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I've been working to create a test suite for determining how well PDBFixer works. The idea is to have an objective way of telling whether or not a code change makes it better. Basically, we need a l…
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Hi, supposed I have my own pdb file which contains my own rna and peptides interaction prediction, how do I that this pipeline to inference? thanks.
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Hey @a-r-j, just pinging back here as promised yesterday with what probably could be considered a design doc for Graphein. I'm excited about this! I also know that my memory is gradually degrading as …
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I encountered a RuntimeError when running the ad.run() function using a dihedral with an atom name containing a single quote (e.g., "O3'"). Here's the code I used:
```py
atom1_alpha_Dihang_residue…
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Hello,
I am running MD simulation on Protein-DNA-RNA complex. However, The DNA and RNA are dissociated in first step of the Equilibration phase. Could you please advise on this matter ?.
Attach…
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Description
When docking a ligand with HOH (water molecules) using either the standard scoring function or the solvation scoring function, I obtain an SDF file containing the docked ligand, the HOH m…
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@ValWood
We have "Proteins with PDB structures". Should we add something similar for RNA structures?
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I've attempted to reproduce some of the results from the paper:
*L. Fu, Y. Cao, J. Wu, Q. Peng, Q. Nie, and X. Xie, "UFold: fast and accurate RNA secondary structure prediction with deep learning",…
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If you like SARS-CoV-2 proteins, drug discovery, and open science, then join the SGC online, and the sgc-ocn team meeting today from 17:00-18:00 BST to discuss pan-coronavirus antivirals.
Join Zoo…
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### A summary and discussion of the 19F NMR fragment screen approach towards the SARS-CoV-2 helicase, Nsp13.
### Current Objectives as of 11th March 2024:
**@TomkUCL:**
- [x] 1. Synthesis…