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aa-score-tool

a tool for protein-ligand binding affinity prediction

acgt

Accerelarting Chemical discovery with Graph Transformer

acpc

Chemoinformatics tool for ligand-based virtual screening

acpype

OFFICIAL: AnteChamber PYthon Parser interfacE

adaptabert

Unsupervised Domain Adaptation of Contextualized Embeddings for Sequence Labeling

af2

To eventually become a Pytorch implementation of Alphafold2, as details of the architecture get released

aizynthfinder

A tool for retrosynthetic planning

alchemical-analysis

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

alchemlyb

the simple alchemistry library

algdock

Molecular docking with Alchemical Interaction Grids

alphafold

Open source code for AlphaFold.

alphafold_non_docker

AlphaFold2 non-docker setup

alphafold_pytorch

An implementation of the DeepMind's AlphaFold based on PyTorch for research

alphaspace2

Protein surface topographical mapping tool

amberti

python package to run AmberTI

amdock

(Linux) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina

apbs

Software for biomolecular electrostatics and solvation calculations

apbs-pdb2pqr

APBS and PDB2PQR software

apbs-rest

Web server and RESTful backend services for APBS and PDB2PQR

apbscore

Atom Pair Based scoring function

apollo1060

Data and models (with prediction scripts) used in publications related to Apollo1060 platform

appfel.py

The Automated Protein-Protein Free Energy tooL (APPFEL.py) is designed to calculate the affinity of any protein-protein complex starting only from the complex three-dimensional structure.

arae_smiles

attentivefp

autodock-gpu

AutoDock for GPUs and other accelerators

autodock-vina

AutoDock Vina

autodockgpu

awesome-molecular-generation

Awesome papers related to generative molecular modeling and design.

bash_run_alphafold_v2.3

run_alphafold.sh for AlphaFold v2.1 and later

bat.py

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