allosteric_pathway_observables

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.

average_structure_calcs

Scripts to average the structure of a substrate from a MD trajectory

bioinformatics_analyses

This repo will hold a set of scripts that I have written to analyze a set of amino acid sequences.

blender_files

Repo where I'm gonna store my important blender files. Startup files, defaults, etc.

cart_pca_projection

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.

clustering_scripts

K-means clustering, silhouette analysis

collective_variable_analyses

Home Repo for an assortment of Collective Variable Analysis methods as well as post-processing analyses (such as PCA)

covar_pca_analyses

Python, MDAnalysis script to perform a covariance analysis of the Cartesian coordinates and principal component analysis on said covar matrix

crystal_water_analysis

Multistep analysis of crystal structures to identify what positions that are well maintained within the body of structures.

csuthesis

Colorado State University LaTeX Thesis/Dissertation Template

dask_workflows

Home for various dask workflows that I am developing

dcd_writer

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.

denv-ns3h

Repository for all scripts used in the DENV-NS3h paper.

dihedral_analysis

Python, MDAnalysis script to calculate certain dihedrals of protein residues.

distance_matrix

Python, MDAnalysis script to create a distance matrix for single frame or for full trajectory

dna_stacking_analysis

Python scripts to perform analysis of stacking of residues

docking_refinement

A repository that will act as a home for testing scripts for post-analysis and modeling of docking results.

download_pdbs

Automation Script to Download PDB files from the RSCB Protein Data Bank.

ensemble_docking

Repo to hold most if not all codes associated with my WIP ensemble docking protocol

exafold

Fast GPU-based protein folding simulations that run from only a protein sequence and set of restraints designed to fold the protein.

fetch_and_write

Fetch a PDB ID's structure and write it out as a PDB file.

fixman_summer_theory_wrkshp_day1

Day1 Files - Introduction to Bash, Python, and VMD

hbond_analysis

hbonding for residue pairs

henm

homology_modeling_scripts

Python, MDAnalysis scripts to perform important steps in prepping/post-processing homology models.

md_program

Molecular Dynamics Program to simulate Liquid Argon; Developed by RBD

minimize_equilibrate_protocol

Minimization and equilibration (heating) protocol; contains config files for each step in the process

molecdynamics

molecularnodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

pan_of_hgf

Repository of simulation and analysis scripts used for modeling the PAN domain of the HGF protein.