u/hyperfinesplitting

Hi all,
I’m preparing a protein receptor for AutoDock Vina screening at pH 7.4.

PROPKA gives three potentially relevant His residues with predicted pKa values of 7.26, 7.35 and 8.07. They are currently modeled as neutral HID/HIE states.

Would you:

• protonate the pKa 8.07 His to HIP,
• keep the borderline ones neutral,
• or test multiple receptor protonation states for docking?

How much weight would you give to PROPKA versus local H-bond geometry / experimental structures when deciding?

Thanks!

Hi all,

I have a 16-aa cyclic peptide with a non-standard thioether linkage, and I generated thousands of 3D conformers with Rosetta SimpleCycPepPredict using -cyclic_peptide:cyclization_type thioether_lariat.

I’d like to dock these conformers in batch against a known protein-protein interface while keeping the thioether intact. Many docking tools, including some supporting cyclic peptides, either cannot handle the non-standard linker or require opening the cycle.

What docking tool or workflow would you recommend?

Thank you so much :)

Hi everyone,

I’m a final(i.e.. 3rd)-year PhD student in Europe, about four months from my expected thesis submission deadline.

For very serious reasons related to my current supervision and academic environment, I am considering whether it is possible to change university and supervisor at this late stage.

I understand this may be very difficult or even impossible in many systems. I would be willing to add extra time to the PhD, potentially up to one additional year, but hopefully not more than that.

I currently have a main supervisor at my home institution and an external co-supervisor at another European university, so I am wondering whether this could make any kind of transfer / re-registration / institutional change more realistic.

My questions are:

1. Has anyone successfully transferred PhD institution very late in the PhD and received the degree from the new university?
2. Are there countries or university systems in Europe where this is administratively possible?
3. Are there universities that allow advanced PhD entry, recognition of previous doctoral work, or transfer of completed PhD research?
4. If a direct transfer is not possible, are there alternatives such as re-enrolling elsewhere with recognition of prior work, converting to a joint/cotutelle arrangement, or changing the awarding institution through an external co-supervisor?

Thank you so much

Hi everyone,

my PI suggested, mainly to save time, that I could buy individually recombinant proteins and try to reconstitute a heterotrimeric protein complex in vitro for a DSF/thermal shift assay, instead of co-expressing and co-purifying the complex.

I’m a bit skeptical because of potential issues with tags, buffers, stoichiometry, stability, and whether the complex would actually form and be homogeneous enough to give interpretable data. The goal would be to test small-molecule stabilizers.

Has anyone successfully done this with commercial recombinant proteins? Did it work well enough for DSF, SEC, SPR, or similar assays? Any practical advice, experience, or opinions would be very helpful.

Thanks!

Hi everyone,

my PI suggested, mainly to save time, that I could buy individually recombinant proteins and try to reconstitute a heterotrimeric protein complex in vitro for a DSF/thermal shift assay, instead of co-expressing and co-purifying the complex.

I’m a bit skeptical because of potential issues with tags, buffers, stoichiometry, stability, and whether the complex would actually form and be homogeneous enough to give interpretable data. The goal would be to test small-molecule stabilizers.

Has anyone successfully done this with commercial recombinant proteins? Did it work well enough for DSF, SEC, SPR, or similar assays? Any practical advice, experience, or opinions would be very helpful.

Thanks!

Hi everyone,

my PI suggested, mainly to save time, that I could buy individually recombinant proteins and try to reconstitute a heterotrimeric protein complex in vitro for a DSF/thermal shift assay, instead of co-expressing and co-purifying the complex.

I’m a bit skeptical because of potential issues with tags, buffers, stoichiometry, stability, and whether the complex would actually form and be homogeneous enough to give interpretable data. The goal would be to test small-molecule stabilizers.

Has anyone successfully done this with commercial recombinant proteins? Did it work well enough for DSF, SEC, SPR, or similar assays? Any practical advice, experience, or opinions would be very helpful.

Thanks!

Hi everyone,

my PI suggested, mainly to save time, that I could buy individually recombinant proteins and try to reconstitute a heterotrimeric protein complex in vitro for a DSF/thermal shift assay, instead of co-expressing and co-purifying the complex.

I’m a bit skeptical because of potential issues with tags, buffers, stoichiometry, stability, and whether the complex would actually form and be homogeneous enough to give interpretable data. The goal would be to test small-molecule stabilizers.

Has anyone successfully done this with commercial recombinant proteins? Did it work well enough for DSF, SEC, SPR, or similar assays? Any practical advice, experience, or opinions would be very helpful.

Thanks!

Hi everyone,

has anyone tried running the NVIDIA NIM version of DiffDock on RunPod? Any tips or known issues? Or alternatives you would suggest?

I need to screen a molecular library (around 40k small molecules, 20 samples per complex) and I'm wondering if this setup is stable and hopefully the fastest / leanest option for a job of this scale. I am also trying to do this without breaking the bank, so any tips on keeping cloud costs down or avoiding known issues would be hugely appreciated.

Thanks!

Hi everyone,

has anyone tried running the NVIDIA NIM version of DiffDock on RunPod? Any tips or known issues? Or alternatives you would suggest?

I need to screen a molecular library (around 40k small molecules, 20 samples per complex) and I'm wondering if this setup is stable and hopefully the fastest / leanest option for a job of this scale. I am also trying to do this without breaking the bank, so any tips on keeping cloud costs down or avoiding known issues would be hugely appreciated.

Thanks!

Hi everyone, I’m trying to choose between 1.67 and 1.74 high-index lenses and would really appreciate your advice.

R: SPH -6.75, CYL -2.25, AXIS 160
L: SPH -7.25, CYL -1.25, AXIS 30

I usually wear contact lenses, but I’d like to start wearing glasses much more often, since I work long hours at a computer and my eyes are starting to suffer from wearing contacts for too many hours.

My optician said she would normally recommend 1.74, but they currently don’t have 1.74 available due to a shortage, so they could only make 1.67 for now.

The frame would be something like Vogue VO5625S 319969, but with clear prescription lenses instead of sunglass lenses. I’m also considering a second pair by replacing the lenses in my current Emporio Armani EA3079 5026 Havana Dark frame.

Would 1.67 be acceptable in these frames, or is it worth waiting/finding another optician for 1.74?

I’ve also read that 1.74 lenses can have more optical compromises, such as chromatic aberration or distortion. Is that true, and should I worry about it?

Thank you!

Hi everyone, I’m trying to choose between 1.67 and 1.74 high-index lenses and would really appreciate advice.

R: SPH -6.75, CYL -2.25, AXIS 160
L: SPH -7.25, CYL -1.25, AXIS 30

I usually wear contact lenses, but I’d like to start wearing glasses much more often, since I work long hours at a computer and my eyes are starting to suffer from wearing contacts for too many hours.

My optician said she would normally recommend 1.74, but they currently don’t have 1.74 available due to a shortage, so they could only make 1.67 for now.

The frame would be something like Vogue VO5625S 319969, but with clear prescription lenses instead of sunglass lenses. I’m also considering a second pair by replacing the lenses in my current Emporio Armani EA3079 5026 Havana Dark frame.

Would 1.67 be acceptable in these frames, or is it worth waiting/finding another optician for 1.74?

I’ve also read that 1.74 lenses can have more optical compromises, such as chromatic aberration or distortion. Is that true, and should I worry about it?

Thank you!

Hi everyone, I’m trying to choose between 1.67 and 1.74 high-index lenses and would really appreciate advice from opticians.

R: SPH -6.75, CYL -2.25, AXIS 160
L: SPH -7.25, CYL -1.25, AXIS 30

I usually wear contact lenses, but I’d like to start wearing glasses much more often, since I work long hours at a computer and my eyes are starting to suffer from wearing contacts for too many hours.

My optician said she would normally recommend 1.74, but they currently don’t have 1.74 available due to a shortage, so they could only make 1.67 for now.

The frame would be something like Vogue VO5625S 319969, but with clear prescription lenses instead of sunglass lenses. I’m also considering a second pair by replacing the lenses in my current Emporio Armani EA3079 5026 Havana Dark frame.

Would 1.67 be acceptable in these frames, or is it worth waiting/finding another optician for 1.74?

I’ve also read that 1.74 lenses can have more optical compromises, such as chromatic aberration or distortion. Is that true, and should I worry about it?

Thank you!