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gmultiwfn

A third-party distribution of Multiwfn for gfortran, 100% free!

hdac6-chenyadong-3d-qsar

the data set from Yadong(2019)

idock

idock is a standalone tool for structure-based virtual screening powered by fast and flexible ligand docking.

in-silico-identification-of-kinase-hinge-binding-fragments

papers about in silico identification of kinase hinge binding fragment

istar

istar is a software-as-a-service platform for bioinformatics and chemoinformatics.

jupyter-notebook-in-cloudam

如何在Cloudam上建立Jupyter Notebookhow to set up a jupter notebook in the cloudam

keras-generating-focussed-molecule-libraries

Working on reimplementing the work presented by Segler et al. in "Generating Focussed Molecule Libraries for Drug Discovery with Recurrent Neural Networks" https://arxiv.org/pdf/1701.01329.pdf

keras-molecules

Autoencoder network for learning a continuous representation of molecular structures.

knime-plants

KNIME nodes to configure, run and analyze PLANTS protein-ligand docking

knime-silicos-it

KNIME nodes and example workflows for software made by Silicos-it, ie. align-it, shape-it

ligdream

Novel molecules from a reference shape!

meeko

A new Python package to prepare small molecules for docking.

mmic_autodock

MMIC for molecular docking with AutoDock Vina

mmpbsa_from_openmm

example demonstrating a free energy estimation starting from OFF and OpenMM

mmpbsa_scripts

molecule_generator

Code for "Multi-Objective De Novo Drug Design with Conditional Graph Generative Model" (https://arxiv.org/abs/1801.07299)

mpi-vina

An MPI based parallel implementation of Autodock Vina

near_ligand_tags

add new tag to the ligand close to specific residue

notebook_examples

off-ffcompare

Compare molecular structures after energy minimization in various force fields.

openbabel_2433

Step to reproduce the OpenBabel PDBQT tree error resulting in re-docking failure.

pareto.py

Nondominated sorting for multi-objective problems

pdbfixer

PDBFixer fixes problems in PDB files

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.

pmapper

3D pharmacophore signatures and fingerprints

propka-3.1

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

protac

publication and patent about protac technology

psikit

psi4+RDKit

pyani_mmff

Python scripts to conduct optimization using a set of optimization algorithms utilizing an ANI energies and forces.