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Molecular Modeling in Peptide and Protein Analysis

Peptides and Proteins

  1. Krzysztof Kuczera

Published Online: 15 DEC 2011

DOI: 10.1002/9780470027318.a1623.pub2

Encyclopedia of Analytical Chemistry

Encyclopedia of Analytical Chemistry

How to Cite

Kuczera, K. 2011. Molecular Modeling in Peptide and Protein Analysis. Encyclopedia of Analytical Chemistry. .

Author Information

  1. University of Kansas, Lawrence, KS, USA

Publication History

  1. Published Online: 15 DEC 2011


This article describes the theoretical background and practical applications of classical molecular mechanics (MM) and molecular dynamics (MD). Following a brief historical outline of molecular modeling, the concept of the molecular potential energy function is introduced and the basic algorithms of MM, namely, energy minimization, normal mode analysis, MD, and Monte Carlo (MC) simulations, are defined. The advantages of molecular modeling methods — speed of calculations and detailed microscopic insight — are described. The shortcomings — approximate nature and difficulties with conformational sampling — are also analyzed. A number of modern approaches aimed at improving the reliability of computer simulations are briefly presented, including advanced energy optimization methods, treatment of long-range forces, and accelerated conformational exploration. Examples of applications of molecular modeling methods to the study of various aspects of the structure, dynamics, and function of peptides and proteins are presented. A brief exposition of the relationship between molecular modeling and some fundamental experimental techniques, such as X-ray crystallography, neutron scattering, nuclear magnetic resonance (NMR), and fluorescence and vibrational spectroscopies, is provided. Finally, an outline of future directions of modeling studies is suggested.