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PMID: 2832829 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

A computer graphics program system for protein structure representation.

Nucleic acids research ·Vol. 16 ·No. 5 ·1988-03-11 ·Pages 1801-12

Ross AM, Golub EE

Abstract

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.

MeSH Terms

Algorithms Amino Acid Sequence Amino Acids/analysis Computer Graphics HIV/analysis HIV Envelope Protein gp120 Protein Conformation Retroviridae Proteins Software/methods Structure-Activity Relationship Viral Envelope Proteins

Chemicals

Amino Acids HIV Envelope Protein gp120 Retroviridae Proteins Viral Envelope Proteins

Authors & Affiliations

2 authors, click to expand affiliations / ORCID

Ross A M

Biochemistry Department, University of Pennsylvania, School of Dental Medicine, Philadelphia 19104.

Golub E E

References (22)

22 references, click to expand

Analysis of the code relating sequence to conformation in globular proteins. Development of a stereochemical alphabet on the basis of intra-residue information.
Biochem J. 1974 Sep;141(3):869-82 PMID: 4463966
Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure.
J Mol Biol. 1974 Oct 5;88(4):857-72 PMID: 4427383
A simple method for displaying the hydropathic character of a protein.
J Mol Biol. 1982 May 5;157(1):105-32 PMID: 7108955
A BASIC microcomputer program for plotting the secondary structure of proteins.
Comput Programs Biomed. 1982 Dec;15(3):163-8 PMID: 6897712
Localization and synthesis of an antigenic determinant of herpes simplex virus glycoprotein D that stimulates the production of neutralizing antibody.
J Virol. 1984 Jan;49(1):102-8 PMID: 6197535
The hydrophobic moment detects periodicity in protein hydrophobicity.
Proc Natl Acad Sci U S A. 1984 Jan;81(1):140-4 PMID: 6582470
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
Biopolymers. 1983 Dec;22(12):2577-637 PMID: 6667333
The complete sequence of the M RNA of snowshoe hare bunyavirus reveals the presence of internal hydrophobic domains in the viral glycoprotein.
Virology. 1984 Sep;137(2):227-40 PMID: 6091326
Fine structure analysis of type-specific and type-common antigenic sites of herpes simplex virus glycoprotein D.
J Virol. 1984 Nov;52(2):431-5 PMID: 6208376
Antigenic variants of CVS rabies virus with altered glycosylation sites.
Virology. 1985 Jan 15;140(1):1-12 PMID: 3966297
Localization of epitopes of herpes simplex virus type 1 glycoprotein D.
J Virol. 1985 Feb;53(2):634-44 PMID: 2578577
Strategies for the economic preparation of Epstein-Barr virus proteins of diagnostic and protective value by genetic engineering: a new approach based on segments of virus-encoded gene products.
IARC Sci Publ. 1984;(63):525-39 PMID: 6100280
Analysis of the 3' region of the sheep elastin gene.
Arch Biochem Biophys. 1985 Sep;241(2):684-91 PMID: 3839997
Computer-assisted analysis of envelope protein sequences of seven human immunodeficiency virus isolates: prediction of antigenic epitopes in conserved and variable regions.
J Virol. 1987 Feb;61(2):570-8 PMID: 2433466
Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins.
J Mol Biol. 1987 Jun 5;195(3):659-85 PMID: 3656427
A computerized version of the Chou and Fasman method for predicting the secondary structure of proteins.
Anal Biochem. 1987 Jun;163(2):292-7 PMID: 3661979
Use of helical wheels to represent the structures of proteins and to identify segments with helical potential.
Biophys J. 1967 Mar;7(2):121-35 PMID: 6048867
Helix probability profiles of denatured proteins and their correlation with native structures.
Proc Natl Acad Sci U S A. 1970 Apr;65(4):810-5 PMID: 5266152
The influence of nearest-neighbor amino acids on the conformation of the middle amino acid in proteins: comparison of predicted and experimental determination of -sheets in concanavalin A.
Proc Natl Acad Sci U S A. 1973 May;70(5):1473-7 PMID: 4514316
Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins.
Biochemistry. 1974 Jan 15;13(2):211-22 PMID: 4358939
Prediction of protein conformation.
Biochemistry. 1974 Jan 15;13(2):222-45 PMID: 4358940
Empirical predictions of protein conformation.
Annu Rev Biochem. 1978;47:251-76 PMID: 354496

Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

0305-1048

DOI

10.1093/nar/16.5.1801

Published

1988-03-11

Pages

1801-12

Language

English

Region

England

NLM ID

0411011

PMCID

PMC338174

Subset

Grants

NIDCR NIH HHS · DE-02623 · United States

External Links

PubMed source DOI: 10.1093/nar/16.5.1801 PMC Full Text View journal details

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