Denoising diffusion probabilistic models for replica exchange
☆25Feb 19, 2022Updated 4 years ago
Alternatives and similar repositories for DDPM_REMD
Users that are interested in DDPM_REMD are comparing it to the libraries listed below
Sorting:
- Demo of diffusion models #DDPM applied to molecular dynamics of small peptide☆14Jan 26, 2024Updated 2 years ago
- DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces☆20May 7, 2025Updated 10 months ago
- Python module for identification of conserved water molecules from molecular dynamics trajectories.☆14Feb 12, 2026Updated 3 weeks ago
- PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Comp…☆16Oct 23, 2025Updated 4 months ago
- DyNoPy☆11Sep 5, 2024Updated last year
- Clustering tool for biomolecular structural ensembles and data in general.☆10Aug 24, 2020Updated 5 years ago
- Python Tools for NAMD☆24May 7, 2025Updated 10 months ago
- Temperature generator for Replica Exchange MD simulations☆29Dec 14, 2022Updated 3 years ago
- Jupyter book and content for "Machine Learning for Molecular Dynamics" course☆13Apr 7, 2022Updated 3 years ago
- GraphVAMPnets combines graph neural networks with variational approach for Markovian process (VAMP) theory to identify the slow collectiv…☆12Feb 20, 2024Updated 2 years ago
- Correlation-based feature selection of Molecular Dynamics simulations☆29Nov 25, 2025Updated 3 months ago
- A simple but powerful VSCode extension for visualizing protein structures using the Molstar framework.☆34Oct 17, 2025Updated 4 months ago
- Multi-Level DBSCAN: A Hierarchical Density-Based Clustering Method for Analyzing Molecular Dynamics Trajectories☆13Dec 6, 2020Updated 5 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Sep 27, 2023Updated 2 years ago
- Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.☆17Feb 27, 2026Updated last week
- ☆18Oct 30, 2023Updated 2 years ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated 10 months ago
- ☆15Apr 7, 2022Updated 3 years ago
- C++11/Python3 library to read/write High Speed AFM data file☆14Apr 14, 2023Updated 2 years ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Jul 2, 2024Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Feb 23, 2026Updated last week
- ☆16Jul 26, 2024Updated last year
- Resources for Generalisable Protein Complex Prediction☆18Oct 16, 2024Updated last year
- Examples and data for performing path similarity analysis (PSA).☆17Oct 23, 2015Updated 10 years ago
- [ICML 2025] Repurposing pre-trained score-based generative models for transition path sampling by minimizing the Onsager-Machlup (OM) act…☆26Jan 14, 2026Updated last month
- Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped refe…☆13Sep 14, 2021Updated 4 years ago
- ☆13Jun 11, 2024Updated last year
- Tools for creating, analyzing and visualizing Conformation Space Networks☆17Aug 31, 2022Updated 3 years ago
- MDToolbox.jl: A Julia package for molecular dynamics trajectories analysis and modeling of biomolecules☆21Mar 21, 2025Updated 11 months ago
- Automatic Martini force field generator for small organic molecules (up to 25 heavy atoms), Martini 3 compatible☆36Feb 16, 2026Updated 2 weeks ago
- A flow matching model for generating conformational ensembles of protein backbones.☆35Jan 7, 2026Updated 2 months ago
- Modeling molecular ensembles with scalable data structures and parallel computing☆37Feb 16, 2026Updated 2 weeks ago
- Robust and stable clustering of molecular dynamics simulation trajectories.☆19Sep 2, 2022Updated 3 years ago
- A deep learning-based framework to uniquely identify an uncorrelated, isometric and meaningful latent representation.☆19Sep 12, 2023Updated 2 years ago
- Spectral Gap Optimization of Parameters☆18Mar 28, 2020Updated 5 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆67Apr 16, 2021Updated 4 years ago
- ☆73Mar 7, 2024Updated 2 years ago
- A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and che…☆18Aug 13, 2021Updated 4 years ago
- Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates☆21Nov 8, 2024Updated last year