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Molecular Modeling

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Systems and Synthetic Biology

Abstract

Recent advances in theoretical methods based on quantum mechanics and classical mechanics with visualization tools have played a very important role in chemistry and biology. Further, computers have a profound influence on the way we do science in the last few decades. The current chapter provides a preliminary exposure to a range of molecular modeling approaches applicable to small to medium sized molecules to proteins. Recent advances in the theoretical and computational methodologies which are aimed to treat large molecules are described. Emphasis is given on methods of computer aided drug design. These are preceded by a simple introduction to quantum mechanics, classical mechanics and molecular dynamics. A major area in modelling biomolecules is a proper quantitative treatment of non-bonded interactions. The importance of understanding various non-bonded interactions is highlighted. The role of these non-bonded interactions which determines the biological structure and functions is described. Thus, the current chapter provides a brief overview of computational methods applied to biomolecules.

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Abbreviations

ANN:

Partial least square, artificial neural network

CADD:

Computer aided drug design

DFT:

Density function theory

FBDD:

Fragment based drug design

FEP:

Free energy perturbation

F-value:

Fisher statistic

FTA:

Fragment tailoring approach

GFA:

Genetic function approximation

HTS:

High-throughput screening

Ki:

Inhibitory constant

LBVS:

Ligand-based virtual screening

MCSCF:

Multi-configurational self-consistent field

MD:

Molecular dynamics

MLR:

Multi-linear regression

MM:

Molecular mechanics

PCR:

Principal component regression

PDE:

Phosphodiesterase

QM:

Quantum mechanics

QM/MM:

Quantum mechanics/molecular mechanics

QSAR:

Quantity structure activity relationship

SBVS:

Structure-based virtual screening

SCF:

Self-consistent field

TI:

Thermodynamic integration

VS:

Virtual screening

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Acknowledgement

Department of Science and Technology, New Delhi is thanked for the Swarnajayanti Fellowship to GNS, Women Scientist Fellowship to PB and INSPIRE Fellowship to CC. Department of Biotechnology and Council of Scientific and Industrial Research, New Delhi are also thanked for financial assistance.

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Authors and Affiliations

  1. Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, 500 607, Hyderabad, India

    Dr. Preethi Badrinarayan, Chinmayee Choudhury & Prof. G. Narahari Sastry

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  1. Dr. Preethi Badrinarayan
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  2. Chinmayee Choudhury
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  3. Prof. G. Narahari Sastry
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Correspondence to G. Narahari Sastry .

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Editors and Affiliations

  1. Centre for Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamshala, India

    Vikram Singh

  2. Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Budh Nagar, India

    Pawan K. Dhar

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Badrinarayan, P., Choudhury, C., Sastry, G. (2015). Molecular Modeling. In: Singh, V., Dhar, P. (eds) Systems and Synthetic Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9514-2_6

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