Workshop Guide

Outline

The full multi-week outline for the ENMs workshop, including references and planned practical sessions.

Week 1: Introduction

Part 1

  • Two widely known ENMs with numerous applications
  • What do ENMs study?
  • Each structure encodes a unique dynamics
  • What do ENMs do?
  • What does a spring actually do?
  • What is the mean-square fluctuation of a two-particle system in a harmonic potential at temperature T?

    Part 2

    Fetching information from PDB website by py-rcsb-api

  • Search API
  • Data API

Week 2-3: Theory

Part 1

  • Recap 5 minutes
  • GNM
    • Network representation (Gaussian fluctuations, Kirchhoff matrix $\Gamma$)
    • Variance-Covariance matrix,
    • Comparison with B factors
    • Pearson Correlation Coefficient
  • GNM databases 2005 - L-W Yang et al., iGNM: a database of protein functional motions based on Gaussian Network Model 2016 - H. Li et al., iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics

    Part 2

  • Recap 5 minutes
  • Check exercises, 15 minutes
  • Fetching information from UniProt website

Week 4: Practice using GNM

Part 1

  • DynOmics website (https://dyn.life.nthu.edu.tw/oENM/index.php)
  • Matlab code for GNM (https://github.com/Yuan-Yu/bioStructureM)
  • ProDy (http://www.bahargroup.org/prody/)
  • Practice
    1. Extract B factors from your PDB structure
    2. Compare these B factors with those obtained from diagonal element $\Gamma^{-1}$ matrix

      Part 2

Week 5: Theory

Part 1

  • ANM

    Part 2

Week 6: Theory

Part 1

  • Perturbation Response Scanning (PRS)
    • Effectivity and Sensitivity

    • Part 2

Reference

Professor Yang’s slides: https://drive.google.com/file/d/1xTXsxh9Lw9cnomhAGVPi41kYqTLW5u73/view?usp=drive_link 2017 - Computational Biophysics Workshop (Pitt) Day 1: https://www.youtube.com/watch?v=6ld8Ee-QCO4 Day 2: https://www.youtube.com/watch?v=0e12cEe_C9U&t=253s 2020 - Network models in biology (Protein Folding and Dynamics Webinar) https://www.youtube.com/watch?v=8DBAlYsvlbI&t=2523s 2021 - #Network Models In Biology : From Molecular Machinery To Chromosomal Dynamics https://www.youtube.com/watch?v=3z6pE_CBwxg&t=113s 2022 - ProDy: Protein Dynamics using Elastic Network Models https://www.youtube.com/watch?v=8JwRC4Dcj_M

Potential topics:

  • PDB parser
  • Structure superimposition
  • Deep Neural Network (DNN) models
  • UniProt API
  • Docker/Singularity