☆30Jul 24, 2026Updated this week
Alternatives and similar repositories for upside2-md
Users that are interested in upside2-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:
- 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 NOTE: this has been superseded by Upside 2: https://github.com/sosnicklab/upside2-…☆28Mar 3, 2022Updated 4 years ago
- A fork of Autodock Vina for DeltaVina scoring function☆10Nov 7, 2016Updated 9 years ago
- Command-line tools for protein structure analysis: convert PDB, mmCIF, PDBML, or XYZR files into atomic sphere data, then compute volumes…☆15Updated this week
- Emap2sec+: Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning☆18Nov 21, 2025Updated 8 months ago
- Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching☆12Sep 17, 2025Updated 10 months 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.
- Shrinking Proteins with Diffusion☆29Jan 8, 2026Updated 6 months ago
- SGPPI: structure-aware prediction of protein-protein interactions in rigorous conditions with graph convolutional network☆15Nov 17, 2022Updated 3 years ago
- TomoNet is a GUI based pipeline package focusing on cryoET and STA data processing☆22Mar 12, 2026Updated 4 months 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
- Neural networks to analyze structural heterogeneity in cryo-electron sub-tomograms☆33Jul 13, 2026Updated 2 weeks ago
- Graphical user interface to integrate cryoEM flexibility analyses with ChimeraX☆24Sep 5, 2024Updated last year
- HiCOPS: Computational framework for peptide identification from MS data through accelerated database search☆10Mar 24, 2023Updated 3 years ago
- MAGPIE☆17May 5, 2024Updated 2 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.
- OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling☆21May 4, 2020Updated 6 years ago
- ☆34Sep 19, 2025Updated 10 months ago
- ☆24May 8, 2026Updated 2 months ago
- Correlation-based feature selection of Molecular Dynamics simulations☆29Jul 20, 2026Updated last week
- Kuhlman Lab Installation of AlphaFold3☆42Mar 26, 2026Updated 4 months ago
- A program fror inter-protein contact prediction from structures of interacting proteins☆21Jun 1, 2024Updated 2 years ago
- Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file☆40Apr 29, 2026Updated 2 months ago
- ☆46Jan 10, 2024Updated 2 years ago
- A program interfacing Segment Anything with cryoSPARC via cryosparc-tools to efficiently identify vesicle-embedded membrane proteins and …☆13Feb 18, 2025Updated last year
- 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.
- Detect and erase gold fiducials in cryo-EM images☆16May 27, 2025Updated last year
- DMFF (Differentiable Molecular Force Field) is a Jax-based python package that provides a full differentiable implementation of molecular…☆199Updated this week
- A command-line interface and Python library for generating AlphaFold3 input files.☆41Jan 2, 2026Updated 6 months ago
- Pipeline for the automatic detection and segmentation of particles and cellular structures in 3D Cryo-ET data, based on deep learning (co…☆42Jan 30, 2024Updated 2 years ago
- Complete saturation mutagenesis of a protein using ESM☆19Feb 20, 2024Updated 2 years ago
- A software package for flexible HPC GPs☆16Jul 8, 2026Updated 2 weeks ago
- Fast and accurate coarse-grained neural network molecular dynamics☆15Jul 13, 2026Updated 2 weeks ago
- Temperature generator for Replica Exchange MD simulations☆30Dec 14, 2022Updated 3 years ago
- Complementary tools for Relion tomo☆12Mar 9, 2024Updated 2 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- ☆35Dec 15, 2023Updated 2 years ago
- Python library that enables scripting access to CryoSPARC, a cryo-EM software package.☆49Updated this week
- Precompiled Windows binaries for GROMACS☆12May 10, 2022Updated 4 years ago
- CryoEM particle picking software enabled continual learning☆11Jan 9, 2022Updated 4 years ago
- Contextual Analysis Tools for cryoET and subtomogram averaging☆41Jul 16, 2026Updated last week
- Python scripts to manipulate Relion tomo STAR files and much more...☆15Mar 23, 2026Updated 4 months ago
- Explainable deep hypergraph learning modeling the peptide secondary structure prediction☆13Feb 27, 2023Updated 3 years ago