Coarse-grained molecular dynamics for protein physics
☆43Sep 15, 2017Updated 8 years ago
Alternatives and similar repositories for Upside-MD
Users that are interested in Upside-MD are comparing it to the libraries listed below
Sorting:
- The BiomolecularStructures package provides several Bioinformatics-related modules for Julia.☆12Jun 13, 2017Updated 8 years ago
- Learning protein structure with a differentiable simulator☆27Jul 8, 2019Updated 6 years ago
- ☆29Jul 10, 2020Updated 5 years ago
- Implementation of Differentiable Molecular Simulations with torchMD.☆16Oct 9, 2023Updated 2 years ago
- Differentiable Markov Chain Monte Carlo☆15Mar 23, 2024Updated last year
- COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM☆15Feb 8, 2026Updated last month
- ☆29Dec 1, 2020Updated 5 years ago
- Physical energy function for protein sequence design☆38May 6, 2023Updated 2 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
- Python/TF1 implementation of DeepAccNet (https://www.biorxiv.org/content/10.1101/2020.07.17.209643v1)☆10Sep 2, 2020Updated 5 years ago
- Auto-differentiated descriptors using Enzyme☆12Apr 2, 2025Updated 11 months ago
- Comparison of principal components analysis with diffusion maps on toy data sets and a molecular simulation trajectory☆17Feb 1, 2017Updated 9 years ago
- Generative diverse protein backbones by protein language model☆34Feb 27, 2026Updated 3 weeks ago
- Add CMAP parameters into common AMBER prmtop file☆14Sep 12, 2021Updated 4 years ago
- Contact map alignment☆43Feb 3, 2021Updated 5 years ago
- A voxel based approach for dynamic cluster analysis of molecular dynamics trajectories.☆32Nov 5, 2025Updated 4 months ago
- Package to perform minimum-distance distribution analyses of complex solute-solvent interactions☆23Mar 5, 2026Updated 2 weeks 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 2 years ago
- A tool to characterize the local structure of liquid water by geometric order parameters.☆15Jul 31, 2024Updated last year
- OpenMM plugin that implements (an)isotropic polarizable point dipoles and multipoles up to octopoles.☆11Feb 7, 2025Updated last year
- A library to perform targeted free energy perturbation with normalizing flows.☆10Sep 1, 2025Updated 6 months ago
- ☆18Dec 29, 2025Updated 2 months ago
- Software for automated processing of alchemical free energy calculations☆11Nov 7, 2022Updated 3 years ago
- ☆12Jun 16, 2023Updated 2 years ago
- Run OpenMM with forces provided by any Python program☆39Dec 25, 2024Updated last year
- Fully convolutional neural networks for protein residue-residue contact prediction☆44Mar 25, 2019Updated 6 years ago
- Deep learning meets molecular dynamics.☆186May 3, 2019Updated 6 years ago
- Code for RL-DIF☆16Jun 24, 2025Updated 8 months ago
- general purpose coarse-grained molecular dynamics simulation package☆35Jan 27, 2023Updated 3 years ago
- Deep convolutional networks for fold recognition☆22Nov 8, 2019Updated 6 years ago
- Gibbs sampling for expanded ensembles and replica exchange simulations☆11Jun 1, 2014Updated 11 years ago
- Graph Inference on MoLEcular Topology☆26Mar 25, 2023Updated 2 years ago
- Turbomoleio is a python package containing a set of tools for the generation of inputs and parsing of outputs for the TURBOMOLE quantum c…☆21Jan 20, 2025Updated last year
- PyTorch library of layers acting on protein representations☆119Jun 30, 2024Updated last year
- The GB99dms implicit solvent force field for proteins, plus scripts and data☆27Sep 19, 2025Updated 6 months ago
- ☆19Feb 6, 2017Updated 9 years ago
- ChainRules.jl integration for Unitful.jl☆13Aug 9, 2022Updated 3 years ago
- A Gene Finder framework for Julia.☆16Jan 16, 2026Updated 2 months ago
- Rigid Body Dynamics with OpenMM☆12May 29, 2018Updated 7 years ago