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3d-generative-sbdd

💊 A 3D Generative Model for Structure-Based Drug Design (NeurIPS 2021)

ab_opt

Official implementation of Generative Diffusion Models for Antibody Design, Docking, and Optimization.

af2bind

af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

af_cluster

Predict multiple protein conformations using sequence clustering and AlphaFold2.

afep

calculate the atom-wise free energy contribution using FEP

ai4sci-micam

This is the code of paper "De Novo Molecular Generation via Connection-aware Motif Mining". Zijie Geng, Shufang Xie, Yingce Xia, Lijun Wu, Tao Qin, Jie Wang, Yongdong Zhang, Feng Wu, Tie-Yan Liu. ICLR 2023.

alchemlyb

the simple alchemistry library

algdock

Molecular docking with Alchemical Interaction Grids

alphaflow

AlphaFold Meets Flow Matching for Generating Protein Ensembles

alphafold

Open source code for AlphaFold.

alphafold-multistate

alphafold2rave

alphamissense

alphaplot

:chart_with_upwards_trend: Application for statistical analysis and data visualization which can generate different types of publication quality 2D and 3D plots with extensive visual customization.

apo2ph4

A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening

arpeggio

Calculation of interatomic interactions in molecular structures

arpeggio-1

Calculation of interatomic interactions in molecular structures

atom-openmm

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

atom_mapper

Atom order in one molecule is made to match that in another

auto3d_pkg

autodock-gpu

AutoDock for GPUs and other accelerators

autodock-vina

AutoDock Vina

bar-fep

BAR and FEP method for free energy calculation

bat.py

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

bbar-pytorch

bfee2

binding free energy estimator 2

c36idpsff

CHARMM36IDPSFF force field for GROMACS

cafe_plugin

a VMD plugin for binding affinity prediction using end-point free energy methods

ccdutils

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit