Russell B. Davidson's Projects
Semi-temporary repo for a collection of metrics used in the literature to describe allostery. Once the "observable" is calculated, a pathway finding algorithm (think Dijkstra algorithm) is used to qualify the pathways of action.
Scripts to average the structure of a substrate from a MD trajectory
This repo will hold a set of scripts that I have written to analyze a set of amino acid sequences.
Repo where I'm gonna store my important blender files. Startup files, defaults, etc.
Python 3 codes to analyze (align and average) a set of MD trajectories, calculate the cartesian coordinates for an atom selection, and perform PCA on these cartesian coordinates to analyze the essential dynamics of selection.
K-means clustering, silhouette analysis
Home Repo for an assortment of Collective Variable Analysis methods as well as post-processing analyses (such as PCA)
Python, MDAnalysis script to perform a covariance analysis of the Cartesian coordinates and principal component analysis on said covar matrix
Multistep analysis of crystal structures to identify what positions that are well maintained within the body of structures.
Colorado State University LaTeX Thesis/Dissertation Template
Home for various dask workflows that I am developing
Python code, using MDAnalysis, to take in a .dcd file and write a new .dcd file. Useful for turncating large .dcd files down to smaller file sizes by removing solvent/unwanted atoms.
Repository for all scripts used in the DENV-NS3h paper.
Python, MDAnalysis script to calculate certain dihedrals of protein residues.
Python, MDAnalysis script to create a distance matrix for single frame or for full trajectory
Python scripts to perform analysis of stacking of residues
A repository that will act as a home for testing scripts for post-analysis and modeling of docking results.
Automation Script to Download PDB files from the RSCB Protein Data Bank.
Repo to hold most if not all codes associated with my WIP ensemble docking protocol
Fast GPU-based protein folding simulations that run from only a protein sequence and set of restraints designed to fold the protein.
Fetch a PDB ID's structure and write it out as a PDB file.
Day1 Files - Introduction to Bash, Python, and VMD
hbonding for residue pairs
Python, MDAnalysis scripts to perform important steps in prepping/post-processing homology models.
Molecular Dynamics Program to simulate Liquid Argon; Developed by RBD
Minimization and equilibration (heating) protocol; contains config files for each step in the process
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
Repository of simulation and analysis scripts used for modeling the PAN domain of the HGF protein.