Building and analyzing residue interaction networks with cofactors (includes tutorial).

Order parameter calculations from Desmond Maestro .csv out files

Efficiently compute off-resonance Raman spectra from first principles calculations (e.g. VASP) using polynomial models and ML/AI.

A Jekyll website for the research guides--UNIX, AMBER, Analysis, and R.

Machine Learning Transition State Analysis (MLTSA) suite with Analytical models to create data on demand and test the approach on different types of data and ML models.

Molecular Dynamics Trajectory Analysis Tools

A package to find collective variables of dynamical systems by training neural networks

A library for the Analysis of Molecular Dynamics Simulations of Self Assembling Peptides. Started during an internship at CNTE, Niguarda Hospital, Milan

A package for multiple-scale simulations on the dynamical and kinetic processes in materials

A Python module for performing data analysis of atomistic trajectories relevant for glasses and supercooled liquids.

"Atomic democracy" for site analysis of surfaces and bulks with known lattice structure(s).

Repository for my senior design project/thesis code

This repository contains Jupyter notebooks used to perform computational analysis of LAT1 (SLC7A5) cholesterol binding sites, as published in JCTC

A python molecular dynamics data analysis tool.

A user-friendly Python package to manipulate input and output files of LAMMPS molecular dynamics code. One Python class per LAMMPS file type. Include conversion into pandas DataFrame.

Reactive molecular dynamics trajectory analysis