MODE-TASK’s documentation

Getting started

• Introduction
  • PyMOL Plugin
  • Cite this project
  • Contributing
  • License
• Installation
  • Platform compatibility
  • Download the project
  • Installing dependencies

Theory

• Normal Mode Analysis (NMA)
• Principal Component Analysis (PCA)
• Kernel PCA (kPCA)
• Incremental PCA
• Multi-dimensional scaling (MDS)
• t-Distributed Stochastic Neighbor Embedding (t-SNE)

Usage

• NMA Scripts
  • Coarse grain
  • ANM
  • Mean square fluctuation
  • Assembly Covariance
  • Conformation mode
  • Combination mode
  • Mode visualisation
• PCA Scripts
  • PCA on Cartesian coordinates
  • PCA on internal coordinates
  • MDS (Multi-dimensional scaling) on MD trajectory
  • t-SNE on MD trajectory

Tutorials

• NMA Tutorial
  • Aim
  • Create a working directory
  • Preparation of structure of the mature capsid
  • Preparation of the structure of the A-particle capsid
  • Coarse grain
  • Mode decomposition
  • Identification of modes that contribute to the conformational change
  • Conformation mode
  • Combination mode
  • Mode visualisation
  • Mean square fluctuation (MSF)
  • Assembly Covariance
• PCA Tutorial
  • PCA of a MD trajectory
  • MDS (Multi-dimensional scaling) on a MD trajectory
  • t-SNE on a MD trajectory

pyMODE-TASK

• pyMODE-TASK- PyMOL plugin