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In this work experts provide a broad perspective of the theoretical tools available today to analyze protein structure and function. Topics at the frontier of computational biophysics are discussed in a pedagogical and complete way: molecular dynamics of globins; global optimization methods; memory associated Hamiltonians; simple models of protein folding; and reaction path studies in proteins. Those entering the field should find the book to be a useful introduction, and it is also intended as a complementary text to existing ones that focus on just one of the above subjects.