Literature DB >> 24186049

Modelling of peptide and protein structures.

S Fraga1, J M Parker.   

Abstract

The modelling of protein structures (whether isolated, in solution, or involved in recognition processes) is reviewed, free of any mathematical apparatus, to provide an overview of the concepts as well as leading references. A general feeling for this field of work is first established by a sampling of some impressions on its difficulties and chances of success. Then, the main body of this work examines the information available (databases and parameters), presents the theoretical foundations for the modelling procedures (with emphasis on the potential energy functions), surveys the existing simulation techniques and prediction methods, and discusses the problems still to be faced. For completeness, a representative list of existing software packages is presented in the Appendix.

Year:  1994        PMID: 24186049     DOI: 10.1007/BF00814159

Source DB:  PubMed          Journal:  Amino Acids        ISSN: 0939-4451            Impact factor:   3.520


  122 in total

1.  Monte Carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space.

Authors:  A Caflisch; P Niederer; M Anliker
Journal:  Proteins       Date:  1992-09

2.  A workbench for multiple alignment construction and analysis.

Authors:  G D Schuler; S F Altschul; D J Lipman
Journal:  Proteins       Date:  1991

3.  Prediction of the secondary structure and functional sites of major histocompatibility complex molecules.

Authors:  S Fraga; E San-Fabian; S Thornton; B Singh
Journal:  J Mol Recognit       Date:  1990-04       Impact factor: 2.137

4.  Prediction of surface and interior regions in proteins--Part II: Predicting secondary structure in regions bound by surface exposed regions.

Authors:  J M Parker; R S Hodges
Journal:  Pept Res       Date:  1991 Nov-Dec

5.  New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites.

Authors:  J M Parker; D Guo; R S Hodges
Journal:  Biochemistry       Date:  1986-09-23       Impact factor: 3.162

6.  Improvements in protein secondary structure prediction by an enhanced neural network.

Authors:  D G Kneller; F E Cohen; R Langridge
Journal:  J Mol Biol       Date:  1990-07-05       Impact factor: 5.469

Review 7.  Intermediates in the folding reactions of small proteins.

Authors:  P S Kim; R L Baldwin
Journal:  Annu Rev Biochem       Date:  1990       Impact factor: 23.643

8.  Prediction of probable pathways of folding in globular proteins.

Authors:  T Kikuchi; G Némethy; H A Scheraga
Journal:  J Protein Chem       Date:  1988-08

9.  Surface tension of amino acid solutions: a hydrophobicity scale of the amino acid residues.

Authors:  H B Bull; K Breese
Journal:  Arch Biochem Biophys       Date:  1974-04-02       Impact factor: 4.013

10.  Dipoles of the alpha-helix and beta-sheet: their role in protein folding.

Authors:  W G Hol; L M Halie; C Sander
Journal:  Nature       Date:  1981-12-10       Impact factor: 49.962

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