Posts categorized under: Advanced

Bayesian Query Comparison


  • Generate some example Virtual Screening data.
  • Construct a bayesian model for predicting probability of activity given a certain similarity score.
  • Use this to compare to different queries.
In [3]:
import numpy as np
import pandas as pd
import scipy as sp
from matplotlib import pyplot as plt

from scipy ...

Clustering Molecules with Fingerprints and DBSCAN


  • Calculate Molecule Similarities
  • Use DBSCAN method to cluster
  • Examine data
In [13]:
import matplotlib.pyplot as plt
import mpld3
%matplotlib inline
import seaborn as sns
colors = sns.color_palette()
# sns.palplot(colors)
do_tooltips = True

import warnings
In [14]:
# import OE tools and data
import ...

Embedding Molecules in 2D-space

Embedding Molecules in a 2D Space

by Matt Geballe

Many times in computational chemistry we want to think about molecules in relationship to each other based on some definition of similarity. Example uses could be evaluating whether a set of molecules is "diverse" or not (for some definition of diversity ...