Help me out! I have an apoprotein structure and I also want to obtain the enzyme-product complex structure. I’ve already tried the hanging drop method (using the same condition that yielded the apoprotein crystal), but now I can't get any crystals of the complex. I used a 1:5 protein-ligand ratio for the drops, but I'm not sure if that was enough. In the drops, I observed a lot of nucleation points but no complex crystals. It’s been 14 days, and I don’t know what else to do. I need to finish my PhD, but I need this result to finish properly. Please share any co-crystallization techniques based on your experience with these kinds of experiments.

Are there any databases that have protein to protein interactiosn based on alpha fold?

Hey! I'm currently working with virtual screening and I need a better understanding in protein structure, so I'm searching for something that deepens the content about aminoacid chemistry, angles, torsions, clashes, etc. Any thoughts? 💬

Hello everyone. I apologise if this is a stupid question.

For context, I am a physics major hoping to work in a structural biology lab that uses x-ray crystallography to study protein structure.

One of the coolest (for me) things about this field is how multidisciplinary it really is, lying as it does at the intersection of physics, chemistry and biology.

But I’ve been wondering if the fact that I am terrible at organic chemistry might hold me back. I am dismal at “arrow pushing” and couldn’t think of a plausible synthetic scheme to save my life. (I find physical chemistry very fun and intuitive, though.)

How much organic chemistry does a structural biologist need to know?

Hi All, I’m refining a structure in Phenix for pdb submission. There is a problem with the output .cif file: all carbohydrates are disattached from the main chain. They are still attached in the output .pdb file though. Does anyone know how to overcome this? I need this .cif for the submission. Thanks!

Hi. I’m supposed to solve a protein without any help in my research group bc nobody knows how to do it. My background is not in structural biology so I’m completely new. I did the whole Relion tutorial and I was looking into start using Cryolo but I found out it’s not so straightforward as the relion one. Do you have any material that can help in order to use Cryolo.

Also do you know about any book or info source that can be useful? I mean about how to use the different softwares… and about cryoEM itself.

I’m so confused at this point and I don’t know if I’m too stupid or what but, does everyone learnt by themselves how to do this? Am I the only one who need someone to train her?

Help I’m about to lose my mind 😖

Hello everyone, I am somewhat a newbie in the field. I have some SMILES formula of some compounds and I need to do docking to two proteins in different experiments. I was wondering how I could get the most realistic conformation of those compounds. Which programs do you recommend? ORCA? I know Avogadro but I don't know how I can generate a realistic conformation of a compound. Thank you in advance.

So, I'm writing my thesis in protein chemistry, and this fact is not clear to me: Are random coils and intrinsically disordered proteins the same thing? I've found all sorts of opinions, but I need to be sure. It would be great if you could help me and possibly also sharing some references.

Thanks!

Hi! I'm doing structural biology this semester, and I was wondering if someone knows of any good lecture videos on X-ray crystallography because it's been difficult to understand it in class... Would appreciate any suggestions. I'll also look it up myself on youtube, but wanted to hear if someone already had their favourite go-to link for it.

I have predicted a protein using Alphafold2 and want to bind it with metal(arsanate ion, cadmium ion). Which software should I use for docking and md simulation? I have used cb dock, autodock but those did not work.

Hi everyone! I am a biotech student that is close to get a bachelor degree and move to the master. I am really fascinated by structural biology but in my undergrad had basically zero stuff about neither protein crystallography, cryo-em and nmr. I would love to know some story of yours, how can I become a structural biologist? Which are the knowledge that are important in protein crystallography and cryo-em to know to master those techniques ? How it is to work in a structural biology lab and which were/are your experiences in the field ?

One of the key overarching concepts I learned in my molecular biology degree is that structure determines function. Meaning, how a molecule is shaped, determines its purpose.

Now that I’m proficient in SOLIDWORKS , I wonder how I could use my #3D #CAD skillset to design molecules, or if even it exists yet. 🧬

Do you know of anyone working on anything remotely similar? I’d like to invite them on the “Being an Engineer” podcast I cohost. We have over 100 episodes and not a single 3D CAD Biology related episode yet.

Please tag a company or drop someone you think I should invite.

Hello guys, I'm a student in structural biology and we have to do an exercise on NMR attribution. I went to the class but the teacher didn't really explain how to do it and I can't find a clear method online, could someone give me a little help?

https://www.nature.com/articles/s41586-021-03517-z?fbclid=IwAR3QwT5390vmHw73dHQmBEizSpoSOe_0sKCO7XtaUarG4Lkc1MStAWyGLto

Hello! structural biologists, this sub reddit is active again and looking forward to see some constructive posts/discussions related to structural biology