Secondary Structure Characterization Based on Amino Acid Composition and Availability in Proteins (Record no. 54113)

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control field MX-MdCICY
005 - DATE AND TIME OF LATEST TRANSACTION
control field 20250625162441.0
040 ## - CATALOGING SOURCE
Transcribing agency CICY
090 ## - LOCALLY ASSIGNED LC-TYPE CALL NUMBER (OCLC); LOCAL CALL NUMBER (RLIN)
Classification number (OCLC) (R) ; Classification number, CALL (RLIN) (NR) B-20008
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245 10 - TITLE STATEMENT
Title Secondary Structure Characterization Based on Amino Acid Composition and Availability in Proteins
490 0# - SERIES STATEMENT
Volume/sequential designation Journal of Chemical information and modeling, 50(4), p.690-700, 2010
520 3# - SUMMARY, ETC.
Summary, etc. The importance of thorough analyses of the secondary structures in proteins as basic structural units cannot be overemphasized. Although recent computational methods have achieved reasonably high accuracy for predicting secondary structures from amino acid sequences, a simple and fundamental empirical approach to characterize the amino acid composition of secondary structures was performed mainly in 1970s, with a small number of analyzed structures. To extend this classical approach using a large number of analyzed structures, here we characterized the amino acid sequences of secondary structures (12?154 ?-helix units, 4592 310-helix units, 16?787 ?-strand units, and 30?811 "other" units), using the representative three-dimensional protein structure records (1641 protein chains)from the Protein Data Bank. We first examined the length and the amino acid compositions of secondary structures, including rank order differences and assignment relationships among amino acids. These compositional results were largely, but not entirely, consistent with the previous studies. In addition, we examined the frequency of 400 amino acid doublets and 8000 triplets in secondary structures based on their relative counts, termed the availability. We identified not only some triplets that were specific to a certain secondary structure but also so-called zero-count triplets, which did not occur in a given secondary structure at all, even though they were probabilistically predicted to occur several times. Taken together, the present study revealed essential features of secondary structures and suggests potential applications in the secondary structure prediction and the functional design of protein sequences.
700 12 - ADDED ENTRY--PERSONAL NAME
Personal name Otaki, J. M.
700 12 - ADDED ENTRY--PERSONAL NAME
Personal name Tsutsumi, M.
700 12 - ADDED ENTRY--PERSONAL NAME
Personal name Gotoh, T.
700 12 - ADDED ENTRY--PERSONAL NAME
Personal name Yamamoto, H.
856 40 - ELECTRONIC LOCATION AND ACCESS
Uniform Resource Identifier <a href="https://drive.google.com/file/d/1GDvTKJFIMRGGrNNGnq-91eTNUGWEWiMq/view?usp=drivesdk">https://drive.google.com/file/d/1GDvTKJFIMRGGrNNGnq-91eTNUGWEWiMq/view?usp=drivesdk</a>
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Source of classification or shelving scheme Clasificación local
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  Clasificación local     Ref1 CICY CICY Documento préstamo interbibliotecario 25.06.2025   B-20008 25.06.2025 25.06.2025 Documentos solicitados