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2020-06-05-py-tutorial

Tutorial for OpenMM and MDAnalysis

3dmol.js

WebGL accelerated JavaScript molecular graphics library

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

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

awesome-chatgpt-prompts

This repo includes ChatGPT prompt curation to use ChatGPT better.

awesome-cheminformatics

A curated list of Cheminformatics libraries and software.

awesome-cryoem

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

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

ball_contrib

Third-party libraries used by the Biochemical Algorithms Library (BALL)

bio-datasets

Free collection of Bio datasets and embeddings

bio-transformers

bio-transformers is a wrapper on top of the ESM/Protbert model, trained on millions on proteins and used to predict embeddings.

biobb_wf_amber_md_setup

This tutorials aim to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package.

biobb_wf_flexserv

This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).

biobb_wf_godmd

This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).