Sequence conservation of protein on 3D structure.
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scop3D command line script added Oct 21, 2015 Update Nov 21, 2016


Project Description

Scop3D (Sequence Conservation On Protein 3D structure) allows the visualization of sequence variation of a protein on its structure.

Scop3D is composed of two parts. The first part focuses on the analysis of sequence conservation, while the second part involves structural annotation.

A command line version is available as well.

Sequence analysis

The starting point for the sequence analysis is a FASTA-file which contains all sequence variants of interest. These variants are aligned with MUSCLE. From the resulting multiple sequence alignment, the consensus sequence is constructed by retaining the most frequently found residue across all variant sequences for each position. This residue should be found more than the conservation threshold which is set be the user. Two matrices are created. The first matrix annotates the consensus sequence with the absolute abundance of each amino acid per position. In the second matrix, these numbers are converted into relative abundances in percent. Finally, a sequence logo is created with WebLogo.

Structure annotation

In this part, a PDB-file is needed. This file can be obtained from the PDB or an own PDB-file can be used. If no protein structure is at hand, scop3D provides the option to retrieve a homologous structure by performing a BLAST search of the consensus sequence against the PDB. The outcome of the structure annotation is two PDB-files with altered B-values and a set of figures. In the first PDB-file, the B-values are replaced by the percent variation (defined as one hundred minus the percentage conservation) at that position. In the second PDB-file, the B-values are replaced by the entropy factor.


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See the wiki for additional information on how to use scop3D for both the graphical user interface and command line versions.

System requirements

The requirements for the graphical user interface and command line version are currently different, as decribed in the wiki.


!!! the use of the space character in file names or directory names should be avoided !!! !!! scop3D does not function when irregular characters are used !!!

When large structures are being analysed, it is possible that only part of the structure is visualized. We therefore implemented the 'see ccp4mg' button in the image pages. This button allows you to start ccp4mg with your structure loaded. This then allows you to center the structure as you wish or to change the representation of the structure.

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Project Support

The scop3D project is grateful for the support by:

Compomics VIB Ghent University
compomics vib ugent

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