Roshan Shrestha

prepmd. Automatically prepare structures from the PDB for molecular dynamics simulation

courses. Anthropic's educational courses

ppt-master. AI generates a real, editable PowerPoint from any document — native shapes & animations, editable charts & tables you can change the data on, speaker notes voiced as audio narration, and the option to follow your own .pptx template, not slide images · by Hugo He

Resume-Matcher. The #1 AI Harness for Building Resumes, PDFs, Cover Letters & more, locally with 100+ LLMs support.

MD_FromBasicsToApplication. Elaborate Tutorial for Teaching Molecular Dynamics directed to university students in their graduate program. The course is designed to be finished within one semester, but can be completed within a couple of weeks technically speaking.

nepal-tts-training. Nepali and Nepal-language Piper/TTS training recipes, review tooling, and serving experiments

protonate_utils. Scripts for protonating proteins and ligands

LAMMPS-AST. HTML

paper-qa. High accuracy RAG for answering questions from scientific documents with citations

2026LLMsForScience. Repo dedicated to materials from the "LLMs for Science" class taught in Spring 2026 at the CUNY Graduate Center.

scientific-agent-skills. Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 160,000+ scientists worldwide. 140 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Pi, Antigravity, and the open Agent Skills standard.

google-colab-cli. Python

MisoTTS. Miso TTS is an 8 billion, highly emotive text-to-speech model

TorchCode. 🔥 LeetCode for PyTorch — practice implementing softmax, attention, GPT-2 and more from scratch with instant auto-grading. Jupyter-based, self-hosted or try online.

PDBe-MCP-Servers. PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.

aider. aider is AI pair programming in your terminal

awesome-harness-engineering. Awesome list for AI agent harness engineering: tools, patterns, evals, memory, MCP, permissions, observability, and orchestration.

claude-code. Claude Code is an agentic coding tool that lives in your terminal, understands your codebase, and helps you code faster by executing routine tasks, explaining complex code, and handling git workflows - all through natural language commands.

airflow. Apache Airflow - A platform to programmatically author, schedule, and monitor workflows

azureml-examples. Official community-driven Azure Machine Learning examples, tested with GitHub Actions.

absolute-stability-predictor. Jupyter Notebook

Martini3-Fullerene. It will have all the tools necessary for building the M3 version of Fullerene.

Martini3-Graphene. This repository contains the tools to build the Martini 3 version of graphene (structure and ITP files)

claude-howto. A visual, example-driven guide to Claude Code — from basic concepts to advanced agents, with copy-paste templates that bring immediate value.

gribouille. Create elegant graphics with the Grammar of Graphics for Typst.

fastai. The fastai deep learning library

Power-CAT-Copilot-Studio-Kit. TypeScript

skills-for-copilot-studio. A skill for AI-coding tools to build and edit Microsoft Copilot Studio agents as YAML — with schema validation, templates, and AI-powered skills. Suited for Claude Code, GitHub Copilot CLI, and more.

awesome-microsoft-copilot-prompts. The definitive Microsoft 365 Copilot prompt library for business teams. 400+ prompts for Office apps, Copilot Studio, security operations, and enterprise deployment. Battle-tested in production environments

AFMForceLipid. Python scripts for constructing CG amorphous silica AFM tips and analyzing AFM tip–lipid membrane interactions using MARTINI 3.

AI-driven-protein-design. Resources for learning AI-driven protein design

skills. Public repository for Agent Skills

parameter-golf. Train the smallest LM you can that fits in 16MB. Best model wins!

openai-apps-sdk-examples. Example apps for the Apps SDK

openai-python. The official Python library for the OpenAI API

openai-agents-python. A lightweight, powerful framework for multi-agent workflows

whisper. Robust Speech Recognition via Large-Scale Weak Supervision

openai-cookbook. Examples and guides for using the OpenAI API

skills. Skills Catalog for Codex

ai4chem_course. EPFL CH-457 "AI for chemistry"

adk-samples. A collection of sample agents built with Agent Development Kit (ADK)

langfun. OO for LLMs

perfetto. Production-grade client-side tracing, profiling, and analysis for complex software systems.

langextract. A Python library for extracting structured information from unstructured text using LLMs with precise source grounding and interactive visualization.

azure-mol-samples-2nd-ed. Supporting resources for "Learn Azure in a Month of Lunches - 2nd edition" (Manning Publications)

azure-cli. Azure Command-Line Interface

azure-quickstart-templates. Azure Quickstart Templates

llm_aided_ocr. Enhances Tesseract OCR output using LLMs (local or API) for error correction, smart chunking, and markdown formatting of scanned PDFs

destructive_command_guard. The Destructive Command Guard (dcg) is for blocking dangerous git and shell commands from being executed by agents.

atlas-session-lifecycle. Session lifecycle management for Claude Code — persistent memory, soul purpose, reconcile, harvest, archive

DPG-tutorial-2026. Automated Workflows and Machine Learning for Materials Science Simulations

themosia2026-cg-interfaces. Hands-on course material for the THEMOSIA Winter School 2026 on coarse-grained modeling of solid–ionic liquid interfaces using the Martini 3 force field

umbrella_sampling. setting up and analysing PMFs

MLforMaterials. Online resource for a practical course in machine learning for materials research at Imperial College London (MATE70026)

deep-learning-v2-pytorch. Projects and exercises for the latest Deep Learning ND program https://www.udacity.com/course/deep-learning-nanodegree--nd101

Chem6_Lab_PythonCode. Code for completing analyses in Chem6 lab

MembraneFission.

fep_tutorial. Rich Text Format

ruff. An extremely fast Python linter and code formatter, written in Rust.

combined-autonomous-coding. Python

statquest.github.io. HTML

awesome-matchem-datasets. Python

aws-ml-enablement-workshop. 組織横断的にチームを組成し、機械学習による成長サイクルを実現する計画を立てるワークショップ

pytorch-examples. Simple examples to introduce PyTorch

NYU-DLSP20. NYU Deep Learning Spring 2020

the-incredible-pytorch. The Incredible PyTorch: a curated list of tutorials, papers, projects, communities and more relating to PyTorch.

dlwpt-code. Code for the book Deep Learning with PyTorch by Eli Stevens, Luca Antiga, and Thomas Viehmann.

theLMbook. This is the official repository for The Hundred-Page Language Models Book by Andriy Burkov

scientific-visualization-book. An open access book on scientific visualization using python and matplotlib

marimo. A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. Stored as pure Python. All in a modern, AI-native editor.

intro-hpc. Scripts used in the "HPC@UAntwerp introduction" course​

BigSolDBv2.0. Jupyter Notebook

Introduction.jl. Jupyter Notebook

pytorchTutorial. PyTorch Tutorials from my YouTube channel

summer-program. Repository for all summer program related programs

mol-view-stories. Molstar Stories Webapp

codex. Lightweight coding agent that runs in your terminal

probability. Probabilistic reasoning and statistical analysis in TensorFlow

ost_pymodules. A set of modules for advanced analysis of molecular structures and MD trajectories using the OpenStructure (http://www.openstructure.org) software.

QUIP. libAtoms/QUIP molecular dynamics framework: https://libatoms.github.io

handson-ml2. ⛔️ DEPRECATED – See https://github.com/ageron/handson-ml3 or handson-mlp instead.

pytorch-deep-learning. Materials for the Learn PyTorch for Deep Learning: Zero to Mastery course.

tensorflow-deep-learning. All course materials for the Zero to Mastery Deep Learning with TensorFlow course.

BCVSPIN2024_Tutorial. This is the repository for BCVSPIN2024 Machine Learning Workshop, Nepal.

NotebookOS. A GPU-efficient Jupyter Notebooks-as-a-Service platform designed for interactive deep learning training (IDLT) workloads (ASPLOS'26)

molecool. This repo is pushed to exclusively by Claude Code

Evo-MD_curvature_sensing. Python

mlcg. Machine Learning tools for Coarse Graining

mlcg-tk. Tools to prepare data for use in training a transferable coarse grained (CG) forcefield using the MLCG package

Automartini_M3. Automatic Martini force field generator for small organic molecules (up to 25 heavy atoms), Martini 3 compatible

apbs. Software for biomolecular electrostatics and solvation calculations

gpu_programming_beginner. Fundamentals of heterogeneous parallel programming with CUDA C/C++ at the beginner level.

database-tutorial-pt2. Python

iqb-2024. Notebooks and environment set up for IQB 2024 workshop - Python for Molecular Docking

iqb-2025. This repository contains notebooks for the workshop Python for Cheminformatics-Driven Molecular Docking held on May 1, 2025 in collaboration with the RCSB Protein Data Bank.

chemiluminescence-of-bleach. Jupyter Notebook

julia-introduction. Introduction to Julia - from https://github.com/JuliaMolSim/MolSSI_workshop - under construction!

auto_slurm. Script for automatically submitting SLURM jobs, significantly simplifying routine calculations.

openmm7tutorials. Tutorials using new features in OpenMM 7

torchmd. End-To-End Molecular Dynamics (MD) Engine using PyTorch

unomd. Python package to run molecular dynamics simulation of a protein-ligand complex in a single line of code.

LAMMPS_Examples. Examples LAMMPS simulations to generate thermodynamic properties of simple molecular models

TensorFlow-Tutorial. Tensor Flow tutorial examples, containing Linear Regression, MLP and CNN examples

ATLAS-UK-ML. ATLAS UK Machine Learning Tutorial notebooks, macros and scripts

QMUL_MLSociety. QMUL ML Society's repository for educational resources. This is a collection of lecture notes, tutorials, and learning materials focused on machine learning and artificial intelligence. Join us in exploring these resources to enhance our understanding and skills in the field! Contributions are welcome!

openmmMartini. adding martini force field to openmm

openmm-cph. Constant pH simulation with OpenMM

interfaceff2gro. A python script to prepare GROMACS input files using INTERFACE forcefield

KE824-Biomolecular-simulations. This is purely for testing how to upload larger filesizes

annotate. Annotate text and publish it on the web

Force-Fields. Force Fields

openmm-setup. An application for configuring and running simulations with OpenMM

SeparatedTopologies. Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).

awesome-pretrain-on-molecules. [IJCAI 2023 survey track]A curated list of resources for chemical pre-trained models

openmm-wheels. Shell

simple-simulate-complex. Simple protein-ligand complex simulation with OpenMM

tldw_server. tl/dw (Too Long, Didn't Watch): Your Personal Research Multi-Tool - a naive attempt at 'A Young Lady's Illustrated Primer' (Open Source NotebookLM)

plumed_scripts. Python

openmm-plumed-tests. Alanine dipeptide OpenMM-Plumed test

a2c_ase. An ASE-friendly implementation of the amorphous-to-crystalline (a2c) workflow.

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.

contact_map. Contact map analysis for biomolecules; based on MDTraj

gmx_MMPBSA. gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

mediapy. This Python library makes it easy to display images and videos in a notebook.

COBY. COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3

MDBenchmark. Scripts and inputs to perform simulations of organic crystals and peptide crystals using GROMACS.

Python. My Python Examples

packmol. Packmol - Initial configurations for molecular dynamics simulations

MDCrow. Molecular dynamics simulations with an LLM agent

python. Exercism exercises in Python.

OpenMMDL. Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes

ConformerDependentCharges. Jupyter Notebook

simple-simulate-complex. Simple protein-ligand complex simulation with OpenMM

ProteinStructureEmbedding. Python

sars-cov-2-proteins.

ParmEd. Parameter/topology editor and molecular simulator

rustlings. :crab: Small exercises to get you used to reading and writing Rust code!

Dhar_IDP_ensemble_docking_25. Code Accompanying "Ensemble Docking for Intrinsically Disordered Proteins" by Anjali Dhar, Thomas R. Sisk and Paul Robustelli.

pygwalker. PyGWalker: Turn your dataframe into an interactive UI for visual analysis

ommprotocol. A command line application to launch molecular dynamics simulations with OpenMM

md-scripts. A collections of scripts for working molecular dynamics simulations

2020-06-05-files. Files for the py tutorial located at https://emleddin.github.io/2020-06-05-py-tutorial/

example_MD_with_MLP. Simple example of creating, training, and running a machine learning potential for molecular dynamics

MDAnalysisWorkshop-Intermediate1Day. Materials for 1-day intermediate workshop

cgen2gmx. Command line tool for organizing and curating molecular dynamics force field parameters

Nance_Enzyme_Encap_MD. Jupyter Notebook

jupytermosaic. A Jupyter Notebook / Jupyter Lab extension allowing for tiling of cells for a customizable and flexible layout reducing white space.

drMD. Molecular Dynamics for Experimentalists

forcebalance. Systematic force field optimization.

bacterial-inner-membrane.

tinydft. A minimalistic atomic Density Functional Theory (DFT) code

md-tracks. MD-Tracks is a statistical analysis toolkit for molecular dynamics and monte carlo simulations.

QuickFF. A Python code to quickly derive ab initio parameterized force fields.

tinyff. Minimalistic force-field implementation for teaching purposes

openmm-tensorflow. OpenMM plugin to define forces with neural networks

openmm-ml. High level API for using machine learning models in OpenMM simulations

rainbow. Read chromatography and mass spectrometry binary files.

wedap. Weighted Ensemble Data Analysis and Plotting

info8004-advanced-machine-learning. Lectures for INFO8004 Advanced Machine Learning, ULiège

info8010-deep-learning. Lectures for INFO8010 Deep Learning, ULiège

dats0001-foundations-of-data-science. Materials for DATS0001 Foundations of Data Science, ULiège

info8006-introduction-to-ai. Lectures for INFO8006 Introduction to Artificial Intelligence, ULiège

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

dabble. Membrane protein builder and parameterizer

mdvwhole. Density based object completion over PBC.

Python. All Algorithms implemented in Python

HierGO. A hierarchical approach of generating MD simulation-ready tiled graphene oxide stacks

scikit-mol. scikit-learn classes for molecular vectorization using RDKit

interfaceff2gro. A python script to prepare GROMACS input files using INTERFACE forcefield

networks-course. A short course on network data science at Johns Hopkins University

academicwriting.

markitdown. Python tool for converting files and office documents to Markdown.

pytim. a python package for the interfacial analysis of molecular simulations

rex_md_tutorial. Simple tutorial for running replica exchange on Infer

Machine-Learning-Fundamentals. A collection of Machine Learning models implemented from math to model in jupyter notebook.

scipy-lecture-notes. Notes used to give tutorials (for example at Euroscipy 2010/2011)

simple-membrane-protein-analysis. This is a short tutorial showing how to use both VMD and MDAnalysis to analyse a molecular dynamics simulation of a membrane protein.

pymol-animations. Tutorials and examples for nicer animations (movies) and images in PyMOL.

IntroToBiophysics. Introduction to Biophysics, requires one semester of calculus-based Physics.

making-prettier-plots. a quick primer on making prettier (and more impactful) plots

persistence_length_tutorial. Calculate the persistence length of polymers using MDAnalysis

PHY494-resources-2016. Resources for ASU PHY494 (Spring 2016)

ASU-PHY494. Class web pages for Spring 2021 ASU PHY494 Computational Methods in Physics.

trieste2017. Material related to the plumed2017 event

scipro-primer. Software and additional material for the book "A Primer on Scientific Programming with Python"

tf_metadynamics. Using neural networks for enhanced sampling in computational biophysics

ab-initio-thermodynamics-of-water. “Ab initio thermodynamics of liquid and solid water” Bingqing Cheng, Edgar A. Engel, JÖrg Behler, Christoph Dellago and Michele Ceriotti

learn-cpp. Codecademy | Learn C++

Numpy-Tutorial-SciPyConf-2016. SciPy 2016 NumPy tutorial

chatgpt-prompts-for-academic-writing. This list of writing prompts covers a range of topics and tasks, including brainstorming research ideas, improving language and style, conducting literature reviews, and developing research plans.

stat_rethinking_2024. R

the-art-of-command-line. Master the command line, in one page

making-it-rain. Cloud-based molecular simulations for everyone

ML-For-Beginners. 12 weeks, 26 lessons, 52 quizzes, classic Machine Learning for all

Python. All Algorithms implemented in Python

acs-2023-notebooks-filled. Jupyter Notebook

enhanced_sampling_tutorials. A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS

python-mastery. Advanced Python Mastery (course by @dabeaz)

openmm_workshops. Jupyter Notebook

PHY494-resources-2017. Data files and scripts for the ASU PHY494 (Spring 2017) class.