Enhanced protein mutational sampling using time-lagged variational autoencoders
☆30Sep 17, 2018Updated 7 years ago
Alternatives and similar repositories for vde_metadynamics
Users that are interested in vde_metadynamics are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Using supervised machine learning to build collective variables for accelerated sampling☆28Jun 26, 2018Updated 8 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- Accelerating Metadynamics-Based Free-Energy Calculations with Adaptive Machine Learning Potentials☆18Jun 9, 2021Updated 5 years ago
- My first ever repository, some notebooks useful, others sucks. Topics include file format conversion with obabel, docking with Auto Dock,…☆26Oct 22, 2025Updated 9 months ago
- Spectral Gap Optimization of Parameters☆18Mar 28, 2020Updated 6 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.
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Dec 19, 2021Updated 4 years ago
- A Python package to improve the accessibility and reproducibility of enhanced sampling simulations☆15May 16, 2018Updated 8 years ago
- Bias-controlled 3D generative framework for structure-based ligand design☆17Nov 2, 2022Updated 3 years ago
- Code for the results of the Paper:☆21May 17, 2018Updated 8 years ago
- Molecular AutoEncoder in PyTorch☆93Jan 16, 2026Updated 6 months ago
- Rethinking Metadynamics: From Bias Potentials to Probability Distributions☆15Sep 18, 2023Updated 2 years ago
- A novel approach to pose selection in protein-ligand docking based on graph theory.☆20Nov 22, 2016Updated 9 years ago
- Useful Collective Variables for OpenMM☆18May 9, 2024Updated 2 years ago
- Version controled, crossreferenced bibliomanager with automatic metadata fetching☆17Apr 8, 2021Updated 5 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆14Feb 20, 2023Updated 3 years ago
- Novel molecules from a reference shape!☆83Jan 30, 2024Updated 2 years ago
- Learning Protein-Ligand Properties with Atomic Environment Vectors☆10Apr 19, 2024Updated 2 years ago
- Variational Autoencoder for Dimensionality Reduction of Time-Series☆189May 1, 2022Updated 4 years ago
- NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms☆16Sep 14, 2018Updated 7 years ago
- MD pharmacophores and virtual screening☆35Dec 15, 2023Updated 2 years ago
- Using neural networks for enhanced sampling in computational biophysics☆16Aug 17, 2017Updated 8 years ago
- Deep learning meets molecular dynamics.☆189May 3, 2019Updated 7 years ago
- A deep learning framework for deubiquitnase-substrate interaction identification☆13Jul 31, 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.
- FlexPose, a framework for AI-based flexible modeling of protein-ligand binding pose.☆56Dec 27, 2023Updated 2 years ago
- ☆29Jul 10, 2020Updated 6 years ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Jan 3, 2026Updated 7 months ago
- ☆12May 3, 2025Updated last year
- Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)☆13Dec 1, 2025Updated 8 months ago
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 5 years ago
- ☆10Jun 28, 2025Updated last year
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆34Jul 31, 2026Updated last week
- Package for reading, analysis and visualization of metadynamics HILLS☆41Nov 28, 2023Updated 2 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.
- DDGScan: an integrated parallel workflow for the in silico point mutation scan of protein☆51Mar 21, 2024Updated 2 years ago
- Normal Mode Analysis for Macromolecules☆18Apr 1, 2017Updated 9 years ago
- Cryptic pocket prediction using AlphaFold 2☆25Nov 27, 2022Updated 3 years ago
- dockECR: open consensus docking and ranking protocol for virtual screening of small molecules☆28Oct 15, 2021Updated 4 years ago
- Development version of plumed 2☆509Jul 31, 2026Updated last week
- SIEVE-Score: interaction energy-based virtual screening method based on random forest.☆14Sep 15, 2023Updated 2 years ago
- ☆13Jul 11, 2023Updated 3 years ago