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Molecular Modeling

APRIL/2015

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Topics
• Introduction
• Drug discovery pipeline
• Molecular Modeling Toolbox
• Molecular Mechanics Methods
• Quantum Mechanics Methods

• Model and Scale


• Molecular Graphics
• Molecular Modeling Software

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Introduction1
Definition. Molecular modelling allow scientists to use computers to
visualize molecules means representing molecular structures numerically
and simulating their behavior with the equations of quantum and classical
physics , to discover new lead compounds for drugs or to refine existing
drugs in silico.

Goal. To develop a sufficient accurate model of the system so that physical


experiment may not be necessary .

Theoretical Physics, Quantum Mechanics 60’s, Quantum Computing 80’s,


Nanothechnology, Richard Feyman

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Introduction1
The term “ Molecular modeling “expanded over the last decades from a
tool to visualize three-dimensional structures and to simulate , predict
and analyze the properties and the behavior of the molecules on an
atomic level to data mining and platform to organize many compounds
and their properties into database and to perform virtual drug screening
via 3D database screening for novel drug compounds

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Drug discovery pipeline

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Computational toolbox

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Model and Scale

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Molecular graphics1

Sticks Ball and Stick

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Molecular graphics2

Space Filling (CPK) Wire Frame

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Molecular graphics2
Protein structures
Primary Structure Secondary Structure

Terciary Structure Quaternary Structure

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Molecular Modeling Software

Molecular Mechanics Quantum Mechanics


• Amber • Gaussian
• Charmm • Spartan
• Gromacs • Siesta
• Discovery Studio • Abinit
• Gromos
• Lammps
• NAMD – VMD, etc

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The end:

Time to rest, you are free for today

Molecular Modeling and Simulation


An Interdisciplinary Guide 2nd edition, Prof. Tamar Schlick

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