leelasd

molfunc

fast functionalisation of molecules

RNA-Science-Toolbox

A platform to do RNA science

SPOT-RNA

RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.

aimnetnse

AIMNet-NSE model

antibody-in-pytorch

Machine learning models for antibody sequences in PyTorch

benchmarking-gnns

Repository for benchmarking graph neural networks

BionoiNet

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

blase

Python module for drawing and rendering ASE (Atomic Simulation Environment) atoms and molecules objects using blender.

DEVELOP

Getting-Things-Done-with-Pytorch

Jupyter Notebook tutorials on solving real-world problems with Machine Learning & Deep Learning using PyTorch. Topics: Face detection with Detectron 2, Time Series anomaly detection with LSTM Autoencoders, Object Detection with YOLO v5, Build your first Neural Network, Time Series forecasting for Coronavirus daily cases, Sentiment Analysis with BERT.

GHOST

GNN_DOVE

Code for "Protein Docking Model Evaluation by Graph Neural Networks"

GNNExplainer_DGL

GNNExplainer implementation using DGL

jupyterlabpymolpysnips

Molecular_Anatomy

OCSR_Review

This repository contains the information related to the benchmark study on openly available OCSR tools

openmm-tutorial-msbs

OpenMM tutorial for the MSBS course

PDB-New-Search-API-Query-with-Python-Example

This is a basic example of querying the RCSB PDB using the new (2021) search API with a python program and json file.

pnab

ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS

Randomdata

rcsbsearch

Python interface for the RCSB search API.

reactome2py

python client for reactome content, analysis, and human functional protein interactions (FI) services api calls.

RNAblueprint

RNAblueprint library for uniform sampling of RNA sequences given structural and sequence constraints

RNANet

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

RNArtistCore

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

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

sbm-openmm

Python library to run structure based model (SBM) simulations using the OpenMM toolkit

torch-dftd

pytorch implementation of dftd2 & dftd3

torchmd

End-To-End Molecular Dynamics (MD) Engine using PyTorch