A computer graphics program system for protein structure representation.
We have developed a computer graphics program system for the schematic representation of several protein secondary structure analysis algorithms. The programs calculate the probability of occurrence of alpha-helix, beta-sheet and beta-turns by the method of Chou and Fasman and assign unique predicted structure to each residue using a novel conflict resolution algorithm based on maximum likelihood. A detailed structure map containing secondary structure, hydrophobicity, sequence identity, sequence numbering and the location of putative N-linked glycosylation sites is then produced. In addition, helical wheel diagrams and hydrophobic moment calculations can be performed to further analyze the properties of selected regions of the sequence. As they require only structure specification as input, the graphics programs can easily be adapted for use with other secondary structure prediction schemes. The use of these programs to analyze protein structure-function relationships is described and evaluated.
Ross
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Biochemistry Department, University of Pennsylvania, School of Dental Medicine, Philadelphia 19104.
Golub
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D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis; D003196:Computer Graphics; D006678:HIV / Q000032:analysis; D015699:HIV Envelope Protein gp120; D011487:Protein Conformation; D012191:Retroviridae Proteins; D012984:Software / Q000379:methods*; D013329:Structure-Activity Relationship; D014759:Viral Envelope Proteins
D000596:Amino Acids; D015699:HIV Envelope Protein gp120; D012191:Retroviridae Proteins; D014759:Viral Envelope Proteins