ljmartin

dockviz. docking visualization with py3dmol and streamlit

dockop. faster docking

pdb_to_pdbqt. download and prepare a pdb file for docking wth Vina-flavoured algorithms

mmpbsa_from_openmm. example demonstrating a free energy estimation starting from OFF and OpenMM

d4-rescore. Re-scoring a set of docked ligands with off-the-shelf algorithms to assess utility in virtual screening

align. aligning molecules

openmm_gamd. Gaussian accelerated Molecular Dynamics in OpenMM

openmm_metadynamics. toy metadynamics example

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

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

df_to_svg. exporting dataframes to svg w nice rendering

sas_mol_surface. Some examples demonstrating Solvent-accessible Surfaces (SAS) meshes of proteins + fun rendering with fresnel

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

molgen. Jupyter Notebook

timemachine. Differentiate all the things!

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

Missing_label_problem. Data and analysis scripts for Missing Label Problem paper

omm_remake_forces. remaking OpenMM forces with Custom*Forces

drug_binding_site. Jupyter Notebook

pbc-fixer. Quickly equilibrates the cell size for simulations using periodic boundary conditions in OpenMM

phytocann_smiles. SMILES codes for the phytocannabinoids from El Sohly textbook

arpeggio-PDBnSDF. Calculation of interatomic interactions in molecular structures

ljmartin.github.io. lew's blog

Science. Scripts for science

tamd_test. testing step-by-step TAMD in openmm

molrec. recsys for ligands

gst. generalized serial tempering

substrate-scope-plot. Jupyter Notebook

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 Scraped data no longer current.

espsim. Scoring of shape and ESP similarity with RDKit

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

fp_generalizability_revision. Python

mgen. Convenient matrix generation functions for python

snippets. snippets

datasets. some molecule datasets for ml

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

what_do_mol_prop_look_like. What do molecular properties look like?

openmm. OpenMM is a toolkit for molecular simulation using high performance GPU code.