AG-Peter / encodermapView external linksLinks
python library for dimensionality reduction
☆32Oct 28, 2025Updated 3 months ago
Alternatives and similar repositories for encodermap
Users that are interested in encodermap are comparing it to the libraries listed below
Sorting:
- Coarse grain to atomistic molecular coordinate and topology converter☆17Mar 13, 2025Updated 11 months ago
- Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)☆14Jan 2, 2026Updated last month
- fragbuilder is a tool to create, setup and analyze QM calculations on peptides.☆15Oct 31, 2014Updated 11 years ago
- mirror of https://zhanglab.ccmb.med.umich.edu/EDTSurf/☆10Jun 20, 2023Updated 2 years ago
- This code allows is for diversity picking across multiple different, and potentially overlapping chemical compound classes, while at the …☆11Oct 30, 2020Updated 5 years ago
- open toolbox for structural comparison☆13Dec 13, 2018Updated 7 years ago
- ☆13Feb 13, 2025Updated last year
- ProteinFeatureAnalyzer extracts, analyzes and visualizes features from protein structures.☆14Mar 14, 2020Updated 5 years ago
- An Explainable Neural Network for Fault Diagnosis With a Frequency Activation Map☆14Dec 30, 2021Updated 4 years ago
- Jupyter notebook for an introduction to atomic-scale machine learning class☆17Nov 14, 2023Updated 2 years ago
- Repository of the data for PLUMED Masterclass 22.3☆14Jul 10, 2024Updated last year
- Comparison of principal components analysis with diffusion maps on toy data sets and a molecular simulation trajectory☆17Feb 1, 2017Updated 9 years ago
- ☆15Jun 26, 2018Updated 7 years ago
- Implementation of AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction☆16Jun 19, 2025Updated 7 months ago
- Automatic Mutual Information Noise Omission☆15Oct 8, 2024Updated last year
- Learning Protein Constitutive Motifs from Sequence Data: RBM toolbox☆20Jan 30, 2019Updated 7 years ago
- Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)☆45May 3, 2020Updated 5 years ago
- aimmd (AI for Molecular Mechanism Discovery) autonomously steers (a large number of) molecular dynamics simulations to efficiently sample…☆19Nov 22, 2025Updated 2 months ago
- Main repository for METAGUI3☆20Jun 19, 2021Updated 4 years ago
- Materials for KDD2023 tutorial: Knowledge-augmented Graph Machine Learning for Drug Discovery: from Precision to Interpretability☆23Aug 8, 2023Updated 2 years ago
- Build conformational representations of Intrinsically Disordered Proteins and Regions by a guided sampling of the protein torsion space☆31Dec 18, 2025Updated last month
- Probabilistic Graphical Models in Python3.☆24Jun 4, 2025Updated 8 months ago
- Fast and accurate protein structure prediction☆57Jan 17, 2025Updated last year
- SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks (Scientific Reports)☆65May 9, 2020Updated 5 years ago
- cime public repository☆32Jan 12, 2023Updated 3 years ago
- ☆63May 2, 2019Updated 6 years ago
- Correlation-based feature selection of Molecular Dynamics simulations☆29Nov 25, 2025Updated 2 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆35Sep 16, 2025Updated 4 months ago
- PDBClean helps create a curated ensemble of molecular structures☆14Oct 23, 2025Updated 3 months ago
- Scores for Hydrophobicity and Charges based on SASAs☆41Jun 12, 2025Updated 8 months ago
- Molecular Dynamics in the Open☆86Oct 27, 2025Updated 3 months ago
- This repository contains the installation zip file, user manual, example data, and source code for the PyXlinkViewer plugin for PyMOL v2☆10Jul 3, 2023Updated 2 years ago
- MDAnalysis wrapper around Packmol☆37May 1, 2023Updated 2 years ago
- VMD Plugin and associated scripts to build lignin structures from topological specifications☆17Jul 17, 2025Updated 6 months ago
- Official repo of the Biomeccanica Multiscala course (prof. Marco A. Deriu) - Master Degree in Biomedical engineering, Politecnico di Tori…☆12Jan 2, 2025Updated last year
- A tool for setting up free energy simulations.☆36Oct 20, 2022Updated 3 years ago
- A fragment-based molecular assembly toolkit☆43Dec 4, 2025Updated 2 months ago
- Graph Network for protein-protein interface including language model features☆34Mar 26, 2024Updated last year
- Unsupervised learning of atomic scale dynamics from molecular dynamics.☆85Dec 14, 2021Updated 4 years ago