Pinned Repositories
ACSESS
ACSESS is the Algorithm for Chemical Space Exploration with Stochastic Search, which is developed by Dr. Aaron M. Virshup in Beratan Group.
BBB-score
A script using RDKit to reproduce the BBB score reported by Gupta.
DLFG
Deep Learning Fragment Generator
DP4
This notebook reproduces the calculation of the DP4 proposed by Goodman group (DOI:10.1021/ja105035r)
keras-molecules
Autoencoder network for learning a continuous representation of molecular structures.
QBMG
QBMG: Quasi-Biogenic Molecule Generator with Deep Recurrent Network
qvina2
a python script to use qvina2 as docking engine to run virtual screening against a database in MDL sdf format
rdkit-scripts
A collection of cheminformatics scripts that use rdkit
vapor-pressure
Vapor pressure prediction using Keras
virtual-screening-validation
A collection of virtual screening benchmarking
gkxiao's Repositories
gkxiao/virtual-screening-validation
A collection of virtual screening benchmarking
gkxiao/DP4
This notebook reproduces the calculation of the DP4 proposed by Goodman group (DOI:10.1021/ja105035r)
gkxiao/rmsd
Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
gkxiao/torchANI2Gaussian
scripts to interface TorchANI to Gaussian package
gkxiao/unidock
some tips for using Uni-Dock
gkxiao/xtb-scan
torsion scan at DFT//xTB-GNF2 theory level with xTB, ORCA and Gaussian
gkxiao/3max
An example of aniline-Zn interaction
gkxiao/covalent-vs
gkxiao/csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
gkxiao/d4-rescore
Re-scoring a set of docked ligands with off-the-shelf algorithms to assess utility in virtual screening
gkxiao/FEP
gkxiao/flare-qm
scripts for flare ligand QM
gkxiao/gaussian-tools
Some tools written for Gaussian 16/09.
gkxiao/gisttools
Post-processing of data generated by the GIST (Grid Inhomogeneous Solvation Theory) action in cpptraj
gkxiao/gnina-scoring-function
Using GNINA scoring function to rank the pose
gkxiao/in-silico-identification-of-kinase-hinge-binding-fragments
papers about in silico identification of kinase hinge binding fragment
gkxiao/meeko_vina
Add molecule name into meeko pdbqt
gkxiao/near_ligand_tags
add new tag to the ligand close to specific residue
gkxiao/notebook_examples
gkxiao/openbabel_2433
Step to reproduce the OpenBabel PDBQT tree error resulting in re-docking failure.
gkxiao/pdbqt_sample
a sample for pdbqt file
gkxiao/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.
gkxiao/pyani_mmff
Python scripts to conduct optimization using a set of optimization algorithms utilizing an ANI energies and forces.
gkxiao/QuantPharmacophore
Code available for the quantitative pharmacophores
gkxiao/sb2021
SB2021 V1 Revision
gkxiao/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/).
gkxiao/strain_energy
gkxiao/very-negative-vina-score
python script results in very negative vina score
gkxiao/waters
solvent thermodynamics in the binding site
gkxiao/xtb_gaussian
xtb gaussian interface