Open Source, Prepare a molecular dynamic simulation from scratch without installing local VMD, use LigParGen for topology, it is one of the most reliable MD for a general solution protein-ligand simulation.
☆13Jul 3, 2023Updated 2 years ago
Alternatives and similar repositories for NAMD-MD
Users that are interested in NAMD-MD are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- This script is designed for evaluating the binding affinity between a protein target and a small molecule, by calculating the binding fre…☆15May 1, 2023Updated 3 years ago
- A python script for PyMol to make protein-ligand interaction images.☆18Apr 1, 2025Updated last year
- Open-Sourced. Millions of small molecules will be downloaded from the ZINC database in 3D SDF file format, with one click, to get ready f…☆13Dec 29, 2023Updated 2 years ago
- A purely functional cheminformatics toolkit written in Scala☆16Jun 7, 2013Updated 12 years ago
- Open Source, Mostly just clicking mouse to finish a simulation with Ambertools and OpenMM. It was designed to use locally but another not…☆37Apr 27, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Explain a SMARTS using SmartsView (K. Schomburg and M. Rarey)☆17Oct 4, 2021Updated 4 years ago
- A Rust reimplementation of PyMOL molecular visualization☆112Apr 16, 2026Updated last month
- Contributed and additional nodes for maize☆22Feb 18, 2026Updated 3 months ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆29Nov 2, 2025Updated 6 months ago
- LigParGen python package version 2.3 (beta)☆14Apr 19, 2025Updated last year
- ☆13May 18, 2025Updated last year
- ☆81Dec 18, 2024Updated last year
- How to get started with computational chemistry research. Directed to new people in our lab, may be useful in general.☆28Jun 4, 2018Updated 7 years ago
- ☆10May 17, 2021Updated 5 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ☆29May 5, 2025Updated last year
- Electronic lab notebook for organic chemistry☆18May 7, 2026Updated 3 weeks ago
- ☆15Nov 7, 2022Updated 3 years ago
- ☆11Oct 1, 2021Updated 4 years ago
- Graph convolutional neural networks for analyzing glycans [LEGACY; use glycowork implementation]☆19Mar 9, 2021Updated 5 years ago
- A deep reinforcement learning library for conformer generation.☆20Apr 15, 2024Updated 2 years ago
- Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab☆11Oct 16, 2022Updated 3 years ago
- a sublime plugin for quick find relative link file on project☆15Jun 30, 2017Updated 8 years ago
- C++/Python Library for Systematic Chemical Space Exploration☆25Dec 21, 2021Updated 4 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Efficient manipulation of protein structures in Python☆68Sep 27, 2025Updated 8 months ago
- Code of "Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model"☆14Jul 8, 2025Updated 10 months ago
- [JCIM'25] AccFG: Functional Group Extraction and Molecular Structure Comparison☆28Dec 27, 2025Updated 5 months ago
- Shape-based alignment of molecules using 3D point-based representation☆23Apr 8, 2026Updated last month
- Python based Graphical User Interface for generating input files for and running molecular dynamic simulation.☆10Aug 27, 2024Updated last year
- Disordered protein ensemble prediction☆14Apr 2, 2026Updated last month
- Code to support the paper: P. van Gerwen, K. R. Briling, C. Bunne, V. R. Somnath, R. Laplaza, A. Krause, C. Corminboeuf, "3DReact: Geomet…☆24Nov 6, 2025Updated 6 months ago
- Dig into an opam switch for doc☆11Apr 8, 2022Updated 4 years ago
- ☆11Jun 16, 2024Updated last year
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆17Apr 10, 2026Updated last month
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆16Apr 3, 2026Updated last month
- ☆16Dec 24, 2016Updated 9 years ago
- ☆15Oct 5, 2024Updated last year
- Demos of many Rosetta applications☆25Jun 10, 2025Updated 11 months ago
- Lamarckian Evolutionary Algorithm for de novo Drug Design☆27Mar 3, 2023Updated 3 years ago
- A light-weight PyTorch extension for equivariant deep learning☆18Feb 20, 2025Updated last year