mdml: Deep Learning for Molecular Simulations
☆55May 17, 2025Updated last year
Alternatives and similar repositories for mdml
Users that are interested in mdml are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆64Aug 5, 2026Updated 2 months ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆19Apr 16, 2025Updated last year
- ☆52Jun 15, 2026Updated 3 months ago
- This repository provides with custom code and analysis scripts to generate structural ensembles of intrinsically disordered proteins by u…☆24Oct 31, 2025Updated 11 months ago
- Combines FRESEAN mode analysis of a protein (based on a CG representation) with enhanced sampling using metadynamics☆17May 7, 2026Updated 5 months ago
- 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.
- Automated Adaptive Absolute alchemical Free Energy calculator☆132Oct 5, 2026Updated last week
- Bayesian Optimization for protein design and mining☆28Jul 2, 2026Updated 3 months ago
- A protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cle…☆40Jul 25, 2024Updated 2 years ago
- ☆16Jun 19, 2026Updated 3 months ago
- Deconvolving mutation effects on protein stability and function with disentangled protein language models☆18May 15, 2026Updated 4 months ago
- Software package for FEP☆24Aug 7, 2026Updated 2 months ago
- Molecular Dynamics for Experimentalists☆72Oct 6, 2026Updated last week
- Weighted Ensemble Data Analysis and Plotting☆27Jul 17, 2026Updated 2 months ago
- PandaDock: Physics based Molecular Docking with GNN Scoring☆106Aug 24, 2026Updated last month
- 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.
- ☆38Oct 14, 2024Updated 2 years ago
- A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS☆168May 9, 2026Updated 5 months ago
- The package of ProBuilder from Longxing Cao lab☆26Jan 19, 2026Updated 8 months ago
- OMNI-P2x: A universal neural network potential for excited states☆16Mar 19, 2026Updated 6 months ago
- Fully automated high-throughput MD pipeline☆109Sep 18, 2026Updated 3 weeks ago
- Efficient manipulation of protein structures in Python☆68Jun 16, 2026Updated 3 months ago
- ☆46Jan 10, 2024Updated 2 years ago
- Model for predicting micro-millisecond motions from protein sequence and/or structure☆117Aug 20, 2026Updated last month
- ☆17May 18, 2026Updated 4 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Deep generative modeling of protein structural ensembles☆41May 27, 2026Updated 4 months ago
- ☆28Jun 2, 2026Updated 4 months ago
- Official Implementation of CompassDock☆21Feb 13, 2026Updated 8 months ago
- ☆12May 16, 2020Updated 6 years ago
- ☆157May 18, 2026Updated 4 months ago
- A machine learned Molecular Mechanics force field with integration into GROMACS and OpenMM☆65Updated this week
- Neural relational inference for molecular dynamics simulations☆60May 30, 2023Updated 3 years ago
- PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.☆153Feb 12, 2025Updated last year
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆89Jan 8, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A flow matching model for generating conformational ensembles of protein backbones.☆53May 22, 2026Updated 4 months ago
- Python application for finding apo and holo structures for user-defined protein-ligand interactions☆10Feb 7, 2023Updated 3 years ago
- Structure prediction and design of proteins with noncanonical amino acids☆147Feb 1, 2026Updated 8 months ago
- Python based Graphical User Interface for generating input files for and running molecular dynamic simulation.☆10Aug 27, 2024Updated 2 years ago
- ☆68Apr 28, 2025Updated last year
- Pytorch implementation for ICML 2024 paper Proteus: Exploring Protein Structure Generation for Enhanced Designability and Efficiency.☆90Jun 23, 2024Updated 2 years ago
- A deep learning-based framework to uniquely identify an uncorrelated, isometric and meaningful latent representation.☆19Sep 12, 2023Updated 3 years ago