Scop3D: three-dimensional visualization of sequence conservation

Proteomics. 2015 Apr;15(8):1448-52. doi: 10.1002/pmic.201400354. Epub 2015 Mar 3.


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: Bioinformatics; Fusion protein; Human respiratory syncytial virus; Mumps virus; Sequence conservation; Sequence variability.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Computer Graphics*
  • Conserved Sequence
  • Humans
  • Models, Molecular
  • Protein Conformation
  • Respiratory Syncytial Virus, Human / chemistry
  • Sequence Analysis, Protein
  • User-Computer Interface*
  • Viral Fusion Proteins / chemistry


  • F protein, human respiratory syncytial virus
  • Viral Fusion Proteins