A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations

Listing of papers about machine learning for proteins.

Machine learning and deep learning resources

Welcome to the Physics-based Deep Learning Book (v0.2)

ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.

The fastai book, published as Jupyter Notebooks

A deobfuscator for PyArmor.

Accompanying code to Casey and Follows, 2020. A flexible and easy-to-use model of microbial acclimation to nutrient availability.

Python library to run structure based model (SBM) simulations using the OpenMM toolkit

My web page containing all the demos from my youtube channel "Ten Minute Physics" www.youtube.com/c/TenMinutePhysics

OpenMM tutorial for the MSBS course

MoleculeKit: Your favorite molecule manipulation kit

Material for a full course on applied nonlinear dynamics, nonlinear timeseries analysis, and complex systems, in Julia

Collection of Pytorch lightning tutorial form as rich scripts automatically transformed to ipython notebooks.

18 Lessons, Get Started Building with Generative AI 🔗 https://microsoft.github.io/generative-ai-for-beginners/

Open Source LLM toolkit to build trustworthy LLM applications. TigerArmor (AI safety), TigerRAG (embedding, RAG), TigerTune (fine-tuning)

Benchmarking common tasks on proteins in various languages and packages

Post-processing of data generated by the GIST (Grid Inhomogeneous Solvation Theory) action in cpptraj

Predict the structure of immune receptor proteins

Secure, cross-platform Git credential storage with authentication to GitHub, Azure Repos, and other popular Git hosting services.

Antibody Numbering and Antigen Receptor ClassIfication

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Protein Graph Library

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

Python / C++ based particle reaction-diffusion simulator