vtlim

permeability

Adaptive biasing force (ABF) & umbrella sampling (US) simulations to calculate membrane permeability

patfam

Web app to determine whether patent applications from different jurisdictions (USPTO, EPO, WIPO, etc.) are of the same family.

plot_potential

Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper torsion (harmonic), van der Waals (Lennard-Jones), electrostatics (Coulomb), and the Morse potential.

advent2021

Advent of Code, https://adventofcode.com/

dihedral-scan

Compute dihedral scan in some molecule, such as to compare an MM force field to QM results.

GLIC

Scripts for fitting GLIC receptor to cryo-EM densities

textsmoosh

Web app to process and combine multi-line text into a single line

vtlim.github.io

Website of Victoria Lim

mismatch

Web app to find mismatched base pairs between hybridized DNA sequences.

alchemlyb

the simple alchemistry library

alchemtest

the simple alchemistry test set

conversion_tofix

d3-flask-blog-post

Blog post on using D3 with flask

drug-computing

Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.

druid

Apache Druid: a high performance real-time analytics database.

druid-website-src

Apache Druid website src

Hv1

Free energy perturbation calculations for Hv1 protein

misc

Miscellaneous scripts for research and data analysis using Python, OpenEye Python Toolkit, VMD/Tcl, or Grace.

off_psi4

Quanformer is a Python-based pipeline for generating conformers, preparing quantum mechanical (QM) calculations, and processing QM results for a set of molecules and their conformers. *** This repo has a new location here:

open-forcefield-data

Datasets for open forcefield parameterization and development

sdsc-summer-institute-2017

SDSC Summer Institute 2017 teaching material

shapes

From Github workshop with Caitlin (2/15/18)

stb_proteinart

stock-market

Exploratory analysis of stock market data in R.

tech-docs

TurbomoleScripts

All scripts I've written for interacting with the quantum mechanical calculation package Turbomole

uci-thesis-latex

LaTeX template for thesis and dissertation documents at UC Irvine

vtlim