SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level

BioData Mining
Florian HeinkeDirk Labudde

Abstract

To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasing number of available structures in databases or structure models produced by automated modeling frameworks this process requires assistance from tools that allow automated structure visualization. In this paper a web server and its underlying method for generating graphical sequence representations of molecular structures is presented. The method, called SequenceCEROSENE (color encoding of residues obtained by spatial neighborhood embedding), retrieves the sequence of each amino acid or nucleotide chain in a given structure and produces a color coding for each residue based on three-dimensional structure information. From this, color-highlighted sequences are obtained, where residue coloring represent three-dimensional residue locations in the structure. This color encoding thus provides a one-dimensional representation, from which spatial interactions, proximity and relations between residues or entire chains can be deduced quickly and solely from color similarity. Furthermore, additional heteroatoms and chemical compou...Continue Reading

References

Jan 1, 1990·Proteins·E G Hutchinson, J M Thornton
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Apr 22, 1999·Protein Science : a Publication of the Protein Society·D R WestheadJ M Thornton
Jan 23, 2003·Bioinformatics·Charles S Bond
Apr 8, 2011·Bioinformatics·Corinna VehlowMichael Lappe
Oct 14, 2011·Bioinformatics·Alex StivalaPeter J Stuckey
Oct 25, 2013·Nucleic Acids Research·Tjaart A P de BeerRoman A Laskowski
Jul 27, 2014·Journal of Computer-aided Molecular Design·Helen M BermanJohn L Markley

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Software Mentioned

TOPS
CMA
HERA
CMView
PROTTER
origami
CEROSENE
PyMOL
Sequence
SequenceCEROSENE

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