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Computer Simulations of Protein Structures and Interactions
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.
The de novo prediction of the tertiary structure of peptides and proteins and, ultimately, the development of molecular switches, synthetic vaccines, pepzymes, peptidomimetics, ... , are the goals of research in biotechnology. This field relies on a cooperative effort between many branches of the life and natural sciences and this work strives to present the corresponding picture, from quantum mechanics to rational drug design, through computer science, synthetic chemistry, immunology, pharmacology, ... We hope that it will serve its dual purpose, as a learning tool and as reference.
1 Introduction
Protein Folding
2 Amino Acids, Peptides, and Proteins
Theoretical Formulation
3 Quantum Mechanics
4 Statistical Mechanics
5 Molecular Mechanics: The Potential Energy Function
6 Molecular Mechanics: Computer Simulations
7 Practical Overview
Experimental and Theoretical Data
8 Databases
Modeling of Isolated Systems and Associations
9 Prediction of Secondary Structures10 Modeling of Tertiary Structures
11 Molecular Associations
12 Structure-Aided Molecular Design