Pinned Repositories
cannabinoid1_scra
rationalising SAR trends using OpenForceField and OpenMM
dockop
faster docking
dockviz
docking visualization with py3dmol and streamlit
generalized_tempering
Generalized serial simulated tempering - free energies along any collective variable in OpenMM
interactive_filtering
Interactive filtering of predicted ligands from virtual screening, using jupyter widgets
mmpbsa_from_openmm
example demonstrating a free energy estimation starting from OFF and OpenMM
nca_jax
Neighborhood component analysis (NCA, a type of metric learning) implemented in JAX
openmm_gamd
Gaussian accelerated Molecular Dynamics in OpenMM
pdb_to_pdbqt
download and prepare a pdb file for docking wth Vina-flavoured algorithms
sas_mol_surface
Some examples demonstrating Solvent-accessible Surfaces (SAS) meshes of proteins + fun rendering with fresnel
ljmartin's Repositories
ljmartin/openmm_metadynamics
toy metadynamics example
ljmartin/fp_low_ave
testing ability of different fingerprints to generalize to out-of-sample
ljmartin/interactive_filtering
Interactive filtering of predicted ligands from virtual screening, using jupyter widgets
ljmartin/sas_mol_surface
Some examples demonstrating Solvent-accessible Surfaces (SAS) meshes of proteins + fun rendering with fresnel
ljmartin/drug_binding_site
ljmartin/Missing_label_problem
Data and analysis scripts for Missing Label Problem paper
ljmartin/molgen
ljmartin/pbc-fixer
Quickly equilibrates the cell size for simulations using periodic boundary conditions in OpenMM
ljmartin/datasets
some molecule datasets for ml
ljmartin/estimating_sem_timeseries
Comparing methods to calculate the standard error of the mean for stationary time series
ljmartin/fp_generalizability_revision
ljmartin/gst
generalized serial tempering
ljmartin/HarmonicOscillator
Toy harmonic oscillator in python, demonstrating the effect of timestep and mass on the Hamiltonian
ljmartin/ipra-table
IPRA Table + Officer Names for Accountability. Work in Progress. Scraped data no longer current.
ljmartin/mgen
Convenient matrix generation functions for python
ljmartin/openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
ljmartin/snippets
snippets
ljmartin/substrate-scope-plot
ljmartin/tamd_test
testing step-by-step TAMD in openmm
ljmartin/cannabinoid1_scra
rationalising SAR trends using OpenForceField and OpenMM
ljmartin/count_cbd_clin_trial
fetch clinical trial data about CBD using API query
ljmartin/enzyme_inhibition_estimation
estimating enzyme inbhibition parameters using PyMC3
ljmartin/filter_my_ligands
Interactive, automated filtration of ranked predictions from docking or virtual screening
ljmartin/lipid_diffusion_colvar_example
Demonstrating a collective variable that defines bilayer diffusion by minimum distance to headgroup atoms
ljmartin/minimc
Just a little MCMC
ljmartin/molembed
molembed
ljmartin/pymc3
Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano
ljmartin/requirements
Simple requirements.txt based example
ljmartin/tamd_jump
Example showing large jump in extended particle coordinates
ljmartin/technical-notes
A place for short, simplified science notes