tica

🚂 Python API for Emma's Markov Model Algorithms 🚂

🏗️ Statistical models for biomolecular dynamics 🏗️

IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook

tICA to capture local loop motion. Describes how to analyse loop movement using TICA and how to run PT-Metad using TIC vectors

How one can use binary classifiers, variational auto-encoder, TICA, PCA, distance and dihedral order parameters as CVs in context of pepsin-like aspartic proteases e.g. BACE1 and plasmepsin-II.

Molecular dynamics pre- and post-processing toolkit.

Reproducible audit of how sampling budget biases apparent state counts from PCA, TICA, and VAE analyses of molecular simulation data.

Enhancement project for TICA, and web application for external users

Production-ready Kubernetes deployment for Open WebUI on the University of Alberta's Vulcan HPC cluster, featuring PostgreSQL, Redis, LDAP auth, RAG, and autoscaling.