Computational Biophysics Project

Project report for the course Computational Biophysics 2022-2023, University of Trento
By Diego Barquero Morera and Anna Pini

Description

The focus of this project is to analyse the dynamics of a protease of interest. The software used to simulate the trajectory is GROMACS, which integrates the equations of motion by means of the Velocity Verlet algorithm. Once the trajectories were obtained they were analysed, focusing on general aspects of the trajectories, as well as frames of interest, the active sites and the distribution of water around the protein. The analysis is mostly performed via Python 3 scripts. The library MDAnalysis facilitates dealing with GRO and XTC files, as well as performing different analysis methodologies. Refer to the repository for source code and initial input files necessary to reproduce all the steps detailed by the report.

About the figures

Some figures in this report are interactive, meaning that they have buttons on top that allow to change between the plots/snapshots of different systems to better compare them.

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Index

• Introduction
• Physical System
• Molecular Dynamics
• Project Structure
• Part 1: Molecular Dynamics
• Input Preparation
• Molecular Dynamics Simulation
• Post Processing
• Part 2: General Analysis
• Calculations
• Ramachandran Map (RAMA)
• Root Mean Square Deviation (RMSD)
• Root Mean Square Fluctuations (RMSF)
• Radius of Gyration (RGYR)
• Contact Map (CMAP)
• Block Analysis (BSE)
• Part 3: Detailed Analysis
• Unsupervised Clustering
• Dynamic Contact Map Differences (DCMD)
• Active Site
• Pyinteraph
• Part 4: Solvent Analysis
• Water Model
• Water Average Local Densities (WALD)
• Solvent Accessible Surface Area (SASA)