luwei0917

DynamicBind

repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

TankBind

Open source code for TankBind. Galixir Tenchnologies

awsemmd_script

LeagueOfLegends

Determining similar sequences across genomes

CG_openMM

coarse-grained force field build on top of openMM

GlpG_Nature_Communication

Code repository for "Energy landscape underlying spontaneous insertion and folding of an alpha-helical transmembrane protein into a bilayer"

openawsem

An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM

awsemmd

Associated memory, Water mediated, Structure and Energy Model (AWSEM) protein simulation code

adv-r

Advanced R programming: a book

awsem_backup

commandcenter

Starcraft 2 Bot

elegant-scipy

1st Edition of Elegant SciPy (O'Reilly Publishers)

EquiBind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

handson-ml

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in python using Scikit-Learn and TensorFlow.

hh-suite

Remote protein homology detection suite.

IEConv_proteins

Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures

jupyterlab

JupyterLab computational environment. This is a very early preview, and is not suitable for general usage yet.

lammps

Public development project of the LAMMPS MD software package

mmCIF2BioLiP

BioLiP2 database curation and web interface

notebooks

The compiled, clean (not run) Jupyter notebooks for Elegant SciPy

open3spn2

An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

openmoltools

An open set of tools for automating tasks relating to small molecules

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

pydata-book

Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media

PythonDataScienceHandbook

Jupyter Notebooks for the Python Data Science Handbook

pytorch_cluster

PyTorch Extension Library of Optimized Graph Cluster Algorithms

SpeedPPI

Rapid protein-protein interaction network creation from multiple sequence alignments with Deep Learning

ThermoNet

ThermoNet is a computational framework for quantitative prediction of the impact of single-point mutations on protein thermodynamic stability. The core algorithm of ThermoNet is an ensemble of deep 3D convolutional neural networks.

WhirlwindTourOfPython

The Jupyter Notebooks behind my OReilly report, "A Whirlwind Tour of Python"