Computer Assisted Modeling: Contributions of Computational by National Research Council, Division on Earth and Life

By National Research Council, Division on Earth and Life Studies, Commission on Life Sciences, Committee on Computer-Assisted Modeling

Common Books booklet date: 2009 unique booklet date: 1987 unique writer: nationwide Academies unique Identifier: NAP:13431 topics: desktop simulation Macromolecules desktops / common know-how

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Extra info for Computer Assisted Modeling: Contributions of Computational Approaches to Elucidating Macromolecular Structure and Function

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Please use the print version of this publication as the authoritative version for attribution. PRIMARY STRUCTURE OF PROTEINS AND NUCLEIC ACIDS 31 one amino acid by another (Dayhoff, 1978; Lipman and Pearson, 1985). Software and Hardware Considerations The computer software and hardware needed to carry out the patternmatching operations on sequences contrast in interesting ways with those required for the intense numerical calculations described in other sections of this report. First, the analyses of patterns in sequences is a problem in symbolic, not numeric, computation.

Please use the print version of this publication as the authoritative version for attribution. P5 andP6, for example, structural domains, may then be recognized as part of an even larger pattern,P7, for example, the tertiary structure of a protein. The hierarchy ofFigure 3-1also represents a computational model for deriving secondary and tertiary structural information from the patterns themselves. This computational model is described below. Methodology The concept of patterns is useful for expanding our view of the primary structure of proteins only if we find some method for labeling the individual amino acids or partial sequences with properties other than identity.

Actually, only about 100 different protein structures have been determined, and of these, many belong to the same families, as do the dehydrogenases or the serine proteases. Equally important, many known protein families—the interferons, for example—have not yet had a single crystal structure determined. The situation is changing rapidly, however, and the prospects appear very good for determining a truly representative set of About this PDF file: This new digital representation of the original work has been recomposed from XML files created from the original paper book, not from the original typesetting files.

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