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zchwang/DeepRMSD-Vina_Optimization #5

RuntimeError: The expanded size of the tensor

Hi, trying to use DeepRMSD-Vina for my docking results. However, I keep getting error: ![Screenshot (237)](https://github.com/zchwang/DeepRMSD-Vina_Optimization/assets/114122870/5f21cfd4-6457-44…

Le-Phung-Hien updated 3 months ago
3
bioexcel/biobb_chemistry #10

Add timeout and parameter to control conformer generation ef…

I have a pipeline using biobb to do a virtual screening. The pipeline admits SDF files or SMILES files for the ligand library. In the case of SMILES, the workflow will generate a protonated conformer …

PabloNA97 updated 3 months ago
3
charnley/rmsd #107

Calculating hungarian RMSD without alignment

Hi, Sorry for the silly question, newbie here. I was wondering whether I could use this program to calculate the hungarian RMSD between two readily aligned molecules (i.e. to calculate RMSD between…

jgarcianafria updated 4 months ago
3
michellab/BioSimSpace #369

Specify ions during system setup

**Is your feature request related to a problem? Please describe.** Hi! I could not find the option to specify the ions to use during system preparation, what in tleap would be addIons2 or pname/nname…

cespos updated 2 years ago
15
saeyslab/nichenetr #269

missing function for circos plot visualization

Hi, Thank you for this nice package! I would like to visualize my NicheNet output in a circos plot following this vignette https://github.com/saeyslab/nichenetr?tab=readme-ov-file#:~:text=Seurat%…

cklee7 updated 5 months ago
2
saeyslab/nichenetr #267

How should I assign a pathway/pathways to the target genes w…

Dear nicheNetR Team, Following my nichnetr analysis, I have generated a list of target genes and I am interested in assigning pathways to these genes. Could you kindly advise if there is a function…

pariaaliour updated 3 months ago
3
openmm/openmm #3929

Porting functionality from LAMMPS for inorganic materials

Spinoff discussion from https://github.com/openmm/openmm/issues/3924 This issue is to discuss whether we can port the AIREBO force field from LAMMPS (https://arxiv.org/pdf/1810.07026.pdf) and the f…

philipturner updated 1 year ago
11
EPiCs-group/obelix-ml-pipeline #12

Add OHE for ligands

akalikadien updated 6 months ago
1
BradyAJohnston/MolecularNodes #510

Ligand / Lipid Name capture

When importing particularly MD trajectories, there are often quite a variety of residue names for water, lipids, ligands, ions and the like. While currently there is mostly just matching against a…

BradyAJohnston updated 4 months ago
1
chemosim-lab/ProLIF #208

bitvector

Hi, Is the bitvectors from prolif comparable between different systems? Or is the interactions captured in a certain order and so do the bitvectors? or it is just useful for 1 protein and 1 li…

Lili-Cao updated 4 months ago
6

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1000+ results for ligands

1000+ results
for ligands