Pinned Repositories
align
aligning molecules
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
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/dockviz
docking visualization with py3dmol and streamlit
ljmartin/dockop
faster docking
ljmartin/align
aligning molecules
ljmartin/pdb_to_pdbqt
download and prepare a pdb file for docking wth Vina-flavoured algorithms
ljmartin/mmpbsa_from_openmm
example demonstrating a free energy estimation starting from OFF and OpenMM
ljmartin/openmm_gamd
Gaussian accelerated Molecular Dynamics in OpenMM
ljmartin/d4-rescore
Re-scoring a set of docked ligands with off-the-shelf algorithms to assess utility in virtual screening
ljmartin/df_to_svg
exporting dataframes to svg w nice rendering
ljmartin/generalized_tempering
Generalized serial simulated tempering - free energies along any collective variable in OpenMM
ljmartin/ljmartin.github.io
lew's blog
ljmartin/omm_remake_forces
remaking OpenMM forces with Custom*Forces
ljmartin/timemachine
Differentiate all the things!
ljmartin/arpeggio-PDBnSDF
Calculation of interatomic interactions in molecular structures
ljmartin/download_chembl
download active ligands associated with a protein target from ChEMBL using web services API
ljmartin/espsim
Scoring of shape and ESP similarity with RDKit
ljmartin/molrec
recsys for ligands
ljmartin/phytocann_smiles
SMILES codes for the phytocannabinoids from El Sohly textbook
ljmartin/what_do_mol_prop_look_like
What do molecular properties look like?
ljmartin/nca_jax
Neighborhood component analysis (NCA, a type of metric learning) implemented in JAX
ljmartin/altair_mols
displaying molecule pictures in altair
ljmartin/cut_tree_balanced
Python function that performs a balanced cut tree of a SciPy linkage matrix
ljmartin/cv
my cv in markdown / pandoc
ljmartin/enzyme_inhibition_pymc3
ljmartin/FASPR-backup
THIS IS A FORK. an ultra-fast and accurate program for deterministic protein sidechain packing
ljmartin/jac_c
jaccard distances in c
ljmartin/libigl
Simple C++ geometry processing library.
ljmartin/meshing_stuff
meshing things
ljmartin/mol_jaccard_for_sih
ljmartin/pdbe-molstar
Molstar PDBe implementation
ljmartin/rdkit
The official sources for the RDKit library