ljmartin/sas_mol_surface ljmartin/sas_mol_surface

  • Stars
    star
    3
  • Rank 3,963,521 (Top 79 %)
  • Language
    Jupyter Notebook
  • Created over 4 years ago
  • Updated about 4 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
ljmartin/sas_mol_surface
github

ljmartin

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

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

More Repositories

1

dockviz

docking visualization with py3dmol and streamlit
HTML
23
star
2

dockop

faster docking
HTML
18
star
3

mmpbsa_from_openmm

example demonstrating a free energy estimation starting from OFF and OpenMM
Jupyter Notebook
10
star
4

pdb_to_pdbqt

download and prepare a pdb file for docking wth Vina-flavoured algorithms
Jupyter Notebook
10
star
5

align

aligning molecules
Jupyter Notebook
9
star
6

openmm_gamd

Gaussian accelerated Molecular Dynamics in OpenMM
Jupyter Notebook
9
star
7

d4-rescore

Re-scoring a set of docked ligands with off-the-shelf algorithms to assess utility in virtual screening
Jupyter Notebook
7
star
8

openmm_metadynamics

toy metadynamics example
Jupyter Notebook
6
star
9

interactive_filtering

Interactive filtering of predicted ligands from virtual screening, using jupyter widgets
Jupyter Notebook
5
star
10

fp_low_ave

testing ability of different fingerprints to generalize to out-of-sample
Python
5
star
11

df_to_svg

exporting dataframes to svg w nice rendering
Jupyter Notebook
3
star
12

drug_binding_site

Jupyter Notebook
2
star
13

Missing_label_problem

Data and analysis scripts for Missing Label Problem paper
Jupyter Notebook
2
star
14

molgen

Jupyter Notebook
2
star
15

generalized_tempering

Generalized serial simulated tempering - free energies along any collective variable in OpenMM
Jupyter Notebook
2
star
16

omm_remake_forces

remaking OpenMM forces with Custom*Forces
Python
2
star
17

pbc-fixer

Quickly equilibrates the cell size for simulations using periodic boundary conditions in OpenMM
2
star
18

molrec

recsys for ligands
Jupyter Notebook
1
star
19

gst

generalized serial tempering
Jupyter Notebook
1
star
20

download_chembl

download active ligands associated with a protein target from ChEMBL using web services API
1
star
21

fp_generalizability_revision

Python
1
star
22

HarmonicOscillator

Toy harmonic oscillator in python, demonstrating the effect of timestep and mass on the Hamiltonian
Python
1
star
23

tamd_test

testing step-by-step TAMD in openmm
Jupyter Notebook
1
star
24

what_do_mol_prop_look_like

What do molecular properties look like?
HTML
1
star
25

phytocann_smiles

SMILES codes for the phytocannabinoids from El Sohly textbook
Python
1
star
26

datasets

some molecule datasets for ml
Jupyter Notebook
1
star
27

Science

Scripts for science
1
star
28

snippets

snippets
Jupyter Notebook
1
star
29

estimating_sem_timeseries

Comparing methods to calculate the standard error of the mean for stationary time series
Jupyter Notebook
1
star
30

ljmartin.github.io

lew's blog
Jupyter Notebook
1
star