gkxiao's repositories
virtual-screening-validation
A collection of virtual screening benchmarking
torchANI2Gaussian
scripts to interface TorchANI to Gaussian package
csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
d4-rescore
Re-scoring a set of docked ligands with off-the-shelf algorithms to assess utility in virtual screening
gaussian-tools
Some tools written for Gaussian 16/09.
gisttools
Post-processing of data generated by the GIST (Grid Inhomogeneous Solvation Theory) action in cpptraj
gnina-scoring-function
Using GNINA scoring function to rank the pose
in-silico-identification-of-kinase-hinge-binding-fragments
papers about in silico identification of kinase hinge binding fragment
meeko_vina
Add molecule name into meeko pdbqt
near_ligand_tags
add new tag to the ligand close to specific residue
openbabel_2433
Step to reproduce the OpenBabel PDBQT tree error resulting in re-docking failure.
pdbqt_sample
a sample for pdbqt file
ph4_selection_using_hydration_site_analysis
Protein Pharmacophore Selection Using Hydration-Site Analysis: an example using Flare 3D-RISM or GIST to select pharmacophore generated by Ligandscout.
pyani_mmff
Python scripts to conduct optimization using a set of optimization algorithms utilizing an ANI energies and forces.
QuantPharmacophore
Code available for the quantitative pharmacophores
sb2021
SB2021 V1 Revision
Solvent_sites_clustering
This repo contains a python script to obtain solvent sites according to https://watclust.wordpress.com/methodology/ using as input molecular dynamics in AMBER format (https://ambermd.org/).
very-negative-vina-score
python script results in very negative vina score
xtb-scan
torsion scan at DFT//xTB-GNF2 theory level with xTB, ORCA and Gaussian
xtb_gaussian
xtb gaussian interface