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2020-06-05-py-tutorial

Tutorial for OpenMM and MDAnalysis

3dmol.js

WebGL accelerated JavaScript molecular graphics library

acid

Auto in silico Consensus Inverse Docking(ACID) is a web server mainly for drug repurposing based on the consensus inverse docking method, which is designed to evaluate the binding affinities between each protein and the given small molecule. ACID is open to the public and shows great potential.

acpype

OFFICIAL: AnteChamber PYthon Parser interfacE

af2bind

alchemical-transfer-method

Simulation input files for the paper Alchemical Transfer Approach to Absolute Binding Free Energy Estimation.

algdock

Molecular docking with Alchemical Interaction Grids

alphafold

Open source code for AlphaFold.

amber-dyes

AMBER DYES Force Field

amberff-in-namd

amberutils

Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods

ampl

The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.

android-cluster-toolkit

The Android Cluster Toolkit helps organize and manipulate a collection of Android devices.

anvio

An analysis and visualization platform for 'omics data

archer-benchmarks

arpeggio

Calculation of interatomic interactions in molecular structures

asgard

ASGARD is a tool that allows via an automated MD workflow to perform MD protein or protein-ligand complex analysis and to generate the corresponding report easily

atom-openmm

OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method

autodock-gpu

AutoDock for GPUs and other accelerators

autodock-vina

AutoDock Vina

autogrow4

AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual library of pre-enumerated compounds. AutoGrow4 is a useful tool for generating entirely novel drug-like molecules and for optimizing preexisting ligands.

awesome-chatgpt-prompts

This repo includes ChatGPT prompt curation to use ChatGPT better.

awesome-cheminformatics

A curated list of Cheminformatics libraries and software.

awesome-code-llm

👨‍💻 An awesome and curated list of best code-LLM for research.

awesome-cryoem

A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

awesome-molecular-docking

We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.

awesome_ai_aided_drug_design_papers

https://chenxingqiang.github.io/Awesome_AI_Aided_Drug_Design_Papers/

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

ball

The Biochemical Algorithms Library