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dockviz
docking visualization with py3dmol and streamlitdockop
faster dockingmmpbsa_from_openmm
example demonstrating a free energy estimation starting from OFF and OpenMMpdb_to_pdbqt
download and prepare a pdb file for docking wth Vina-flavoured algorithmsalign
aligning moleculesopenmm_gamd
Gaussian accelerated Molecular Dynamics in OpenMMd4-rescore
Re-scoring a set of docked ligands with off-the-shelf algorithms to assess utility in virtual screeningopenmm_metadynamics
toy metadynamics exampleinteractive_filtering
Interactive filtering of predicted ligands from virtual screening, using jupyter widgetsfp_low_ave
testing ability of different fingerprints to generalize to out-of-samplesas_mol_surface
Some examples demonstrating Solvent-accessible Surfaces (SAS) meshes of proteins + fun rendering with fresneldf_to_svg
exporting dataframes to svg w nice renderingdrug_binding_site
Missing_label_problem
Data and analysis scripts for Missing Label Problem papermolgen
generalized_tempering
Generalized serial simulated tempering - free energies along any collective variable in OpenMMomm_remake_forces
remaking OpenMM forces with Custom*Forcespbc-fixer
Quickly equilibrates the cell size for simulations using periodic boundary conditions in OpenMMmolrec
recsys for ligandsgst
generalized serial temperingdownload_chembl
download active ligands associated with a protein target from ChEMBL using web services APIfp_generalizability_revision
HarmonicOscillator
Toy harmonic oscillator in python, demonstrating the effect of timestep and mass on the Hamiltoniantamd_test
testing step-by-step TAMD in openmmwhat_do_mol_prop_look_like
What do molecular properties look like?phytocann_smiles
SMILES codes for the phytocannabinoids from El Sohly textbookdatasets
some molecule datasets for mlScience
Scripts for sciencesnippets
snippetsljmartin.github.io
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