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ligand-binding-db-bindingdb

Downloads and converts the BindingDB to ChEMBL triples

ligand-binding-pathsampling

Using path sampling to study ligand binding/unbinding kinetics

lime

Lime: Explaining the predictions of any machine learning classifier

making-it-rain

Cloud-based molecular simulations for everyone

manifold

A model-agnostic visual debugging tool for machine learning

mapping-protein-kinases-binding-sites

Algorithms in Structural Bioinformatics

mat

The official implementation of the Molecule Attention Transformer.

match_ligand_binding_sites

Extract ligand binding sites from PDB. Match the binding sites to de novo scaffolds.

moad_ligandfinder

A script able to extract ligands from pdb structure(s) and remove them from the original structure. The ligands are identified according to the *valid* ligands found in the binding MOAD database. The ligand can be extracted as a pdb or as a xyz (coordinate) file. Other options such as converting the queried pdb to pqr are available .

moldqn-pytorch

A PyTorch Implementation of "Optimization of Molecules via Deep Reinforcement Learning".

moleculenet

Moleculenet.ai Datasets And Splits

molegular

Repository for MoleGuLAR: Molecule generation using Reinforcement Learning and Alternating Rewards

molstar

A comprehensive macromolecular library

morph-kgc

Powerful RDF Knowledge Graph Generation with [R2]RML Mappings

moses

Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models

navigo

Tools for analyzing and visualizing Gene Ontology gene function terms

nbval

A py.test plugin to validate Jupyter notebooks

nntox

opa2vec

Turning Ontologies Plus Annotation Properties into Vectors

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

pocket2drug

Pytorch implementation of Pocket2Drug: a generative deep learning model to predict binding drugs for protein ligand-binding sites.

pocketprotectors

Simulate the binding of drugs to targets by identifying the shape and location of regions that may be stabilized through binding of targeted molecules, and correlate with structural changes in the protein active site or lack of drug binding stabilization.

pointsite

PointSite: a point cloud segmentation tool for identification of protein ligand binding atoms

prolif

Protein-Ligand Interaction Fingerprints

propythia

Python generic modular semi-automated platform containing functions for the classification of proteins based on their physicochemical properties using ML.

pubvenn

PubMed meets Venn diagrams

puresnet

Predicting protein-ligand binding sites using deep convolutional neural network

pyada

A cheminformatics package to perform Applicability Domain of molecular fingerprints based in similarity calculation.

pycheckmol

Application for detecting functional groups of a molecules.