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deepchem

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

deepclip

This repository contains all DeepCLIP Python code

deepcseqsite

Protein-ligand binding sites prediction toolkits

deepdock

An experimental package for deep learning for molecular docking

deepdrug3d

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

deepdtaf

a deep learning architecture for protein-ligand binding affinity prediction

deepligand

deeplytough

DeeplyTough: Learning Structural Comparison of Protein Binding Sites

deepram

End-to-end deep learning toolkit for predicting protein binding sites and motifs.

deepsurf

A surface-based deep learning approach for the prediction of ligand binding sites on proteins

drugex

Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology

edtsurf

mirror of https://zhanglab.ccmb.med.umich.edu/EDTSurf/

etox-allies

eTOX ALLIES is an open source framework that allows the automated prediction of ligand-binding free energies requiring the ligand structure as only input.

fesetup

A tool for setting up free energy simulations.

fragalysis

A repo for analysis of ensembles of protein-ligand complexes

fragment_expansion

Software tools for fragment-based drug discovery (FBDD)

gaudi

GaudiMM: A modular optimization platform for molecular design

gbff

Tools for Bayesian forcefield development

get-binding-pockets-dataset

A repo with the source code to get a dataset of real binding sites composed by atoms distances matrices and atoms types vectors.

gnn_dove

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

govisualizer

gpathfinder

Identification of ligand binding pathways by a multi-objective genetic algorithm

graph-app-kit

Go from graph data to a secure and interactive visual graph app in 15 minutes. Batteries-included self-hosting of graph data apps with Streamlit, Graphistry, RAPIDS, and more!

graphdta

GraphDTA: Predicting drug-target binding affinity with graph neural networks

graphsite

GraphSite: protein-DNA binding site prediction using graph transformer and predicted protein structures

hitl_chem

hots

HoTS: Sequence-based prediction of binding regions and drug-target interactions.

jupyter-docker-stacks

Opinionated stacks of ready-to-run Jupyter applications in Docker. Forked to add GPU capabilities.

kalasanty

Fork of kalasanty repository

kglab

Graph Data Science: an abstraction layer in Python for building knowledge graphs, integrated with popular graph libraries – atop Pandas, NetworkX, RAPIDS, RDFlib, pySHACL, PyVis, morph-kgc, pslpython, pyarrow, etc.