ljmartin/interactive_filtering

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ljmartin/interactive_filtering

ljmartin

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

dockviz

docking visualization with py3dmol and streamlit

dockop

mmpbsa_from_openmm

example demonstrating a free energy estimation starting from OFF and OpenMM

Jupyter Notebook

pdb_to_pdbqt

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

Jupyter Notebook

align

aligning molecules

Jupyter Notebook

openmm_gamd

Gaussian accelerated Molecular Dynamics in OpenMM

Jupyter Notebook

d4-rescore

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

Jupyter Notebook

openmm_metadynamics

toy metadynamics example

Jupyter Notebook

fp_low_ave

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

sas_mol_surface

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

Jupyter Notebook

df_to_svg

exporting dataframes to svg w nice rendering

Jupyter Notebook

drug_binding_site

Jupyter Notebook

Missing_label_problem

Data and analysis scripts for Missing Label Problem paper

Jupyter Notebook

molgen

Jupyter Notebook

generalized_tempering

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

Jupyter Notebook

omm_remake_forces

remaking OpenMM forces with Custom*Forces

pbc-fixer

Quickly equilibrates the cell size for simulations using periodic boundary conditions in OpenMM

molrec

recsys for ligands

Jupyter Notebook

gst

generalized serial tempering

Jupyter Notebook

download_chembl

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

fp_generalizability_revision

HarmonicOscillator

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

tamd_test

testing step-by-step TAMD in openmm

Jupyter Notebook

what_do_mol_prop_look_like

What do molecular properties look like?

phytocann_smiles

SMILES codes for the phytocannabinoids from El Sohly textbook

datasets

some molecule datasets for ml

Jupyter Notebook

Science

Scripts for science

snippets

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estimating_sem_timeseries

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

Jupyter Notebook

ljmartin.github.io

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