Jan Kosinski
@jankosinski
Followers
6,070
Following
288
Media
141
Statuses
1,359
I solve molecular puzzles. We are hiring:
Hamburg, Germany
Joined June 2010
Don't wanna be here?
Send us removal request.
Explore trending content on Musk Viewer
Apple
• 544825 Tweets
Pelosi
• 139479 Tweets
renjun
• 107273 Tweets
iOS 18
• 93491 Tweets
OpenAI
• 82829 Tweets
National Guard
• 79591 Tweets
Lakers
• 76341 Tweets
ARMY FOREVER BANGTAN FOREVER
• 67524 Tweets
iPad
• 64780 Tweets
#امن_الحج_خط_احمر
• 45960 Tweets
Siri
• 45614 Tweets
Benny
• 37691 Tweets
Arda
• 35807 Tweets
Semih
• 33744 Tweets
ESTREIA NA CAMA COM PITANDA
• 33444 Tweets
Ubisoft
• 32774 Tweets
Nodal
• 31474 Tweets
Thelma
• 31327 Tweets
Comicstorian
• 30021 Tweets
Palacio Nacional
• 27566 Tweets
kcon
• 26984 Tweets
Darthes
• 25804 Tweets
Grok
• 24132 Tweets
Jordan Ayew
• 22448 Tweets
Cazzu
• 21673 Tweets
Ángela Aguilar
• 20392 Tweets
Airbnb
• 19954 Tweets
Aye Alfonso
• 18946 Tweets
Chiquita Brands
• 18702 Tweets
Samet
• 16563 Tweets
#WWERaw
• 16310 Tweets
#ローソン盛りすぎチャレンジ
• 10896 Tweets
Barış Alper
• 10297 Tweets
Pinned Tweet
The final version of the PyTME paper published in
@SoftXJournal
! PyTME enables fast CPU and GPU-based template matching in
#cryoET
and fitting in
#cryoEM
. More in the thread with plenty of screenshots👇
1
18
71
This is the end of the world as we know it, if this is reproducible! The new era of functional modeling has begun. I took a transcription factor with an unknown structure and folded it with its recognition sequence embedded in longer DNA. AlphaFold3 accurately positioned the
176
911
5K
We combined
#AlphaFold
and
#cryoEM
to build a new model of the nuclear pore complex, the largest complex in the human cell!
The structure covered by the model is 15x bigger than the human ribosome and 2x bigger than old nuclear pore models. 1/7
Read how:
31
632
3K
AlphaFold3 is insane. MutS protein (green) recognizes base mismatches in DNA (gray), after which it slides off to find MutL matchmaker protein (blue), which positions and activates MutH nuclease (pink) to nick a hemimethylated GATC sequence (red) to activate removal and repair of
32
345
2K
I think this is BIG. MutS protein recognizes mismatches in DNA. AlphaFold3, when given the MutS sequence and long DNA with the mismatch, finds the mismatch and models the complex in the correct conformation.
@rfleiro
You won't believe... Left - crystal structure of MutS bound to G:T mismatch, in red (PDB ID: 1E3M). Right - AlphaFold3 model with longer and different DNA and A:C mismatch, in red... It managed to find the mismatch?? 🤯The models are here:
5
17
111
14
122
685
Might attempt to model a flotillin cage using the AlphaFold3 web server was super fun (original paper: ). Read the thread for a crazy plot twist!🧵👇
8
88
639
Here is a AlphaFold/ColabFold tutorial we have recently presented - from basic to more advanced usage, enforcing alternative conformations, modeling interactions, and analysis with ChimeraX and PICKLUSTER. Maybe you find it helpful 🎓 ! Commenting enabled in the doc so feel free
5
144
538
A candidate novel cannabinoid receptor modeled within a lipid-like membrane bilayer using a trick by
@caco3cz
: adding oleic acids (OLA) as ligand 🤯
8
75
450
🌟 Our new Computational Structural Biology Conference! We're committed to making this a must-attend biennial event in the field! 🧬
✅Register & submit abstract👉
🔬
#EMBOComp3D
#ComputationalStructuralBiology
#Bioinformatics
#StructuralBiology
1/4
3
141
422
Can AlphaFold model large RNA structures? I attempted to model the structure of an intron that was released today:
9
91
397
An attempt to model the structure of a large protein complex using the AlphaFold3 webserver. Did it work?
8
46
326
#AlphaFold
,
#RoseTTAfold
,
#ColabFold
, and multiple other tools marked a new era in structural biology with modeling playing the central role. Apply for positions in our group to develop and apply modeling software in this new era:
2
76
313
Our Assembline software, which we used for modeling nuclear pore and other complexes, is published today in
@NatureProtocols
! Paper: Website:
3
79
312
It works for at least two cases. Consider the applications: computing a baseline gene regulatory network for the entire human genome, recomputing for patients in personalized medicine based on SNPs in their genome, and recomputing for already sequenced cohorts and correlating
This is the end of the world as we know it, if this is reproducible! The new era of functional modeling has begun. I took a transcription factor with an unknown structure and folded it with its recognition sequence embedded in longer DNA. AlphaFold3 accurately positioned the
176
911
5K
10
49
288
An in silico protein-protein interaction screen using AlphaFold2, followed by experimental validation, enabled the discovery of a new interaction by the
@WojtekGalej
lab. This showcases the power of 🖥️➡️🧪 approach!
Online Now: Structural basis of the Integrator complex assembly and association with transcription factors
0
35
173
2
47
280
Once an open source copy of AlphaFold3 is available and works as good, we might be able to predict sequence specificity of all transcription factors computationally. I think that would be HUGE, right?
@fabian_theis
?
5
16
243
We cannot directly visualize atoms in cells with
#cryoEM
, but we can do it using computer modeling. In our new article in
@ScienceMagazine
, we show at the atomic level how nuclear pores constrict in cells upon depletion of energy:
3
48
232
Here we contribute 2 more meters of Dr. Rer. Nat. and 250 pages of excellent doctoral thesis! Congrats Kai Karius, the first PhD from our lab!
12
4
228
Here is our AlphaPulldown Python package, by
@dingquan_yu
from our lab, which streamlines the usage of AlphaFold-multimer for interaction screens and modeling parts of large complexes
AlphaPulldown - a Python package for protein-protein interaction screens using AlphaFold-Multimer
#bioRxiv
2
117
475
2
41
219
OpenFold published! 🥳 This is one of the very few AI-based structure prediction programs that are fully open-source i.e. including training code (next to Uni-Fold and not sure if anything else)
OpenFold developed by
@gahdritz
,
@NazimBouatta
, and
@MoAlQuraishi
is a trainable, open-source implementation of AlphaFold2. It is fast and memory efficient, and the code and training data are available under a permissive license.
6
149
421
0
44
211
A new version of AlphaPulldown by
@dingquan_yu
. Includes experimental support for multimeric templates in AlphaFold by
@DmitryMolo90428
and interface to crosslink-based modeling AlphaLink2 of
@RappsilberLab
6
57
195
In this paper published today in
@nature
we characterize the *in-cell* structure and turnover of yeast nuclear pore complexes, modeling work by
@RantosVasileios
from my lab and in collab. with
@Beck_Laboratory
,
@Matteoffm
@ZimmerliChris
&
@WilflingFlorian
3
35
189
We don't know yet whether it does, but if this sequence specificity generalizes to CRISPR, zinc fingers, TALENs, restriction nucleases - how much income 🤑 that could generate to AlphaFold3 owners?
This is the end of the world as we know it, if this is reproducible! The new era of functional modeling has begun. I took a transcription factor with an unknown structure and folded it with its recognition sequence embedded in longer DNA. AlphaFold3 accurately positioned the
176
911
5K
5
27
185
I feel like playing with DALLE... The models look great but when you look closer some things are new and impressive, but some things seem hallucinated. Care and experimental validation thus as always required!
AlphaFold3 is insane. MutS protein (green) recognizes base mismatches in DNA (gray), after which it slides off to find MutL matchmaker protein (blue), which positions and activates MutH nuclease (pink) to nick a hemimethylated GATC sequence (red) to activate removal and repair of
32
345
2K
4
22
155
I think I won't model anything today, so just reposting what we modeled 2,5 years ago using AlphaFold2, shortly after it came out 🥹
We combined
#AlphaFold
and
#cryoEM
to build a new model of the nuclear pore complex, the largest complex in the human cell!
The structure covered by the model is 15x bigger than the human ribosome and 2x bigger than old nuclear pore models. 1/7
Read how:
31
632
3K
2
21
142
Like this post if you want to know whether AlphaFold3 correctly recapitulated sequence and methyl group binding specificity of MutH, and whether I should use my last job today for adding the missing ion 😂
4
2
141
Wondered how do we model nuclear pores? Now you can do it too!
@RantosVasileios
, Kai Karius, and I present Assembline - our assembly line of macromolecular assemblies! Website: , preprint:
5
31
141
This is the transcription factor I took and this is the DNA sequence I used CAGGATCCTAATTATGGATCCTGTGTATCTTCAGT. Have i missed anything that could leak structural information?
6
12
141
Thanks for liking this story! As promised - yes, AlphaFold3 did get the sequence binding correctly and put N6-methyl-deoxy-adenosine in the right place, as in the crystal structure! Will this sequence specificity work for transcription factors too? NOTE: the crystal structure was
Like this post if you want to know whether AlphaFold3 correctly recapitulated sequence and methyl group binding specificity of MutH, and whether I should use my last job today for adding the missing ion 😂
4
2
141
2
15
135
I submitted a request for modeling the complete cage using the "feedback" button, please share and like this post so maybe they notice and do it for me 😂 🙏
@GoogleDeepMind
@demishassabis
@OVKovalevskiy
@tfgg2
@elonmusk
3
9
128
It was a wonderful
#EMBOComp3D
meeting with 500 onsite and virtual participants! Latest news, algorithms fresh from oven, tips & tricks, spotlights on achievements and challenges, community building across disciplines. Mark calendars for the next one in 2025 and please repost!
🌟 Our new Computational Structural Biology Conference! We're committed to making this a must-attend biennial event in the field! 🧬
✅Register & submit abstract👉
🔬
#EMBOComp3D
#ComputationalStructuralBiology
#Bioinformatics
#StructuralBiology
1/4
3
141
422
1
30
122
Does anyone have a public domain slide deck about AlphaFold that the community could use in academic lectures and tutorials? I mean intro slides about CASP performance, how AF works, confidence metrics, ColabFold, OpenFold, RoseTTAFold, ChimeraX plugins, etc. Asking for a friend.
8
19
123
Here is another one, with a different structural fold (FOX)
5
11
114
Neither cryoEM nor AlphaFold alone is sufficient, you need both! Colleagues from the Löw group
@EMBLHamburg
and co, resolve one conformational state using cryoEM, model two others with AlphaFold, and use clever biophysics to assign function of a new membrane transporter.
Finally, out!
MFSD1 functions as a general dipeptide uniporter in lysosomes!
This was a real team effort. Many thanks to
@Kathaschnatta
,
@DammeMarkus
,
@OceaneGuelle
and Bruno Gasnier,
@AhmadRezaMehdi1
,
@abu_remaileh
, and everyone else involved!
See:
0
11
56
2
11
112
@rfleiro
You won't believe... Left - crystal structure of MutS bound to G:T mismatch, in red (PDB ID: 1E3M). Right - AlphaFold3 model with longer and different DNA and A:C mismatch, in red... It managed to find the mismatch?? 🤯The models are here:
5
17
111
And then the structure forms a barrel! 🤯 Phospho in red. The structure is still incorrect (flotilin1 and 2 should alternate; the twisting of the subunits is wrong etc.), but to me it is amazing that it reacts to the physiologically relevant phosphorylation and "getting in the
1
10
105
Some structures are known (MutS-MutL Nter, MutH-DNA, MutL Cter dimer, and model agrees with them) but not MutL-MutH. I spent large part of my PhD characterizing the interaction site of MutH or MutL with biochemistry and computational docking. The model is spot on with what I got
4
4
104
Did I mention yet that we have PhD and postdoc positions available here in Hamburg, Germany?
Germany passes law to legalise cannabis allowing users to possess and grow a limited amount, but it will remain hard to buy
186
263
1K
5
19
102
We are looking for a Senior Scientific Software Engineer to develop new software tools for modeling large molecular complexes. Perfect balance between academic research and software development.
#python
#programming
,
#AlphaFold
,
#cryoEM
. Apply here:
1
56
95
Here is the Introduction to
#AlphaFold
presentation I compiled based on your slides (
@LindorffLarsen
@arneelof
@sokrypton
Sameer Velankar): . Thank you again!!
3
8
96
So far, we have ~ 250 on-site, > 200 virtual participants, 150 posters; 40 talks and >20 flash talks, late program change with John Jumper from
@GoogleDeepMind
joining us to give a talk, and invitations to register for PhD/postdoc job fair coming soon. Have you registered yet?
🌟 Our new Computational Structural Biology Conference! We're committed to making this a must-attend biennial event in the field! 🧬
✅Register & submit abstract👉
🔬
#EMBOComp3D
#ComputationalStructuralBiology
#Bioinformatics
#StructuralBiology
1/4
3
141
422
1
16
92
Last days to apply and join us in pushing the new era of structural biology!
We are looking for a Senior Scientific Software Engineer to develop new software tools for modeling large molecular complexes. Perfect balance between academic research and software development.
#python
#programming
,
#AlphaFold
,
#cryoEM
. Apply here:
1
56
95
1
31
90
6 - 9 Dec 2023, at
@EMBL
Heidelberg, we will organize a new
@EMBOevents
Computational Structural Biology conference! . Together with
@RommieAmaro
,
@ChristineOrengo
, and Sameer Velankar. More details soon, but please block the dates!
1
19
85
The most beautiful seminar room ever (note the view at the lake! 🤩) for Spring School of DFG grad school VISION where we will teach ChimeraX, Pymol, AlphaFold, ColabFold, AlphaFold Database, PICKLUSTER, FoldSeek and more!
1
2
83
The template database for AlphaFold3 server is from 2021-09-30 ‼️ That means - any structures published after are not used. Still, when testing using structures published after that date we should check for highly similar structures. A thread how 👇
@jankosinski
@GoogleDeepMind
Thank you Jan for the intensive testing and interesting findings! For the templates, it is the same cutoff as mentioned in the paper, i.e. 2021-09-30. We will add this to the Server FAQ for clarity and will let users know if we change this date
2
5
19
2
21
80
@ATinyGreenCell
Ah, right, using the AlphaFold3 server, . The magic is that I did not do anything special! I googled what is a database of transcription factors, found JASPAR, went there, filtered to get some human ones, took some random two that do not have structures
3
6
79
Just reposting for the new followers - consider applying for the course in Hamburg where we teach how to solve macromolecules using experimental and computational approaches! We just need to update the AlphaFold tutorial now 😅
#EMBOStructBio
is open for applications 🧬🧩🕵🏻
Learn how to analyse and interpret experimental data and construct structural models across different resolution scales. 💻👌🏻
📅 17 – 24 Nov 2024
📍
@EMBLHamburg
✍🏻 Apply by 25 Aug
➡️
#EMBL50
#AI
0
18
47
0
14
77
But I would be happy if someone checks if I haven't confused sth here, if it is consistent for other transcription factors, and whether the scores can be used to discriminate specific and unspecific sequences.
3
1
76
@sniperinthewND
Chatgpt summary: Jan Kosinski is excited about using a new computer program called AlphaFold3, which can predict how proteins, the machines inside our cells, shape themselves and attach to DNA. DNA contains the instructions for building proteins, and understanding how proteins
7
15
76
AlphaFold3 will be released as a standalone software? 🤩🥹
We love the excitement & results from the community on AlphaFold 3 and are doubling the AF Server daily job limit to 20. Happy to also share that we're working on releasing the AF3 model (incl weights) for academic use, which doesn’t depend on our research infra, within 6 months.
27
202
904
1
4
74
Four jobs more and I go check what kids are doing upstairs
AlphaFold3 is out with improvements on structural models that include DNA/RNA and small molecules. Unfortunately, there is no code, no binary to run at scale and only a limited webserver. Why even publish?
12
125
592
5
0
70
Modeling took less than 30 minutes. It took me more to prepare the input.
2
1
69
@dingquan_yu
AlphaPulldown-a Python package for protein-protein interaction screens using AlphaFold-Multimer now published in Bioinformatics. In response to users and reviewers, we added MMSeqs2 support thanks to ColabFold by
@sokrypton
@thesteinegger
1
12
69
Work is in full swing on AlphaPulldown by
@dingquan_yu
and
@DmitryMolo90428
, but with so many users, thousands of downloads, and 34 open issues, incl. many exciting feature requests, help would be welcome! If you want to contribute, feel free to fork and submit a pull request!
3
17
66
As
#AlphaFold
big fan, I was thrilled to meet the delegation from
@DeepMind
, incl.
@demishassabis
and John Jumper! Very interesting discussions about the future of
#AlphaFold
and applications of
#AI
in biology. What problem shall they solve next?
EMBL Heidelberg welcomed representatives from DeepMind including Demis Hassabis and John Jumper.
They shared their story of developing the AI tool AlphaFold, met with EMBL scientists and learnt more about our research and services.
0
25
182
0
4
67
Wait a minute - MutL has been hypothesized to bind DNA too but in my model DNA is too short... What if I make it longer? 🤯 I need more jobs or code!!
🚀The era of modeling function began today 🚀
1
2
65
November 2022,
@EMBL
Hamburg: Maya Topf, Arjen Jakobi and myself will hold the next edition of our EMBO Practical integrative structural biology!
#CryoEM
,
#MX
,
#SAXS
,
#MS
,
#NMR
,
#MD
,
#modeling
. See the program and apply:
Apply now! Registration is now open for EMBO Practical Course on Practical integrative structural biology
06 – 13 November 2022 in Hamburg, Germany
#EMBOstructuralBiology
0
1
6
1
32
64
Hold my beer and fasten your seat belts ;-)
A team led by
@aschuller17
&
@schwartzlabmit
found a way to analyze the nuclear pore complex directly inside cells. The pore has larger dimensions than previously thought—showing just how vital it is to study complex molecules in their native environments:
0
14
53
3
2
63
And another one, maybe without the training bias. Should bind specifically promoter region ATTTTAGTCGCGCCTAAAAT and it does again! Left is crystal structure, right is the AlphaFold3 model. Promoter is in red.
3
6
62
We are recruiting two PhD students 🎓 this round! Dry lab 💻: AI-based structural modeling method development and application. Wet lab 🧪: In-cell cryoET and/or crosslinking mass spectrometry of viral infection. Apply ✍️ by 11 March! ⌛️
1
36
60
Sad that code is not released but I am testing the server and it is not bad and super fast (7 minutes for 1700 residues of a protein-RNA complex).
Thrilled to announce AlphaFold 3 which can predict the structures and interactions of nearly all of life’s molecules with state-of-the-art accuracy including proteins, DNA and RNA. Biology is a complex dynamical system so modeling interactions is crucial
205
2K
8K
0
5
58
Nuclear pore structures by
@aobarska
now available for download! With
#AlphaFold
's confidence score pLDDT in the b-factor column!
305 new entries to the PDB this week, including this constricted form of the Human nuclear pore complex (7R5K) from scientists
@embl
&
@MPIbp
(
@jankosinski
,
@Beck_Laboratory
, Hummer labs), published in
@ScienceMagazine
. Latest entries:
0
32
217
0
11
58
That's it! 2022
@EMBOevents
Practical integrative structural biology by Arjen Jakobi, Maya Topf, and myself ends with integration over Limoncello. Full-day intense structural biology, late-night visits to The Library, and sprints across
@EMBLHamburg
@CssbHamburg
and
@desy
5
6
57
🤯🤯👇👇👇👇👇👇🤯🤯
1
8
57
I love playing with molecular puzzles and cannot stop 😂 Just added some plot twist and new insight on how to push AlphaFold3 webserver to get sth a bit better!
An attempt to model the structure of a large protein complex using the AlphaFold3 webserver. Did it work?
8
46
326
4
4
57
From the
#CryoEM
resolution revolution to
#evolution
: Our opinion article with
@Beck_Laboratory
about how
#CryoEM
helps to understand evolutionary relationships
0
19
55
AlphaFold3 also fails to correctly predict the sequence for the restriction nuclease BamHI, despite the availability of five structures, including four with DNA (). On the left is the model, and on the right, the crystal structure. Given that some of these
6
19
55
Special issue of
@JMolBiol
about how Alphafold impacts biology, including our contribution on how it empowers integrative structural biology, has been just published. Some of our predictions like modeling complexes already came true, sooner than I thought:
2
21
54
On my way to Heidelberg for our
#EMBOComp3D
conference 🏎️ Safe travel to all participants! 🌨️ Can’t guess what one of you is bringing in this AlphaTruck… Looking forward to learn about the latest developments in computational structural biology! 😋
🌟 Our new Computational Structural Biology Conference! We're committed to making this a must-attend biennial event in the field! 🧬
✅Register & submit abstract👉
🔬
#EMBOComp3D
#ComputationalStructuralBiology
#Bioinformatics
#StructuralBiology
1/4
3
141
422
2
3
54
In this perspective article, we discuss how accurate modeling methods like
@UWproteindesign
's
#RoseTTAfold
and
@DeepMind
's
#AlphaFold
will empower integrative structural biology, we highlight selected challenges, and dare to envision new avenues for
#AI
0
14
53
Before leaving for the holiday break, check out the summary of our recent
@NatureProtocols
and
@ScienceMagazine
publications about our modeling software Assembline and structures of the nuclear pore complex as it opens and closes inside cells. By
@d_badowska
@EMBLHamburg
Watching molecules in the cell at atomic resolution:
EMBL Hamburg’s Kosinski Group,
@Beck_Laboratory
& colleagues have visualised how the nuclear pore complex dilates and contracts in living cells, using a newly developed software.
0
16
61
0
11
52
, no structure, TCCTGTGTATCTTCAGTGTAAACATTCCAAGCCT, and
3
3
51
So, run out of jobs and friends accounts are busy with other molecules so follow me tomorrow to see what happens when I add more ions, ATP, longer DNA and the mismatch!
3
1
49
Great day because we can now predict protein structures accurately (using Google's and
@DeepMind
's
#AlphaFold2
), bad day because we cannot do it (the software is not available). Tweet, RT, shout for
#OpenFold
1
19
48
16 rising stars of integrative structural biology together with (some) tutors of our EMBO Integrative course! All motivated, engaged, interested, discussing their projects all the time, and even already having a WhatsUp group!
@EMBLEvents
@EMBLHamburg
4
6
46
Almost forgot to share: here is my little software package to relax (energy minimize) PDB structures with a simple command . Written to relax unrelaxed AlphaFold etc. models from larger screens but turns out useful in general. Thanks
@MSiggel
for advice.
1
9
44
🚨COUNTDOWN: Only 11 days left for abstract submissions!🚨 Dive into the latest in comp structural biology, network, explore job fair, enjoy parties, visit the Christmas market, and win the special
#EMBOComp3D
Pub Quiz! 🎉🧬
✅ Submit your abstract NOW 👉
🌟 Our new Computational Structural Biology Conference! We're committed to making this a must-attend biennial event in the field! 🧬
✅Register & submit abstract👉
🔬
#EMBOComp3D
#ComputationalStructuralBiology
#Bioinformatics
#StructuralBiology
1/4
3
141
422
0
16
45
Another pore bites the dust! This one features an extra ring 🤯and is particularly stiff, which might aid in tackling challenging environments. By
@aobarska
@Beck_Laboratory
@HummerLab
& co, with a bit of bioinformatics assistance from
@lenka_cernik
(1/2)
#nuclearpores
facilitate rapid changes in nuclear size in response to osmotic stress. This is relevant under changing environmental conditions.
Work
@pc_hoffmann
Henry Kim
@aobarska
and others in collaboration with
@HummerLab
now online:
1
24
102
0
8
45
@demishassabis
I forgot to include Mg2+ in the MutH active site but have only one job remaining and still want to try sth else. A limit of 20 or another access model would be nice, look what could be done with this 😜
2
1
44
FYI just added to my large RNA modeling thread
BTW. AlphaFold3 nicely places the DNA strand and ions in the expected active site but I don't know whether this comes from templates or not (some templates have RNA there).
1
3
17
1
10
42
Closing
#EMBOComp3D
party 🎉 But we remain serious. We won’t be late for tomorrow morning session.
1
3
43
Wow, our recent
#EMBOComp3D
conference tweet is doing great, especially for a no-Blue account. Hopefully, it means we'll have a solid turnout. 😊 Fancy helping us reach even more people? A Like or RT on the original post would go a long way!🙏🙏👇👇
🌟 Our new Computational Structural Biology Conference! We're committed to making this a must-attend biennial event in the field! 🧬
✅Register & submit abstract👉
🔬
#EMBOComp3D
#ComputationalStructuralBiology
#Bioinformatics
#StructuralBiology
1/4
3
141
422
0
9
39
@KentLangley
Only of the world as we know it ;-) I feel this is a first step towards a predictive computational and personalised model of whole genome regulation, which will accelerate research and medicine. But let's see first if the results hold and was no data leak!
2
4
39
Look with what twist the restriction nuclease story continues... win or fail?
FYI: restriction nuclease HpaI gets placed on the correct cleavage sequence GTT/AAC after I removed all other palindromes and quasi-palindromes from the cleavage sequence. Otherwise, it sticks to them, sometimes with better scores than the correct one.
1
2
20
1
11
40
Overwhelmed by the fantastic response to
#EMBOComp3D
! Due to a very nice number of registrations & abstract submissions, we'll most likely close abstract submission as planned tomorrow at 23:59 German time. So act now: ✅ Register & submit: 🚀🔬
🌟 Our new Computational Structural Biology Conference! We're committed to making this a must-attend biennial event in the field! 🧬
✅Register & submit abstract👉
🔬
#EMBOComp3D
#ComputationalStructuralBiology
#Bioinformatics
#StructuralBiology
1/4
3
141
422
0
8
36
I am looking forward to visiting iMol Institute for the first time! I will talk about the "old" cool NPC stuff and computational modeling but also about a new story related to viral infection coming from our wet lab 🤩 Do zobaczenia!
Join our next edition of IMol Science Club with Dr.
@jankosinski
. Jan is a Group Leader and Co-chair of Infection Biology Transversal Theme at
@embl
in Hamburg. His group investigates viruses and parasites using structural and systems biology approaches.
@NCN_PL
1
1
14
1
3
35
@aobarska
modeled individual proteins with AlphaFold, sub-complexes with
@sokrypton
's AlphaFold/ColabFold, and then put all the pieces together using our software Assembline guided by cryo-ET maps of pores from isolated envelopes and directly from cells.
1
1
36
We're recruiting a PhD student! Structural and/or systems biology of influenza A virus infection, dry lab: structural or systems modeling software development or applications, wet lab: proteomics, imaging. More about us:
0
28
35
In summary, the AlphaFold3 web server cannot replace the experimental structure determination in some cases, as others have also noted. In addition, incompatible functional states may get mixed up in one model as in my earlier experiment .
AlphaFold3 is insane. MutS protein (green) recognizes base mismatches in DNA (gray), after which it slides off to find MutL matchmaker protein (blue), which positions and activates MutH nuclease (pink) to nick a hemimethylated GATC sequence (red) to activate removal and repair of
32
345
2K
1
8
35