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updates oct-23

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2 views

updates oct-23

Uploaded by

premsing212
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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Drug discover weekly Updates..

Weekly update : October – 23, 2021

Updates by : Prem Singh Bist


Understanding chemical information
System
 How to represent compound in philosophy of bits?
 Structural concerns areas : has to searchable
 Address concerns of searching such as :
 Structures those exactly match target structure
 Those contains a target structure
 Those are contained in a target structure
 Those are Tautomeric with target St. (Isomers with different arrangements)
 Those having common features with target structure
 Those which match patterns of atoms and bonds

 https://www.daylight.com/meetings/emug02/Bradshaw/Training/
Updates by : Prem Singh Bist
MDL molfile format

 Graphics entry systems stored the information in the form of a


connection table
 Limitation: It is not possible to represent a molecule in a MDL molfile
where only some of the stereocentres are known.

Updates by : Prem Singh Bist


SMILE

 Linear representation of structure valid for Paper system and computer


System
 Represents the structure in terms of atoms and bonds
 No white space
 Uses the only symbols in the periodic table to represent atoms
 symbols - = # : represents single bond, double bond , triple bond and
aromatics
 full stop or period '.’ represents no bond
 (=) represents branching via double bonds
 c1ccccc1Nc2cc(S(=O)(=O)O)cc3c2cc(N(C)C)cc3

Updates by : Prem Singh Bist


SMILE..

 Atoms represented by : atomic symbols


 Metals by : []
 Brackets can be omitted for B, C, N, O, P, S and Halides
 Cyclic structure are represent by : Same start and end letter same
 Aromatic compound : Represent by upper Letter
 Aliphatic Compound : lower case
 https://www.youtube.com/watch?
v=V4mDkcErJFU&ab_channel=QuickLearn360

Updates by : Prem Singh Bist


Fingerprints

 A chemical fingerprint is a list of binary values (0 or 1) which


characterize a molecule.
 How to create it ?
 One way is : MACCS keys
 Answers questions about chemical structure (True or false)
 Eg: is there s-s bond (yes), ring of size 4 (No)?
 The answers are frequently written as a list of bits (also called a bitstring).
 The bit string for the above structure is : 10

 Can be used for Similarity comparison and database filtering

Updates by : Prem Singh Bist


How comparison is done?

 Comparing two molecules directly is a hard problem.


 MACCS
RDKIT Introduction

 Generate molecule structure from Smile String


 Get Smile String from Structure
Code..

import sys

from rdkit import Chem >>Draw >> IPythonConsole


from rdkit.Chem Descriptors
from rdkit.Chem import AllChem
from rdkit import DataStructs
import numpy as np
from rdkit Import Chem mol = Chem.MolFromSmiles('CCCC')
 Draw >> IPythonConsole smiles = Chem.MolToSmiles(mol)
 Descriptors
 AllChem #Get Molecular weight
mv = Descriptors.MolWt(mol)

#Draw
img = Draw.MolsToGridImage(mol_list, molsPerRow=1)
from rdkit import DataStructs

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