Coarse-grained molecular dynamics for protein physics. NOTE: this has been superseded by Upside 2: https://github.com/sosnicklab/upside2-md
☆26Mar 3, 2022Updated 4 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:
- ☆29Updated this week
- ML toolset for creating TED: The Encyclopedia of Domains☆26May 29, 2025Updated last year
- OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling☆21May 4, 2020Updated 6 years ago
- OPUS-Rota4: A Gradient-Based Protein Side-Chain Modeling Framework Assisted by Deep Learning-Based Predictors☆11Apr 14, 2022Updated 4 years ago
- ☆45Jan 10, 2024Updated 2 years ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- ☆27Feb 16, 2022Updated 4 years ago
- Metal and Water prediction☆14Feb 5, 2025Updated last year
- RNA Structural Bioinformatics Crash Course & Data Science in Python☆14Oct 19, 2022Updated 3 years ago
- ☆143Jun 18, 2025Updated 11 months ago
- Code for our paper "Protein sequence design with a learned potential"☆34Aug 5, 2021Updated 4 years ago
- Deep ResNet-based protein contact prediction☆19Mar 30, 2020Updated 6 years ago
- ☆18Mar 13, 2024Updated 2 years ago
- A cross-platform C++11 implementation of the CMM language interpreter☆11Jul 18, 2025Updated 10 months ago
- FermiKit small variant calls for public SGDP samples☆17Sep 22, 2016Updated 9 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- APBS - software for biomolecular electrostatics and solvation☆132Jul 27, 2020Updated 5 years ago
- MAGPIE☆17May 5, 2024Updated 2 years ago
- ☆33Sep 19, 2025Updated 8 months ago
- Lipid identification software for discovery LC-MS/MS☆12Mar 29, 2019Updated 7 years ago
- a deep learning-based retention time alignment tool for large cohort LC-MS data analysis☆15Dec 6, 2023Updated 2 years ago
- Molecular dynamics without molecules: searching the conformational space of proteins with generative neural networks☆11Jun 13, 2022Updated 3 years ago
- Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file☆39Apr 29, 2026Updated last month
- Note that current version does not include search of very large metagenome data. For some proteins, metagenome data is important. We will…☆99Jan 26, 2022Updated 4 years ago
- A software package for flexible HPC GPs☆16May 18, 2026Updated last week
- 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.
- Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)☆85Apr 21, 2026Updated last month
- Command-line tools for protein structure analysis: convert PDB, mmCIF, PDBML, or XYZR files into atomic sphere data, then compute volumes…☆15Apr 16, 2026Updated last month
- Complementary tools for Relion tomo☆12Mar 9, 2024Updated 2 years ago
- Temperature generator for Replica Exchange MD simulations☆30Dec 14, 2022Updated 3 years ago
- Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching☆12Sep 17, 2025Updated 8 months ago
- Optimized Generative Adversarial Network with Graph Convolutional Networks for Novel Molecule Design☆12Jan 2, 2024Updated 2 years ago
- pyFoldX: python bindings for FoldX.☆57Aug 16, 2021Updated 4 years ago
- DL model to predict HLA peptide presentation☆16Jan 31, 2024Updated 2 years ago
- ☆15Apr 7, 2022Updated 4 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Protocol for finding informative protein families and then using them to score omic samples☆19Jul 27, 2022Updated 3 years ago
- ☆18Dec 22, 2017Updated 8 years ago
- Code for ApoDock☆20Apr 7, 2025Updated last year
- RELION external reconstruct functionality☆11Sep 11, 2020Updated 5 years ago
- A Python module for reading, writing, and manipulating NMR-STAR files.☆30May 15, 2026Updated 2 weeks ago
- Describe and apply transformation on molecular structures and topologies☆144Updated this week
- Learning protein structure with a differentiable simulator☆27Jul 8, 2019Updated 6 years ago