Getting Started

You can easily install PyCoM using pip, from our GitHub respository.

pip3 install git+https://github.com/scdantu/pycom

Now, you are ready to use PyCoM:

from pycom import PyCom, CoMAnalysis
import matplotlib.pyplot as plt

pyc = PyCom(remote=True)
prots = pyc.find(        # search for proteins with:
    min_length=200,      # 200-210 residues
    max_length=210,
    disease='cancer',    # that are associated with cancer
    has_substrate=True,  # have a known substrate
    page=1,
    matrix=True          # and load their coevolution matrices
)

CoMAnalysis().add_contact_predictions(prots)  # add contact predictions

plt.axis('off'); plt.title(f'Contact Map for uniprot_id={prots.uniprot_id[0]}')
plt.imshow(prots.contact_matrix[0])  # plot the contact map

print(prots.iloc[0])  # print the protein's details
Output:
Output of the code above 
uniprot_id                    P62070
neff                          12.754
sequence_length                  204
sequence           MAAAGWRDGSGQEK...
organism_id                     9606
helix_frac                   0.29902
turn_frac                   0.019608
strand_frac                 0.220588
has_ptm                            1
has_pdb                            1
has_substrate                      1
matrix             [[0.0, 0.268, ...
contact_matrix     [[0.0, 0.0,   ...
Name: 0, dtype: object

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Optionally download the database locally, to speed up the loading: https://pycom.brunel.ac.uk/downloads/

Quick guides

Here are some quick guides on starting up using PyCoM:

You can use PyCoM in three different ways:

There is also a Alignment File Repository, where 370,000+ alignment files are available for download. See: https://pycom.brunel.ac.uk/alignments/

More indepth tutorials are available in the Tutorials section.

Differences

You can work with PyCoMdb in three different modes:

  1. PyCoM (local): Download the database to your computer and use PyCoM.

  2. PyCoM (remote): Work with the database on PyCoM server using PyCoM.

  3. WebAPI: Work with the WebAPI without using PyCoM.

Using PyCoM (local) allows access to all the functional features, while PyCoM (remote) and the WebAPI has some limitations as shown in the table below:

Functionality

PyCoM Library

===================+=======================================

Database is Local | Remote database on pycom.brunel.ac.uk

Web API

Query the database

Y

Y

Y

Load matrices

Y

Y

Y

Display basic properties of each entry1

Y

Y

Y

Provides access to

Y

N

N

1.     Diseases

2.     CATH

3.     EC ID

4.     PDB id list

5.     Organism taxonomy

6.     Substrates list

7.     List of Cofactors

8.     PTM’s

9.     List of Ligands

10.  Molecular functions

11.  biological processes

12.  cellular components

13.  protein domain

14.  coding sequence diversity

15.  developmental stage