Coarse-grained molecular dynamics for protein physics
☆49Sep 15, 2017Updated 9 years ago
Alternatives and similar repositories for Upside-MD
Users that are interested in Upside-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:
- Topological Data Analysis on protein structures from crystalized structures and AlphaFold DB.☆12Feb 4, 2026Updated 8 months ago
- Coarse-grained molecular dynamics for protein physics. NOTE: this has been superseded by Upside 2: https://github.com/sosnicklab/upside2-…☆28Mar 3, 2022Updated 4 years ago
- Learning protein structure with a differentiable simulator☆27Jul 8, 2019Updated 7 years ago
- ☆29Jul 10, 2020Updated 6 years ago
- Implementation of Differentiable Molecular Simulations with torchMD.☆15Oct 9, 2023Updated 3 years ago
- 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.
- Differentiable Markov Chain Monte Carlo☆15Mar 23, 2024Updated 2 years ago
- Contact map alignment☆44Feb 3, 2021Updated 5 years ago
- ☆29Dec 1, 2020Updated 5 years ago
- Python/TF1 implementation of DeepAccNet (https://www.biorxiv.org/content/10.1101/2020.07.17.209643v1)☆10Sep 2, 2020Updated 6 years ago
- Corrections to the text of the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford Un…☆32Mar 21, 2023Updated 3 years ago
- Contact map alignment☆16May 10, 2018Updated 8 years ago
- Fully convolutional neural networks for protein residue-residue contact prediction☆44Mar 25, 2019Updated 7 years ago
- Auto-differentiated descriptors using Enzyme☆12Apr 2, 2025Updated last year
- Comparison of principal components analysis with diffusion maps on toy data sets and a molecular simulation trajectory☆17Feb 1, 2017Updated 9 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A voxel based approach for dynamic cluster analysis of molecular dynamics trajectories.☆34Nov 5, 2025Updated 11 months ago
- Add CMAP parameters into common AMBER prmtop file☆14Sep 12, 2021Updated 5 years ago
- COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM☆15Jul 14, 2026Updated 3 months ago
- A tool to characterize the local structure of liquid water by geometric order parameters.☆15Jul 31, 2024Updated 2 years ago
- ☆12Jun 16, 2023Updated 3 years ago
- ☆19Oct 2, 2026Updated 3 weeks ago
- ☆32Updated this week
- Deep learning meets molecular dynamics.☆190May 3, 2019Updated 7 years ago
- DeepContact Software☆26Jun 16, 2018Updated 8 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Graph-building for AtomicGraphNets☆12Nov 20, 2023Updated 2 years ago
- ☆10Jul 24, 2022Updated 4 years ago
- ☆24Aug 6, 2026Updated 2 months ago
- A versatile tool to investigate membrane☆11Dec 12, 2024Updated last year
- collection of thermodynamic models, using ThermoState.jl☆10Nov 28, 2020Updated 5 years ago
- Symmetric matrix as a list of the values in its upper or lower triangular part. Useful for representing pairwise measures or comparisons …☆20Sep 14, 2023Updated 3 years ago
- Generative diverse protein backbones by protein language model☆35Feb 27, 2026Updated 8 months ago
- ProLint 2.0: a scalable framework for the analysis of biomolecular interactions in MD simulations.☆12Jun 14, 2026Updated 4 months ago
- Physical energy function for protein sequence design☆46May 6, 2023Updated 3 years 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.
- Finding a lowest-energy pathway on a multidimensional landscape☆10Aug 4, 2023Updated 3 years ago
- Massively parallel hybrid particle-field molecular dynamics (hPF-MD) simulation method in Julia☆12Jan 14, 2022Updated 4 years ago
- OpenMM plugin for simulating electrochemical systems☆22Sep 23, 2024Updated 2 years ago
- Easily fetch biological sequences from online sources☆12Oct 6, 2022Updated 4 years ago
- Note that current version does not include search of very large metagenome data. For some proteins, metagenome data is important. We will…☆100Jan 26, 2022Updated 4 years ago
- Multivariate Gaussian Direct Coupling Analysis for residue contact prediction in protein families - Julia module☆24Jan 27, 2022Updated 4 years ago
- A library to perform targeted free energy perturbation with normalizing flows.☆11Aug 11, 2026Updated 2 months ago