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2019_drug_approvals

2019_drug_approvals

2023_xff_paper

alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations

alchemical-best-practices

Best practice document for alchemical free energy calculations going to livecoms journal

alchemlyb

the simple alchemistry library

alchemlyb-0.5.0

amber-membrane_protein_tutorial

Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen

amber_tutorials

Some tutorials on how to use AMBER simulation package. Especially for Amber22+AmberTools23.

articleswechat

This repo is used to hold some public files and scripts on WeChat articles

atom-picker

auto3d_pkg

autodock-gpu

AutoDock for GPUs and other accelerators

autodock-vina

AutoDock Vina

bat.py

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems.

biopython

Official git repository for Biopython (originally converted from CVS)

colvars

Collective variables library for molecular simulation and analysis programs

courses

To place what I noticed for learning some courses

cuda-code

diffnet

dihedralcal

Calculate Dihedral

dockstring

A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discovery.

fastmbar

A fast solver for large scale MBAR/UWHAM equations

fmap_v1

Codes to use funnel-metadynamics and funnel metadynamics automated protocol

free_energy_papers

To summarize the key points in papers about (alchemical) free energy simulations and calculations

freeenergy

geogebra

GeoGebra apps (mirror)

gromacs_pca_porcupine

Do PCA analysis using Gromace and display by Porcupine plot

himap

High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP)

holoware-testcases

jupyterlabpymolpysnips