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Scop3D : three-dimensional visualization of sequence conservation

(2015) PROTEOMICS. 15(8). p.1448-1452
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
The integration of a protein's structure with its known sequence variation provides insight on how that protein evolves, for instance in terms of (changing) function or immunogenicity. Yet, collating the corresponding sequence variants into a multiple sequence alignment, calculating each position's conservation, and mapping this information back onto a relevant structure is not straightforward. We therefore built the Sequence Conservation on Protein 3D structure (scop3D) tool to perform these tasks automatically. The output consists of two modified PDB files in which the B-values for each position are replaced by the percentage sequence conservation, or the information entropy for each position, respectively. Furthermore, text files with absolute and relative amino acid occurrences for each position are also provided, along with snapshots of the protein from six distinct directions in space. The visualization provided by scop3D can for instance be used as an aid in vaccine development or to identify antigenic hotspots, which we here demonstrate based on an analysis of the fusion proteins of human respiratory syncytial virus and mumps virus.
Keywords
MUTATIONS, MODEL, SPECIFICITY, COMMUNICATION, PROTEIN, BIOINFORMATICS, MATHEMATICAL-THEORY, MUMPS OUTBREAKS, NEUTRALIZING ANTIBODY, VIRUS FUSION GLYCOPROTEIN, Sequence variability, Sequence conservation, Mumps virus, Fusion protein, Human respiratory syncytial virus, Bioinformatics

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Chicago
Vermeire, Tessa, Stijn Vermaere, Bert Schepens, Xavier Saelens, Steven Van Gucht, Lennart Martens, and Elien Vandermarliere. 2015. “Scop3D : Three-dimensional Visualization of Sequence Conservation.” Proteomics 15 (8): 1448–1452.
APA
Vermeire, T., Vermaere, S., Schepens, B., Saelens, X., Van Gucht, S., Martens, L., & Vandermarliere, E. (2015). Scop3D : three-dimensional visualization of sequence conservation. PROTEOMICS, 15(8), 1448–1452.
Vancouver
1.
Vermeire T, Vermaere S, Schepens B, Saelens X, Van Gucht S, Martens L, et al. Scop3D : three-dimensional visualization of sequence conservation. PROTEOMICS. 2015;15(8):1448–52.
MLA
Vermeire, Tessa, Stijn Vermaere, Bert Schepens, et al. “Scop3D : Three-dimensional Visualization of Sequence Conservation.” PROTEOMICS 15.8 (2015): 1448–1452. Print.
@article{6896481,
  abstract     = {The integration of a protein's structure with its known sequence variation provides insight on how that protein evolves, for instance in terms of (changing) function or immunogenicity. Yet, collating the corresponding sequence variants into a multiple sequence alignment, calculating each position's conservation, and mapping this information back onto a relevant structure is not straightforward. We therefore built the Sequence Conservation on Protein 3D structure (scop3D) tool to perform these tasks automatically. The output consists of two modified PDB files in which the B-values for each position are replaced by the percentage sequence conservation, or the information entropy for each position, respectively. Furthermore, text files with absolute and relative amino acid occurrences for each position are also provided, along with snapshots of the protein from six distinct directions in space. The visualization provided by scop3D can for instance be used as an aid in vaccine development or to identify antigenic hotspots, which we here demonstrate based on an analysis of the fusion proteins of human respiratory syncytial virus and mumps virus.},
  author       = {Vermeire, Tessa and Vermaere, Stijn and Schepens, Bert and Saelens, Xavier and Van Gucht, Steven and Martens, Lennart and Vandermarliere, Elien},
  issn         = {1615-9853},
  journal      = {PROTEOMICS},
  keyword      = {MUTATIONS,MODEL,SPECIFICITY,COMMUNICATION,PROTEIN,BIOINFORMATICS,MATHEMATICAL-THEORY,MUMPS OUTBREAKS,NEUTRALIZING ANTIBODY,VIRUS FUSION GLYCOPROTEIN,Sequence variability,Sequence conservation,Mumps virus,Fusion protein,Human respiratory syncytial virus,Bioinformatics},
  language     = {eng},
  number       = {8},
  pages        = {1448--1452},
  title        = {Scop3D : three-dimensional visualization of sequence conservation},
  url          = {http://dx.doi.org/10.1002/pmic.201400354},
  volume       = {15},
  year         = {2015},
}

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