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2015

Public material for CS109

adv-r

Advanced R programming: a book

awsem_backup

awsemmd

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

awsemmd_script

cg_openmm

coarse-grained force field build on top of openMM

commandcenter

Starcraft 2 Bot

cs344

Introduction to Parallel Programming class code

datasciencecoursera

coursera

datasharing

The Leek group guide to data sharing

discussions

need help with nodeschool? or just wanna ask a question? open an issue on this repo!

dynamicbind

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

edx-learning-from-data-solutions

Homework Answers

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

flask-feedback

glpg_nature_communication

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

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

leagueoflegends

Determining similar sequences across genomes

mmcif2biolip

BioLiP2 database curation and web interface

neovim

vim's rebirth for the 21st century

node-addon-examples

Node.js C++ addon examples from http://nodejs.org/docs/latest/api/addons.html

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

openawsem

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

openfold

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