Molecular modeling is a technique used to develop simplified models and simulations of molecular systems and chemical reactions. It allows scientists to investigate, interpret, and discover new phenomena that are difficult to study experimentally. Molecular modeling uses parameterized potential functions to describe molecular interactions and can be performed with specialized software. It has various applications including aiding drug design through direct and indirect methods, analyzing experimental data, and predicting molecular properties.

1. ANKITA A. SHUKLA

2. ANKITA A. SHUKLA

3. ANKITA A. SHUKLA

4. Modeling is a tool for doing
chemistry. Models are central
for understanding of chemistry.
Molecular modeling is a
discipline concerned with
developing models of
molecular system , chemical
reactions.
Models are some kind of
representation of a system,
usually simplified, that allows
for description and prediction
of properties of interest
Molecular modeling can be
performed by currently
available software.
ANKITA A. SHUKLA

5. A. Molecular modeling allows us to do and teach chemistry better by providing better
tools for Investigating , Interpreting, Explaining, and Discovering new phenomena
(for Drug)
B. Due to the advance in methodology and computer technology an alternative approach
become feasible namely molecular simulation.
C. Fluids consist of molecules and their thermo physical properties are determined by the
molecular interaction.
D. Molecular models describe these molecular interactions by means of parameterized
potential function.
ANKITA A. SHUKLA

6.  To help with analysis and interpretation of
experimental data
 To uncover new laws and formulate new theories
 To help solve problems and hint solutions before doing
experiments
 To help design new experiments
 To predict properties and quantities that is difficult or
even impossible to observe experimentally
ANKITA A. SHUKLA

7. a) Level of simplification: very simple to very
complex
b) Generality: general or specific, i.e. relate only to
specific systems or problems
c) Limitations: one must always be aware of the
range of applicability and limits of accuracy of
any model.
d) Cost and efficiency: CPU time, memory,
disk space
ANKITA A. SHUKLA

8.  The tools of the trade have
gradually evolved from physical
models and calculators, including
the use of programmable
calculators as visualization aids,
computers running analysis pack-
ages such as sylbyl and most
recently integration using
internet based tools and work
benches in HTML, Java script,
etc.
ANKITA A. SHUKLA

9. • Various classes of computers are
required formolecular modeling.
• For chemical information systems the
choice of a computer is generally larger,
and many packages run on VAX, IBM,
or PRIME machines.
• The computational chemistry
programmes allow scientists to generate
and present molecular data including
geometries, energies and properties.
ANKITA A. SHUKLA

10. Direct drug
design
Indirect drug
design
ANKITA A. SHUKLA

11. ANKITA A. SHUKLA
DIRECT DRUG
DESIGN
In the direct approach, the three
dimensional features of the known
receptor site are determined from X-ray
crystallography to design a lead molecule.
In direct design the receptor site geometry
is known; the problem is to find a
molecule that satisfies some geometry
constraints is also a good chemical match.
After finding good candidates according to
these criteria a docking step with energy
minimization can be used to predict
binding strength.

12. ANKITA A. SHUKLA
INDIRECT DRUG
DESIGN
The indirect drug design approach
involves comparative analysis of structural
features of known active and inactive
molecules that are complementary with a
hypothetical receptor site.
If the site geometry is not known, as is
often the case, the designer must base the
design on other ligand molecules that
design on the other ligand molecules that
bind well to the site.

13. The first step to derive a new lead, also called
secondary lead, will be to study the stereo electronic
properties of the selected primary leads.
The next step is to find compounds which contain it
embedded in their structure by three- dimension
database searching.
Prerequisites for effective three-dimensional searching
are large databases of three-dimensional structures and
suitable software to perform this search.
When the lead is available then the next step is lead
optimization
ANKITA A. SHUKLA

14. Molecular mechanics
Dispersion and repulsion
Geometry
Electrostatics
Quantum mechanics
ANKITA A. SHUKLA

15. Molecular mechanics describes the energy
of a molecule in terms of a simple
function which accounts for
distortion from “ideal” bond distances
and angles, as well as and for nonbonded van der
Waals and Coulombic interactions.
ANKITA A. SHUKLA

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17. 
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ANKITA A. SHUKLA

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20. ANKITA A. SHUKLA
Molecular
simulation method
Molecular
dynamics
Periodic
boundary
condition

21. ANKITA A. SHUKLA
Molecular dynamics
Molecular dynamics is an
approach to mimic the
movement of molecule in an
ensemble.
Periodic boundary condition
By applying PBC the
amount of interaction
partners of a molecule in
a simulation theoretically
rises to infinity

22. ANKITA A. SHUKLA
Applications
1
• Generation of Chemical Structures
2
• Molecular Structure Visualization
3
• Modeling of Drug Receptor Interactions

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