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alphafold

Open source code for AlphaFold.

alphafold-structural-space

Structural space exploration of AlphaFold DB

alphafold2_vs_swissmodel

Data for the comparison of AlphaFold2 predictions with the SwissModel repository

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.

bio_embeddings

Get protein embeddings from protein sequences

biobb_wf_virtual-screening

biopython

Official git repository for Biopython (originally converted from CVS)

caviar

Protein cavity identification and automatic subpocket decomposition

chemminetools

ChemMine Tools: open source web framework for small molecule analysis

clusterprofiler

:bar_chart: A universal enrichment tool for interpreting omics data

coral

cpa

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

cys-accessibility

cysdb_app

Integrating chemoproteomics, protein structures, and functional annotations to understand the role of cysteines in the human proteome.

datamol

Molecular Manipulation Made Easy.

deepdrug3d

A convolutional neural network for classifying binding pockets based on spatial and chemical information extracted from the pockets.

deeplearning-models

A collection of various deep learning architectures, models, and tips

deeplytough

DeeplyTough: Learning Structural Comparison of Protein Binding Sites

deeppocket

Ligand Binding Site detection using Deep Learning

diffdock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

dromics

Dose Response for Omics

drugex

An exploration strategy improves the diversity of de novo drug design using deep reinforcement learning

equibind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

folding_tools

A collection of *fold* tools

fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).

geometricus

A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.

ghost

graphein

Protein Graph Library

htmd

HTMD: Programming Environment for Molecular Discovery