All-atom simulations of proteins

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The successful deciphering of the human genome has highlighted an old challenge in protein science: For most of the resolved protein sequences, we do not know the corresponding structures and functions. Neither do we understand in detail the mechanism by which a protein folds into its biologically active form. Computer experiments offer one way to evaluate the sequence-structure relationship and the folding process but are extremely difficult for detailed protein models. Only over the last few years have algorithms been developed that allow an efficient sampling of relevant protein configurations. Important examples of these new techniques will be introduced in the context of all-atom simulations of small proteins. For these molecules, the folding mechanism and the relation between secondary structure formation and folding are explored. Limitations of current energy functions are discussed. © 2008 Springer-Verlag Berlin Heidelberg.

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Lecture Notes in Physics