ljmartin Goto Github PK

align

aligning molecules

altair_mols

displaying molecule pictures in altair

arpeggio-pdbnsdf

Calculation of interatomic interactions in molecular structures

cannabinoid1_scra

rationalising SAR trends using OpenForceField and OpenMM

count_cbd_clin_trial

fetch clinical trial data about CBD using API query

cut_tree_balanced

Python function that performs a balanced cut tree of a SciPy linkage matrix

cv

my cv in markdown / pandoc

d4-rescore

Re-scoring a set of docked ligands with off-the-shelf algorithms to assess utility in virtual screening

datasets

some molecule datasets for ml

df_to_svg

exporting dataframes to svg w nice rendering

dockop

faster docking

dockviz

docking visualization with py3dmol and streamlit

download_chembl

download active ligands associated with a protein target from ChEMBL using web services API

drug_binding_site

enzyme_inhibition_estimation

estimating enzyme inbhibition parameters using PyMC3

enzyme_inhibition_pymc3

espsim

Scoring of shape and ESP similarity with RDKit

estimating_sem_timeseries

Comparing methods to calculate the standard error of the mean for stationary time series

faspr-backup

THIS IS A FORK. an ultra-fast and accurate program for deterministic protein sidechain packing

filter_my_ligands

Interactive, automated filtration of ranked predictions from docking or virtual screening

fp_generalizability_revision

fp_low_ave

testing ability of different fingerprints to generalize to out-of-sample

generalized_tempering

Generalized serial simulated tempering - free energies along any collective variable in OpenMM

gst

generalized serial tempering

harmonicoscillator

Toy harmonic oscillator in python, demonstrating the effect of timestep and mass on the Hamiltonian

interactive_filtering

Interactive filtering of predicted ligands from virtual screening, using jupyter widgets

ipra-table

IPRA Table + Officer Names for Accountability. Work in Progress. Scraped data no longer current.

jac_c

jaccard distances in c

libigl

Simple C++ geometry processing library.

lipid_diffusion_colvar_example

Demonstrating a collective variable that defines bilayer diffusion by minimum distance to headgroup atoms