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A computational server for potential inhibitor and scaffold prediction of nuclear receptors

Project description

PisNRs

PisNRs is a Python module for potential inhibitor and scaffold prediction of nuclear receptors built on top of RDKit, scikit-learn and distributed under the MIT license.

Installation

Dependencies

pisnrs requires:

  • Python (>= 2.6)
  • rdkit (>= 2018.03.2.0)
  • scikit-learn (>= 0.19.1)
  • pandas (>= 0.23.1)

You can configure the environment of the pisnrs through Ancaconda.

1. Introduction to anaconda

Conda is an open-source, cross-platform, software package manager. It supports the packaging and distribution of software components, and manages their installation inside isolated execution environments. It has several analogies with pip and virtualenv, but it is designed to be more "python-agnostic" and more suitable for the distribution of binary packages and their dependencies.

2. How to get conda

The easiest way to get Conda is having it installed as part of the Anaconda Python distribution. A possible (but a bit more complex to use) alternative is provided with the smaller and more self-contained Miniconda. The conda source code repository is available on github and additional documentation is provided by the project website.

3. How to install RDKit with Conda

Creating a new conda environment with the RDKit installed requires one single command similar to the following:

  $ conda create -c rdkit rdkit

4. Install scikit-learn

Install scikit-learn using pip :

    pip install -U scikit-learn

or conda :

    conda install scikit-learn

5. Install pisnrs

If you already have a working installation of rdkit and scikit-learn, the easiest way to install pisnrs is using pip :

    pip install --upgrade pisnrs

Example

1. import pisnrs and load model

    import pisnrs
    model = pisnrs.pisnrs()
    print(model.getNRs()) #print NR proteins in model
    print(model.getLigandDescriptors()) # print Ligand descriptors in model

2. predict the activity and scaffold of one ligand

    ### moltype includes : smiles, mol, block, sdf
    ### You can find the example .mol and .sdf file in the 'example/' folder
    ### Example: https://github.com/ddhmed/pisnrs/tree/master/example
    # 1. smiles input
    smiles = 'CC1OC(C2=CC=CC=C2)=NC=1CN(CC1=CC(=C(C(=C1)C)OC(C(O)=O)(C)C)C)CC1OC=CC=1'
    protein = 'NR1C1'
    des = model.calPCMDecriptorFromMolText(smiles, protein, moltype='smiles') # create descriptors
    print(model.preProba(des)) # predict

    # 2. .mol file input
    molfile = 'example/example.mol'
    protein = 'NR1C1'
    des = model.calPCMDecriptorFromMolText(molfile, protein, moltype='mol')
    print(model.preProba(des))

    # 3. mol block input
    block = '''
     RDKit          2D

 36 39  0  0  0  0  0  0  0  0999 V2000
    4.9515   -5.4554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4879   -6.8820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3696   -8.0956    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4879   -9.3091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9515  -10.7357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4187  -11.0475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8822  -12.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8785  -13.5888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4113  -13.2770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9478  -11.8504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0613   -8.8456    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0613   -7.3456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8478   -6.4639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4775   -7.0740    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3207   -8.5658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0496   -9.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2631   -8.2942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6335   -8.9043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7902  -10.3961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5767  -11.2778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2064  -10.6676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7335  -12.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1606  -11.0062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3174  -12.4980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4741  -13.9897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8445  -14.5999    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2606  -14.8714    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8091  -12.3412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8256  -12.6548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8470   -8.0226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7360   -6.1923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5792   -4.7005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6939   -3.6968    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0838   -2.3265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4079   -2.4833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7198   -3.9505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
  4 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 19 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 25 27  2  0
 24 28  1  0
 24 29  1  0
 18 30  1  0
 14 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
 34 35  2  0
 35 36  1  0
 12  2  2  0
 21 16  1  0
 36 32  2  0
 10  5  1  0
M  END
    '''
    des = model.calPCMDecriptorFromMolText(block, protein, moltype='block')
    print(model.preProba(des))

    # 4. .sdf file input
    sdffile = 'example/example.sdf'
    protein = 'NR1C1'
    des = model.calPCMDecriptorFromMolText(sdffile, protein, moltype='sdf')
    print(model.preProba(des))

3. Batch mode

    smiles_list = ['CCCC', 'CCC']
    protein_list = ['NR1C1', 'NR1C2']
    print(model.preBatch(smiles_list, protein_list=protein_list)) # predict activity of every ligands and proteins in list 
    print(model.preBatch(smiles_list)) # predict activity of every ligands in list and all proteins in model

4. Create molecule images

    smiles = 'CC1OC(C2=CC=CC=C2)=NC=1CN(CC1=CC(=C(C(=C1)C)OC(C(O)=O)(C)C)C)CC1OC=CC=1'
    model.image_from_smile(smiles, name='example.png', dir='example/') # output image of smiles to 'examole/' folder

Important links

Source code

You can check the latest sources with the command:

git clone https://github.com/ddhmed/pisnrs.git

Project details


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