Michael Tung - ChemE Grad at University of Washington
This repository contains Python Code for research projects and exercises including: Analyze protein simulation results from lagre data sets, Animation of time-dependent data, Explore several crucial protein properties (e.g.,free energy, ionics effects, folding rate..), Statistical Analysis, Machine Learning and Genomics Data Science....still updating.
- MDAnalysis package
- H-bond vs simulation time
- Ions numbers around protein vs time
- Ions to hydrophobic core distance vs time
- Recover time-idenpentent free energy surface
- Free energy surface contourplot
- Idenitfy basins in reaction coordinates
- Covergence test of single state
- Poisson Process
- Cumulative Distribution function (CDF)
- Empirical Cumulative Distribution Funciton (ECDF)
- p-value an KS-test
- Automation Sampling
- Animation of Time-dependent data
- matplotlib.animation
- Optimized parameter in MD force filed for calculating Adsorption Energy
- Read FASTA file
- GC percent
- Open Reading Frame (ORF)
- Repeats
- Sequence Similarity Search