Scooby-domain: prediction of globular domains in protein sequence

Scooby-domain (sequence hydrophobicity predicts domains) is a fast and simple method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure. The prediction method successfully identifies sequence regions that will form a globular structure and those that are likely to be unstructured. The method does not rely on homology searches and, therefore, can identify previously unknown domains for structural elucidation. Scooby-domain is available as a Java applet at http://ibivu.cs.vu.nl/programs/scoobywww. It may be used to visualize local properties within a protein sequence, such as average hydrophobicity, secondary structure propensity and domain boundaries, as well as being a method for fast domain assignment of large sequence sets.

[1]  R. A. George,et al.  Snapdragon: a Method to Delineate Protein Structural Domains from Sequence Data , 2022 .

[2]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[3]  D. Eisenberg.  Three-dimensional structure of membrane and surface proteins. , 1984, Annual review of biochemistry.

[4]  Stephen H. Bryant,et al.  Domain size distributions can predict domain boundaries , 2000, Bioinform..

[5]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[6]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[7]  S H White,et al.  Statistical distribution of hydrophobic residues along the length of protein chains. Implications for protein folding and evolution. , 1990, Biophysical journal.

[8]  R. A. George,et al.  Protein domain identification and improved sequence similarity searching using PSI‐BLAST , 2002, Proteins.

[9]  Jaap Heringa,et al.  An analysis of protein domain linkers: their classification and role in protein folding. , 2002, Protein engineering.

[10]  Cathy H. Wu,et al.  InterPro, progress and status in 2005 , 2004, Nucleic Acids Res..

[11]  P. Y. Chou,et al.  Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. , 1974, Biochemistry.

[12]  H. F. Fisher,et al.  A LIMITING LAW RELATING THE SIZE AND SHAPE OF PROTEIN MOLECULES TO THEIR COMPOSITION. , 1964, Proceedings of the National Academy of Sciences of the United States of America.

[13]  K. Dill.  Theory for the folding and stability of globular proteins. , 1985, Biochemistry.

[14]  K. R. Woods,et al.  Prediction of protein antigenic determinants from amino acid sequences. , 1981, Proceedings of the National Academy of Sciences of the United States of America.