I’ve been thinking a lot lately about how many small repetitive tasks eat up time in structural biology/computational workflows, especially the things that aren’t “hard science” but still somehow take hours every week.

Things like:

• file conversions/cleanup
• repetitive PyMOL scripting
• structure preprocessing
• batch analyses
• figure generation
• parsing messy outputs
• chain renumbering
• trajectory analysis
• moving data between incompatible tools

Curious what people here find most annoying or time-consuming in their day-to-day work.

I want to pursue my career in structural biology and I want to purchase a new laptop. My budget is upto 60k. So can someone guide me which laptop I should buy? I mostly want to run pymol, chimera, chimera x and maybe sometimes coot and even blender

I've been working on synth-pdb, a tool to generate Protein Data Bank (PDB) files. It may be useful for researchers who need high-quality synthetic PDB data for benchmarking, software testing or training models.

• Realistic Generation: Builds full atomic PDB files using NeRF construction and backbone-dependent rotamer libraries.
• Physics: Includes integration with OpenMM for energy minimization.
• NMR Simulations: Optionally, generates synthetic NOE, Chemical Shift, RDC and Relaxation rates.
• Deep Learning Ready: Supports zero-copy handover to PyTorch, JAX and MLX.
• Educational Context: The codebase is heavily documented with comments explaining the biophysics behind the implementation. Also many Google Colab tutorials are available.

Github: https://github.com/elkins/synth-pdb

Pypi: https://pypi.org/project/synth-pdb/

Docs: https://elkins.github.io/synth-pdb/

I’d love to hear how you might use this or any features you'd like to see added.

I am a masters student with expertise in protein expression, purification, little bit biochemical techniques and macro molecular crystallography mainly just crystallizing protein sample (screening to optimization but haven't solved any structure yet).

I want to work on macromolecular complexes involved in DNA damage repair. I am looking for stratergy to switch to Cryo-EM and Cryo-ET from crystallography since it might not be a suitable approach for large complexes.

Should I move forward as a PhD and learn during this period or maybe get expertise in Cryo-EM laboratories as project assistant and move onto PhD with more complex projects.

Hi,

I built one of these ultrafast grid plungers during my thesis work and my lab never reimbursed me for out-of-pocket purchase of the components, so it is mine to keep or sell. Since I am not making grids at home I figured I'd offer it up here. If anyone would like to add fast grid freezing capabilities to their lab's repertoire, this is a cheap way to get it done (other option being purchase of a Chameleon for who knows how much ). Nanowire grids are now commercially available for purchase from Quantifoil so the biggest barrier for any lab wanting to use this system is no longer in place.

Total cost for the components at time of purchase was $700. Assembly of the components including soldering of the circuitry not reflected in that price, obviously. If anyone is interested please message me here on reddit with an offer.

Hi! I’m looking for someone who knows about NMR analysis and organic structure elucidation.

I have raw data files for:

• ¹H NMR

• ¹³C NMR

• COSY

• HSQC

• HMBC

Plus IR, UV and MS spectra.

I need:

• Processing of the raw NMR data

• Peak picking, integration, coupling assignment

• Full spectral interpretation

• *Structure elucidation* (or justified candidate structures)

Please send me a DM..

Hey all I wanted to share HBAT 2, a Python package for analyzing hydrogen bonds and non-covalent interactions in macromolecular structures (PDB format).

HBAT 2 detects classical hydrogen bonds, weak hydrogen bonds, halogen bonds, π interactions, π-π stacking, carbonyl interactions, and n-π interactions using geometric criteria.

Key Features:

• GUI, CLI, and Python API interfaces
• Automated PDB fixing with OpenBabel/PDBFixer
• Cooperativity chain detection and visualization
• Built-in presets for different structure types
• Multiple export formats (text, CSV, JSON)
• Cross-platform support
• Interactive Jupyter notebooks with 3D visualisations

GitHub: https://github.com/abhishektiwari/hbat Docs: https://hbat.abhishek-tiwari.com

MIT licensed. Perfect for structural biology, drug design, and bioinformatics workflows.

Feedback and contributions welcome!

To try and limit the number of pedantic self-described scientists coming here to post insults: I obviously did not break physics. I am pointing to the fact that I have an image of what appears to be a Coulombic potential map that matches surprisingly well with the 2D classes of the same sample. Two interesting points are the scale difference between the 2D classes and the projected image (~1x10⁷) and the fact that the image is produced using light in the 400 nm range. The scale of the features resolved in the 2D classes are well beyond the Nyquist limit for light of that wavelength. So, I thought some would find it interesting that such an image can be made using a $20 laser and a mirror.

Laser projection of sample's diffraction pattern was focused using a concave lens. 2D classes for comparison.

I only know this is a plant Protein with 7 RGD motifs.

How could I reverse engineer the origin?

I'm curious to know if there is a naturally occurring protein out there that produces graphene, and if not which protein produces a structure that's very similar to graphene?

Good day

Hello people! I wanted to ask you all what’s some research that you find absolutely fascinating/can’t wait to tell people about? Or what’s some research that you think deserves more attention?

Hi everyone,

I’m a PhD student at DTU working on a project that connects large language models (LLMs) with molecular dynamics (MD) simulations. My focus is on predicting protein thermostability and identifying key sites that contribute to thermal resistance.

The core idea is to combine sequence/structural embeddings from LLMs with MD-derived features to build models that can more accurately link protein dynamics to thermostability. I already have some preliminary results, but I’d like to collaborate with peers who are interested in:

• Protein stability prediction
• AI/ML applied to molecular simulations
• Computational biophysics or structural bioinformatics

I believe a collaborative effort could strengthen the methodology and lead to more impactful publications.

If you’re working in a similar area, or just curious about the intersection of LLMs and MD, feel free to reach out. Happy to discuss ideas, share data, or explore joint writing.

Thanks!

— DTU PhD student

Hello again people! I’m going to join a lab soon that specializes in solving protein structures using cryo-em and then the computational part. I wanted to get an introduction to not only the basics but also some in depth stuff related to cryo-em and computational biology (that follows cryo-em). I’ve tried searching up videos on YouTube but they don’t seem to be very helpful. Anything (journals, books, videos, blogs, etc.) will help! Thank you so much!!

Hello! I am considering R1 universities in USA for my PhD and I’m leaning towards structural/computational biology. I don’t have a lot of experience besides good ol’ molecular docking using autodock but I will be joining a lab in my current masters program for a few months that specialises in structural/computational biology. My current work is with my professor looking at the chemistry of xenoestrogens and their binding in ER-alpha.

I’ve looked at UMass Amherst and BostonU (I love the cold climate) and shortlisted a couple of labs in there (specialising in protein folding and functioning of GPCRs) but I wanted to know more universities that are well known for their work in the community! I have a bachelors in biochemistry and a masters in biotechnology. Hope you guys can give me some insight/advice!

Hi there!

Im working on a metal binding protein that is highly specific more manganese, and all related enzymes have manganese in their active site. I crystalized the enzyme and solved the structure, and placed manganese in the active site through Coot. However, I cant get rid of the green density. Ive tried magnesium, sodium, potassium, chlorine and copper, but still the green density. if anyone could suggest a way I can properly fit the correct metal Ion in there I would be very appreciative!

Alphafold models contain B factors per amino acid. How do you get per atom B-factors, what refinements you use.

Hi everyone! 👋

I’m an indie iOS developer working on a molecular visualization app built specifically for Apple Vision Pro.
The app supports:
📦 Multiple structural representations (primary, secondary, tertiary, quaternary)
🔬 Visualization modes like ball-and-stick, space-filling, surface, and ribbon
🧠 Designed for education, research, and immersive exploration of protein structures (PDB files)

Since I don’t currently have a Vision Pro myself, I’m looking for a few testers who help me to evaluate usability, performance, interaction, and visuals in the real environment.

💡 If you’re interested in trying the app and sharing feedback:
• You’ll get early access
• And the app for free when it launches on the App Store

Whether you’re a molecular biology enthusiast, student, AR/VR developer, or just curious about spatial computing – I’d love your help.

If this sounds interesting, drop a comment or DM me. I’ll follow up with TestFlight details.

Thanks a lot! 🙏

Hello all, new to the group. I studied Cellular Biology at undergrad and loved my structural biology course and have been thinking about advancement that might have happened since then. Back during my undergrad (10 years ago), all structures were determined by either X-ray or Cryo-EM, both of which involve fixing/freezing the protein somehow (in my understanding?). What is the latest these days? Have we advanced at all in being able to gain structural insights of proteins in a more nascent state? Like do we have any imaging modalities that visualise proteins still suspended in unfrozen fluid?

I hope that makes some sense to someone... I am doing hobby research project in Protein Folding and am desperate to know answers!