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AutoDock-Vina

AutoDock Vina

molecule-slide-generator

Generate images of molecules and their properties for use in presentations and reports

pdb_eda

A Python tool for parsing and analyzing electron density maps data available from the worldwide Protein Data Bank

uvadlc_notebooks

Repository of Jupyter notebook tutorials for teaching the Deep Learning Course at the University of Amsterdam (MSc AI), Fall 2021

ViennaRNA

The ViennaRNA Package

B3DB

A large benchmark dataset, Blood-Brain Barrier Database (B3DB), complied from 50 published resources.

BionoiNet

BionoiNet is a deep learning-based software to classify ligand-binding sites.

Coconut-TMAP-SVM

datamol

Molecular Manipulation Made Easy.

dftbplus-3ob-parameters

DFTB3 Parameters for Organic and Biomolecules

drude_prepper_analysis

Analysis scripts for the CHARMM GUI Drude Prepper Paper

epistasis

A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.

FastMBAR

A fast solver for large scale MBAR/UWHAM equations

FLEXS

Fitness landscape exploration sandbox for biological sequence design.

FPSim2

Simple package for fast molecular similarity searches

gamer

Geometry-preserving Adaptive Mesher

GraKeL

A scikit-learn compatible library for graph kernels

graphml-tutorials

Tutorials for Machine Learning on Graphs

graphtransformer

Graph Transformer Architecture. Source code for "A Generalization of Transformer Networks to Graphs", DLG-AAAI'21.

ibm3202

Google Colab Tutorials for IBM3202

Img2Mol

InteracDome

Compute Site-Based Ligand-Binding Frequencies across the InteracDome

making-it-rain

Cloud-based molecular simulations for everyone

MAPD

Model-based Analysis of Protein Degradability

MolScore

An automated scoring function to facilitate and standardize the evaluation of goal-directed generative models for de novo molecular design

openpharmacophore

First steps of an open library to work with pharmacophoric points and pharmacophores.

ProLIF-1

Protein-Ligand Interaction Fingerprints

RNANet

Multiscale dataset of non-coding RNA structures, including sequences, secondary structures, non-canonical interactions, 3D geometrical descriptors, and sequence homology.

RNArtist

RNArtist allows you to design and paint your RNA 2D structures interactively. Coupled with the 3D viewer UCSF Chimera, use your 2D as a map to explore RNA 3D architectures.

RNArtistCore

A Kotlin DSL and library to create and plot RNA 2D structures