Thomas Evangelidis

Founder, CEO & CTO at AI|ffinity ( Computer-Aided Drug Design & NMR. Strictly science-related posts.

[Thomas Evangelidis @tevangelidis]

NMR structure determination at record time⚡!
Watch how in AI|ffinity (https://t.co/xC2macpHO2) we fold proteins from just two 4D spectra:

https://t.co/EcKkn2WyyW

#ai #software #nmr #structuralbiology #proteomics #drugdesign #proteinengineering #biotechnology #pharma

[Thomas Evangelidis @tevangelidis]

@Andrew_Akbashev On one hand your posts are descriptive, concise and accurately reflect academic reality. On the other hand, if you spent less time writing on social media maybe you would have a wealthier publication record and would get the funding. 😁

[Thomas Evangelidis @tevangelidis]

@Andrew_Akbashev But the majority of academic research groups tend to fulfill a greater number of the points you mentioned. 😀

[Thomas Evangelidis @tevangelidis]

Thrilled with my decision to subscribe to ChatGPT! 🎉Its performance surpasses Google Bard by leaps and bounds - truly an investment worth making! 🚀🌟 #AI #ChatGPT #GoogleBard https://t.co/beQAqyd7YP

[Thomas Evangelidis @tevangelidis]

@DFlemmingHansen @LiliMasoumzad1 I am curious to see what will be the outcome. 🙂

[Thomas Evangelidis @tevangelidis]

@joe_fenrir @andrei_yudin In our recent preprint, we demonstrate that explicit calculation of ligand deformation energy and
ligand conformation entropy on the PM6-D3H4X/COSMO level has no positive effect on protein-ligand scoring, despite the huge computational burden they entail.
https://t.co/OuPgDgi7gR

[Thomas Evangelidis @tevangelidis]

@joe_fenrir @andrei_yudin Well, I don't know whether most of the ligands do not bind in a local minimum conformation, but what I can tell for sure is that the contribution of the strain energy and conformational entropy to ligand binding is overrated.

[Thomas Evangelidis @tevangelidis]

@Andrew_Akbashev It couldn't be more true! Postdoc salaries are not only disgraceful for the skills and efforts of the employee, but are usually barely enough for someone to live alone. Imagine having a family to support financially and children to raise with this money...🤯

[Thomas Evangelidis @tevangelidis]

@datamol_io Awesome library and initiative! 👏 👏 👏 Thank you so much! 🙏

[Thomas Evangelidis @tevangelidis]

Structure calculations: NOE distance restraint creation and subsequently Replica Exchange Molecular Dynamics simulations with Solute Tempering from the extended peptide conformation using MELD software. (3 days on a commodity PC with Intel Core i9-12900KF processor and A4000 GPU)

[Thomas Evangelidis @tevangelidis]

Ultra-fast small protein NMR structure determination from just one 4D spectrum⚡!
Watch how we fold proteins in AI|ffinity (https://t.co/3xjdUkoRQR):

https://t.co/zS89nPxeTB

#ai #compchem #nmr #structuralbiology #proteomics #drugdesign #proteinengineering #biotechnology #pharma

[Thomas Evangelidis @tevangelidis]

Protein: https://t.co/AUVhQ7insx, 78 residues
NMR experiments: 4D HCNH NOESY (4 days)
Spectra processing: 2 days including resonance assignment with our 4D-GRAPHS software.

[Thomas Evangelidis @tevangelidis]

@LabSchanda In AI|ffinity we develop a new version rewritten from scratch, which is based on AI and allows whole protein resonance assignment from only one 4D spectrum. Stay tuned to learn more soon. 😉

[Thomas Evangelidis @tevangelidis]

NMR structure determination at record time⚡!
Watch how in AI|ffinity (https://t.co/xC2macpHO2) we fold proteins from just two 4D spectra:

https://t.co/EcKkn2WyyW

#ai #software #nmr #structuralbiology #proteomics #drugdesign #proteinengineering #biotechnology #pharma

[Thomas Evangelidis @tevangelidis]

@LabSchanda Well, according to our Nat Comm paper and also to this video, resonance assignment was conducted with our software 4D-CHAINS. 🙂

[Thomas Evangelidis @tevangelidis]

@ANicoli90 @UCSFChimeraX It would also be nice to display the P-L interactions being formed and disrupted.

[Thomas Evangelidis @tevangelidis]

Structure calculations: Replica Exchange Molecular Dynamics simulations with Solute Tempering using MELD software. (10 days on a commodity PC with Intel Core i9-12900KF processor and A4000 GPU)

[Thomas Evangelidis @tevangelidis]

Protein: MS6282, 145 residues
NMR experiments: 4D HCNH TOCSY (5 days), 4D HCNH NOESY (5 days)
Spectra processing: 3 days including resonance assignment with our 4D-CHAINS software.

[Thomas Evangelidis @tevangelidis]

@Bioinfo_dr None of them! I vote for Glide! 🤣

[Thomas Evangelidis @tevangelidis]

@raghurama123 R^2 is not a good evaluation metric for free energy methods. In the D3R GC they used RMSE and affinity ranking correlation coefficients to evaluate participants' predictions. After all in lead optimization is the ranking power that matters.

[Thomas Evangelidis @tevangelidis]

@ATuerkova I know another one. Those who speak a lot think less, and conversely for the quiet ones. 😁