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Hello, I will be conducting molecular dynamics for several protein-ligand complexes. Is it possible to calculate the interaction energy between the protein and the ligand for individual simulation ste…
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[GROMACS tutorial](http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html )
[GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design](https://doi.org/10.1021/acs.jcim.2c0004…
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Got this strange bug I haven't seen elsewhere in which I was modelling some data in Rex and the first 101 residues to be exact, posterior estimates are identical and so giving no resolution in any of …
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I was trying to use the Google colab based Notebook "Making it Rain" to perform molecular dynamics simulation of one of my proteins with the small molecule inhibitor. But I am getting issues in te fol…
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- [ ] [Correlated gene modules uncovered by high-precision single-cell transcriptomics](https://www.pnas.org/doi/abs/10.1073/pnas.2206938119)
- [x] [Dynamics of single-cell protein covariation during…
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**Aim:**
This issue addresses how to apply LigGrep to filter through docked ligand poses to check that they retain key interactions with the protein that are observed in crystallographic fragment-p…
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### Discussed in https://github.com/aristoteleo/dynamo-release/discussions/423
Originally posted by **Ckenen** September 21, 2022
When I run dyn.tl.dynamics(adata, group="group", NTR_vel=True)…
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Dear Xiaojie,
My data is pulse-chase data from scNT-seq, three temperatures were used for processing, but an error occurs when running dyn. tl. dynamics(adata, group = 'temp'), here's my run co…
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Not many people are using scfix with Martini3 proteins even though it improves side-chain conformations and dynamics. Perhaps it would be best to make this option default.
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Hi, I am a beginning user of openmm toolkit. I followed [this tutorial](https://htmlpreview.github.io/?https://github.com/openmm/pdbfixer/blob/master/Manual.html) and everything seems good. However, I…