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University College London, SoP

Shanghai, China

@Tokelauislands

SallyS.'s starred repositories

DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

Language:PythonMIT1012 17 211

morfeus

A Python package for calculating molecular features

Language:PythonMIT157 8 14

3DInfomax

Making self-supervised learning work on molecules by using their 3D geometry to pre-train GNNs. Implemented in DGL and Pytorch Geometric.

Language:Python147 3 19

RadonPy

RadonPy is a Python library to automate physical property calculations for polymer informatics.

Language:PythonBSD-3-Clause131 4 7

ESP_DNN

A Graph-Convolutional Deep Neural Network for predicting electrostatic potential surfaces

Language:PythonApache-2.084 6 6

VSFlow

Language:PythonMIT80 8 8

DiffusionProteinLigand

Language:PythonApache-2.072 3 6

SELFormer

SELFormer: Molecular Representation Learning via SELFIES Language Models

Language:Python66 2 13

pymol-color-alphafold

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

Language:PythonMIT56 1 3

pyCHARMM-Workshop

pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the University of Michigan by Charles Brooks' Group, June 20-24.

Language:Jupyter NotebookMIT55 3 3

Free-Wilson

An implementation of the Free-Wilson SAR analysis method using the RDKit

Language:PythonMIT54 10 4

lig3dlens

Language:PythonMIT49 2 5

medchem_moves

Language:PythonNOASSERTION44 5 4

protwis

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

Language:PythonApache-2.034 4 51

pyCADD

A python package for computer-aid drug design.

Language:PythonGPL-3.027 4 1

resp

A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4

Language:PythonBSD-3-Clause25 7 11

neutromeratio

Tautomer ratios in solution

Language:Jupyter NotebookMIT24 13 4

FASTDock

FASTDock: A Pipeline for Allosteric Drug Discovery - example scripts and jupyter notebook

Language:Rich Text FormatMIT18 4 1

awesome-quantum-chemistry

Quantum Chemistry is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.

Language:PythonMIT18 10

MacFrag

Language:Python18 1 2

KDD2023_KaGML_DrugDiscovery_Tutorial

Materials for KDD2023 tutorial: Knowledge-augmented Graph Machine Learning for Drug Discovery: from Precision to Interpretability

parKVFinder

parKVFinder: thread-level parallel KVFinder

Language:PythonGPL-3.012 4 3

cheminformatics

Perform operations on chemical structures using Python.

Language:Jupyter NotebookMIT12 1 1

CGUI-IFD

Language:Rich Text Format900

esp-surface-generator

Generate electrostatic potential surfaces using the output from Astex's ESP_DNN method

Language:JavaScriptApache-2.0600

Potential_solver

A Python module for solving electrostatic potential of a distribution of point charges using periodic boundary conditions.

Language:PythonGPL-3.06 60

ProteinDesignPlugin

Language:Python4 120

analysis_libraries_chapter

Analysis libraries for molecular trajectories: a cross-language synopsis

Language:Python1 20

babelruns

lalalalal

Language:Shell100

mollib

A simple python module for reading, writing, fetching and manipulating biomolecules

Language:PythonGPL-3.01 2 59