Jan Choutka
@choutkaj.bsky.social
Interested in:
- Computational biophysics
- Medicinal chemistry
- ME/CFS research
- Computational biophysics
- Medicinal chemistry
- ME/CFS research
Not Banksy, it's based on Loretto but it's been edited.
March 5, 2025 at 6:59 AM
Not Banksy, it's based on Loretto but it's been edited.
Cool stuff. Is GOAT reactive? The epoxide is supposed to react with the thiol, right?
February 26, 2025 at 11:31 AM
Cool stuff. Is GOAT reactive? The epoxide is supposed to react with the thiol, right?
Very informative. Thanks.
January 9, 2025 at 2:40 PM
Very informative. Thanks.
Another recent paper about MBE fragmentation on protein-ligand systems:
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Protein–Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions
Quantum-chemical fragmentation methods offer an attractive approach for the accurate calculation of protein–ligand interaction energies. While the molecular fractionation with conjugate caps (MFCC) sc...
pubs.acs.org
January 3, 2025 at 9:35 AM
Another recent paper about MBE fragmentation on protein-ligand systems:
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Maybe set enforcePeriodicBox=True when appending the reporter?
December 14, 2024 at 2:50 PM
Maybe set enforcePeriodicBox=True when appending the reporter?
Do you think most humans would be able to fix your latex problem?
December 10, 2024 at 3:34 PM
Do you think most humans would be able to fix your latex problem?
Good idea, I will check it out. Thanks.
December 7, 2024 at 5:30 PM
Good idea, I will check it out. Thanks.
I've recently collated affinities for over 1000 inhibitors of Galectin-1 and -3, all measured by a single assay (fluorescence anisotropy). Ligands are provided as SMILES. Paper is pending.
Anyone is welcome to test their method on this set.
github.com/choutkaj/GFA...
Anyone is welcome to test their method on this set.
github.com/choutkaj/GFA...
GitHub - choutkaj/GFA-ligand-set: Set of galectin ligands with known affinities.
Set of galectin ligands with known affinities. Contribute to choutkaj/GFA-ligand-set development by creating an account on GitHub.
github.com
December 7, 2024 at 12:50 PM
I've recently collated affinities for over 1000 inhibitors of Galectin-1 and -3, all measured by a single assay (fluorescence anisotropy). Ligands are provided as SMILES. Paper is pending.
Anyone is welcome to test their method on this set.
github.com/choutkaj/GFA...
Anyone is welcome to test their method on this set.
github.com/choutkaj/GFA...
Ok, now I get it. Thanks!
November 28, 2024 at 1:36 PM
Ok, now I get it. Thanks!
I don't see how vacuum would be relevant. The water is not choosing between the binding site and vacuum. It's choosing between the binding site and bulk.
November 28, 2024 at 10:55 AM
I don't see how vacuum would be relevant. The water is not choosing between the binding site and vacuum. It's choosing between the binding site and bulk.
If it's unfavorable (positive deltaG compared to bulk) for the water to be in that position, why it stays there?
November 28, 2024 at 10:28 AM
If it's unfavorable (positive deltaG compared to bulk) for the water to be in that position, why it stays there?
Just tried it out. This is next level stuff.
November 25, 2024 at 9:50 PM
Just tried it out. This is next level stuff.
Molecular nodes are great. Might I ask if you plan to add support for double/triple bonds, and delocalized bonds in aromatic rings? Thx
November 25, 2024 at 3:45 PM
Molecular nodes are great. Might I ask if you plan to add support for double/triple bonds, and delocalized bonds in aromatic rings? Thx
I would say there is a breaking point if the method is so costly that you can only access timescales that do not give you any meaningfull information about the system.
E.g. with QM dynamics, you can maybe simulate a protein for a few ps. That is pretty useless.
E.g. with QM dynamics, you can maybe simulate a protein for a few ps. That is pretty useless.
November 23, 2024 at 2:48 PM
I would say there is a breaking point if the method is so costly that you can only access timescales that do not give you any meaningfull information about the system.
E.g. with QM dynamics, you can maybe simulate a protein for a few ps. That is pretty useless.
E.g. with QM dynamics, you can maybe simulate a protein for a few ps. That is pretty useless.
For simulating lets say a protein of 2000-5000 atoms in explicit water, more than 100x slowdown will hurt a lot.
Having said that, if the increased cost is paid off by increased accuracy, then there is always a merit.
Having said that, if the increased cost is paid off by increased accuracy, then there is always a merit.
November 23, 2024 at 2:35 PM
For simulating lets say a protein of 2000-5000 atoms in explicit water, more than 100x slowdown will hurt a lot.
Having said that, if the increased cost is paid off by increased accuracy, then there is always a merit.
Having said that, if the increased cost is paid off by increased accuracy, then there is always a merit.
Would be a funny plottwist if bluesky changed its name to twitter.
November 19, 2024 at 1:45 PM
Would be a funny plottwist if bluesky changed its name to twitter.
Throw in HolyC to spice it up.
November 19, 2024 at 7:18 AM
Throw in HolyC to spice it up.
This is really great paper. I have been going back to it multiple times. Thanks for all your work.
November 17, 2024 at 1:08 PM
This is really great paper. I have been going back to it multiple times. Thanks for all your work.