Algorithms for Molecular Biology Fall Semester, 2001

Abstract

Introduction 12.1.1 Background Proteins are long chains of Amino Acids (AA). There are 20 di#erent AAs that serve as building blocks for proteins. Each AA has a specific chemical structure which contains a carbon backbone similar to all amino acids and a residue which varies between the AAs. The length of a protein chain can range from 50 to 1000-3000 AA (200 on the average). Proteins are known to have many important functions in the cell, such as enzymatic activity, storage and transport of material, signal transduction, antibodies and more. An important property of a protein is the length and composition of the AA chain. The series can be obtained automatically from the gene that encodes for the protein. Another interesting property is the unique folding. The AA composition of a protein will usually uniquely determine (on specific environment conditions) the 3D structure of the protein (e.g., two proteins with the same AA sequence will have the same 3D structure in natural conditi