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Molecular Modelling and Structure Elucidation

The document outlines the B.Sc Pass course in Chemiinformatics, focusing on molecular modeling and QSAR modeling in drug discovery. It covers key topics such as molecular encoding, feature selection, model training, and the application of machine learning techniques in QSAR modeling. Additionally, it includes multiple-choice questions and true/false statements related to bioinformatics and protein structure analysis.

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16 views13 pages

Molecular Modelling and Structure Elucidation

The document outlines the B.Sc Pass course in Chemiinformatics, focusing on molecular modeling and QSAR modeling in drug discovery. It covers key topics such as molecular encoding, feature selection, model training, and the application of machine learning techniques in QSAR modeling. Additionally, it includes multiple-choice questions and true/false statements related to bioinformatics and protein structure analysis.

Uploaded by

Annu yadav
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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B.

Sc Pass course (PCM)

Paper Title:-
Chemiinformatics

Unit –I : Introduction to Chemiinformatics


Topic: Molecular Modelling and Structure
Elucidation

Name of Faculty: Dr. Azharulla Khan


Designation: Associate Professor
School of Life & Basic Sciences
MolecularModelling-QSAR Modeling

The standardized procedure for building QSAR


models in drug discovery encompasses a series of
modular steps that incorporate the afore-discussed
chemoinformatics and machine learning techniques.
By following the protocol, QSAR modeling aided by
ML and DL (deep learning) can predict the properties
or activities of chemical compounds, toxicity, and
other related physiochemical properties
Molecular Encoding
Molecular encoding is like chemical data
representation transformation, as discussed before.
Compounds’ chemical characteristics and attributes
are directly deduced from their chemical structures
or by looking up experimental findings. This
process involves extracting relevant information
from the molecular structure, such as atom types,
bond types, functional groups, and
physicochemical properties.
Feature Selection
Feature selection in QSAR aims to identify the most
informative and relevant features from a larger set. It
involves techniques such as univariate analysis, filter
methods, wrapper methods, and embedded methods.
To determine the most pertinent attributes and lessen
the dimensionality and collinearity of the feature
vector, hybrid feature selection, feature learning
methodologies, and unsupervised learning techniques
are applied. These techniques have successfully
preserved a fair computing effort without reducing the
precision of the final QSAR models
Model Training
During the model training and learning phase of
QSAR modeling, a supervised machine learning
model is generally employed to uncover an empirical
function that effectively maps input feature vectors to
biological responses. This function is optimized to
achieve the best possible mapping. It is crucial to
carefully select and consider the SAR datasets and
descriptors used for training and model validation to
ensure the development of accurate QSAR models.
Machine-Learning-Based QSAR
Modeling : Unsupervised learning and
supervised learning are two categories of machine
learning models. In supervised learning, a model is
trained with labeled data to produce predictions based
on known input–output correlations (for example,
support vector machines and linear regression).
Unsupervised learning analyzes unlabeled data to
discover underlying patterns and relationships
without explicit guidance (e.g., clustering and
dimensionality reduction).
Structure elucidation
In order to develop statistical machine learning
methods in chemoinformatics, whether supervised or
unsupervised, including predictive classification,
regression and clustering of molecules and their
properties, the need for large and well-annotated
datasets has been already pointed out; furthermore, it
is crucial to organize these datasets in rapidly
searchable databases and to develop computational
methods to rapidly extract or predict useful
information for each molecule.
Structure elucidation-Scheme
Q.1 MCQ
i. All are sequence alignment tools except:
a. Rasmol
b. BLAST
c. FASTA
d. Clustal W
Answer: a. Rasmol
ii. The science of collecting and analyzing complex
biological data such as genetic codes is known
as…?
a) Bioinformatics
b)Histology
c) Microbiology
d) Entomology
Ans : a) Bioinformatics
iii. Which is a multiple sequence alignment tool?
a) Clustal W
b) Chime
c) Dismol
d) PDB
Answer: a) Clustal W

iv. When was the SWISSPROT protein sequence


database initiated?
(a) 1988
(b) 1985
(c) 1986
(d) 1987
Solution: (d) 1987.
i. ……………..Smith-Waterman describe
. the algorithm for local alignment.
a)1950
b) 1970
c) 1981
d) 1925
Ans: c) 1981

ii. …… task is performed in Bioinformatics.


a)Analysis of gene variation
b)Mapping and analyzing DNA
c)Analysis of protein structure
d)All of these
Answer: d) All of these
.

iii.The chemical used for strand cleavage in the


Maxam-Gilbert method is:
a) Piperidine
b) Hydrazine
c) Formic acid
d) DMSO
Answer: a) Piperidine
Q.3 Wheater the statemnt is true or false
i. Study of the structure and function of proteins is
know as Proteomics.
Ans : True
ii. The process of finding the relative location of genes on
a chromosome is known as gene tracking.
Ans : false
ii. Pauline Hogeweg is a scientist coined the term
bioinformatics.
Ans: True
.

References
i. Engel T., Gasteiger J. Chemoinformatics:
Basic Concepts and Methods, 2018, Wiely
VCH

ii) Mitra P. Algorithms for protein modelling and


engineering. IIT Kharagpur
.https://onlinecourses.nptel.ac.in/noc
21_cs100/preview

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