By National Research Council, Division on Earth and Life Studies, Commission on Life Sciences, Committee on Computer-Assisted Modeling
ISBN-10: 0309062284
ISBN-13: 9780309062282
ISBN-10: 0309568293
ISBN-13: 9780309568296
Normal Books book date: 2009 unique ebook date: 1987 unique writer: nationwide Academies unique Identifier: NAP:13431 topics: machine simulation Macromolecules pcs / basic expertise
Read Online or Download Computer Assisted Modeling: Contributions of Computational Approaches to Elucidating Macromolecular Structure and Function PDF
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Additional info for Computer Assisted Modeling: Contributions of Computational Approaches to Elucidating Macromolecular Structure and Function
Example text
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.
Beta structures are formed from hydrogen bonding between the backbone amides of extended polypeptide strands. Although such features are properly considered tertiary structure, they are often discussed as secondary structure. They are named according to whether the strand pairs run parallel or antiparallel to each other (based on a vector drawn from the N to C termini of the feature) and whether the sheets are folded or rolled into a barrel (Richardson, 1981). , 1985). They are characterized according to local geometric features.
Patterns can be derived by examining the secondary and tertiary structures of known proteins, and relating spatial information back to patterns in the primary structure. In essence, we attempt to map what is known about spatial configurations into the one-dimensional world of sequences. This mapping itself can be done hierarchically, closely related to the hierarchy shown above, as shown from the bottom up inFigure 3-1. The scheme symbolized inFigure 3-1represents the fact that a sequence can be analyzed to determine patterns of partial sequences, illustrated by the boxed elements.
Computer Assisted Modeling: Contributions of Computational Approaches to Elucidating Macromolecular Structure and Function by National Research Council, Division on Earth and Life Studies, Commission on Life Sciences, Committee on Computer-Assisted Modeling
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