Ebook: Computer Simulations of Protein Structures and Interactions

Lecture Notes in Chemistry Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs, vaccines, and industrial enzymes. Computer assisted simulations play an important role, as an auxiliary tool, in this task. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.

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Lecture Notes in Chemistry Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs, vaccines, and industrial enzymes. Computer assisted simulations play an important role, as an auxiliary tool, in this task. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.

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Lecture Notes in Chemistry Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs, vaccines, and industrial enzymes. Computer assisted simulations play an important role, as an auxiliary tool, in this task. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.
Content:
Front Matter....Pages I-XII
Introduction....Pages 1-2
Front Matter....Pages 3-3
Amino Acids, Peptides, and Proteins....Pages 4-25
Front Matter....Pages 26-26
Quantum Mechanics....Pages 27-57
Statistical Mechanics....Pages 58-70
Molecular Mechanics: The Potential Energy Function....Pages 71-97
Molecular Mechanics: Computer Simulations....Pages 98-127
Practical Overview....Pages 128-129
Front Matter....Pages 130-130
Databases....Pages 131-138
Front Matter....Pages 139-139
Prediction of Secondary Structures....Pages 140-163
Modeling of Tertiary Structures....Pages 164-195
Molecular Associations....Pages 196-213
Front Matter....Pages 214-214
Structure-Aided Molecular Design....Pages 215-234
Back Matter....Pages 235-284

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Lecture Notes in Chemistry Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs, vaccines, and industrial enzymes. Computer assisted simulations play an important role, as an auxiliary tool, in this task. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.
Content:
Front Matter....Pages I-XII
Introduction....Pages 1-2
Front Matter....Pages 3-3
Amino Acids, Peptides, and Proteins....Pages 4-25
Front Matter....Pages 26-26
Quantum Mechanics....Pages 27-57
Statistical Mechanics....Pages 58-70
Molecular Mechanics: The Potential Energy Function....Pages 71-97
Molecular Mechanics: Computer Simulations....Pages 98-127
Practical Overview....Pages 128-129
Front Matter....Pages 130-130
Databases....Pages 131-138
Front Matter....Pages 139-139
Prediction of Secondary Structures....Pages 140-163
Modeling of Tertiary Structures....Pages 164-195
Molecular Associations....Pages 196-213
Front Matter....Pages 214-214
Structure-Aided Molecular Design....Pages 215-234
Back Matter....Pages 235-284
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