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3dmolms

3DMolMS: prediction of tandem mass spectra from 3D molecular conformations

alphapulldown

auto_autodock-gpu

Tools that help high-throughput protein-ligand docking in batch mode using AutoDock-GPU.

blogs

Jupyter notebooks that support my graph data science blog posts at https://bratanic-tomaz.medium.com/

cryodrgn

Neural networks for cryo-EM reconstruction

cspred

UCBShift is a program for predicting chemical shifts for backbone atoms and β-carbon of a protein in solution. It utilizes a machine learning module that makes predictions from features extracted from the 3D structures of the proteins.

dd_protocol

Official repository for the Deep Docking protocol

deep_learning_for_biologists_with_keras

tutorials made for biologists to learn deep learning

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

deeplearning-biology

A list of deep learning implementations in biology

dgl-lifesci

Python package for graph neural networks in chemistry and biology

dockstring

A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discovery.

fingernat-dna-interaction

Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.

fpsim2

Simple package for fast molecular similarity searches

fret_x_fingerprinting_simulation

graph-neural-networks-in-life-sciences

graphml-tutorials

Tutorials for Machine Learning on Graphs

gromacs_ff

Trusted force field files for gromacs

hdxer

HDXer is a package to compute Hydrogen-Deuterium exchange data from biomolecular simulations, compare to experiment, and perform ensemble refinement to fit a structrual ensemble to the experimental data

hotmaps

Detects hotspot regions for somatic mutations in 3D protein structures

hotspot3d

3D hotspot mutation proximity analysis tool

hotspots

A knowledge-based method for determining small molecule binding "hotspots".

ibm3202

Google Colab Tutorials for IBM3202

idpgan

knowledge-graph-learning

A curated list of awesome knowledge graph tutorials, projects and communities.

knowledge-graph-tutorials-and-papers

Insightful Tutorials and Papers about Knowledge Graphs

machine-learning-articles

🧠💬 Articles I wrote about machine learning, archived from MachineCurve.com.

making-it-rain-md-simultion

Cloud-based molecular simulations for everyone

massformer

Tandem Mass Spectrum Prediction with Graph Transformers

maw

Metabolome Annotation Workflow