
Fascinating review by
@ricalessandri
, Fabian Grünewald and
@CG_Martini
.
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So excited to release this project into the wild. 🥳
ATOM3D started as a coffee break discussion with
@raphaeljlt
and escalated into a huge data curation and benchmark project with
@PatriciaSuriana
,
@awfderry
and many more joining in. Big thanks to everyone in this amazing team!
Looking for new challenges for machine learning in structural biology?
Check out our recent release: ATOM3D, a unified collection of diverse benchmark datasets for biological problems that deal with atom coordinates in 3D space. ⚛️⚛️⚛️
[1/4]
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Rotational diffusion in membrane protein simulations depends on the box size!
Luckily, these effects turned out to be easier to estimate than for translational diffusion.
We
@MPIBP
even found an easy rule for the size of the simulation box to avoid them.
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Google Maps is showing a picture I took as the top preview for Pier 39, one of San Francisco's most visited tourist attractions.
This has probably more impact than any research I've ever published. 🙃
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Nice article about thermodynamics in the microscopic realm in honor of the 25th anniversary of Jarzynski’s equality.
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German word of the day: Lustkauf
(literally: pleasure purchase)
An impulsive and unreasonable buy of an expensive item that brings the buyer joy.
Example: “My new zoom lens really was a lustkauf.”
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Last week I recorded a talk in which I claim that protein structure prediction is a hard and yet unsolved problem. When the talk will stream next week, this
#CASP14
result will make me look like an clown. 😅
CASP14
#s
just came out and they’re astounding—DeepMind looks to have solved protein structure prediction. Median GDT_TS went from 68.5 (CASP13) to 92.4!!!! Cf. their 2nd best CASP13 struct scored 92.8 (out of 100). Median RMSD is 2.1Å. I think it's over
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Obituary for Berni Alder, inventor of molecular dynamics simulations.
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“The Unknown Postdoc Weeping Over the Rejected Manuscript”
— Marble sculpture, 1908
#PostdocAppreciationWeek
#NPAW
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My phone auto-corrects latex to LaTeX and I've never felt more understood.
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Good news for molecular simulations:
@CompBioPhys
@VytasGapsys
confirm that the simulation box size only minimally affects thermodynamics and kinetics of typical biomolecular systems:
... in contrast to diffusive dynamics. 😉
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Happy
#LGBTQSTEMDay
!
Even some of the G protein-coupled receptor complexes I'm currently simulating are in pride mood.
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New PENSA release: Version 0.2 comes with state-specific information (SSI) analysis, a method that was originally designed to discover signaling pathways involving microswitches but turns out to be much more generally useful.
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Cool paper on the mechanism of a blood-brain-barrier lipid transporter – with MD simulations by my amazing colleague
@DenizAydinPhD
.
#lipids
#biophys
#compchem
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Our ATOM3D paper was selected for an oral presentation at
#NeurIPS2021
in the first ever Datasets and Benchmarks Track.
🎉🍾🎉
Big thanks to the reviewers who "note the importance of the problem, the clarity of the presentation, and the scope of the work."
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Pro tip for all junior scientists:
Create a Google Scholar profile for yourself!
This is little effort but helps many people to find your papers - especially if they only remember your name or pieces of the title.
#AcademicTwitter
#ScienceTwitter
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My parents in Germany finally received a COVID-19 vaccine. 💉🩹🥳
While this already helps me sleep better, I strongly hope that my country will also help people in current hot spots like India and Brazil. 😰
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"On a scale from 1 to 10, how confusing is life in the US?"
"Is the scale in metric or imperial units?"
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So I've bought a new phone and we're having a difficult start. 🙄😅
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Whenever my phone shows an AMBER alert, I think for a second that something must have really gone wrong with my simulations. 🙃
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I used to be super impressed when actors in Hollywood movies would just punch holes into walls.
Now I know how houses in California are built and I'm already disappointed if they don't just walk through.
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"My proteins do wiggle wiggle, then fold."
TikTok is hiring a computational chemist to "speed up classical molecular dynamics and quantum chemistry algorithms with artificial intelligence and high-throughput computational methods"🤯
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The
@lindaunobel
meeting is over - a fantastic week with amazing people. 😍
I learnt a lot about great discoveries in physics and visions for its future. We also discussed a lot about our roles in science and how to make it more open, welcoming, and beneficial to society.
#LINO19
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Membrane proteins rotate differently in dilute and in crowded membranes. Javanainen et al. show how crowding alters rotational diffusion:
They also use our correction formula, yay! 🙂
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"The hypercompetitive academic environment offers a ‘survival benefit’ for people with personality traits such as boldness, dominance, meanness and disinhibition. These personality traits have been clearly associated with bullying behaviours."
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I'm pretty imressed by this large dataset of protein-ligand MD trajectories! 🤩
... and happy they implemented it in line with ATOM3D. 😁
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