Amino acid substitution clash detection

This tool identifies if an amino acid substitution would cause clashes in protein structure or not. Taking PDB format file or PDB accession codes as input, for each position of interest substitutions are modeled using backbone-dependent rotamer library (Shapovalov and Dunbrack, 2011). Sterical clashes are calculated based on the distance between atoms.

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Amino acid substitution clash detection

This tool was developed for protein variation analysis. With the help of this tool, structural reasons behind the loss of stability in protein structure due to amino acid substitution can be analysed; also, unknown protein variants can be modeled and conclusions on sterical effect of substitutions can be made.
The tool calculates the distaces between atoms of the new substituted amino acids and the surrounding atoms in the protein structure and identifies if clashes in the structure would form or not. Clash is considered to be a strong overlap between van der Waals radii of the atoms.

The input can be provided in 2 ways: either uploading your own PDB format file or listing PDB database accession codes. In both cases, a list of specific positions and/or substitutions can be provided - otherwise, all possible subsitutions in all possible positions would be analysed. Note that in the latter case the process would become much longer.

Submit queries

1. Submitting structures by PDB accession codes

PDB accession codes and positions/substitutions of interest should be provided in fasta format. If no substitutions or positions are provided for an accession code, all possible substitutions for that protein structure would be analysed (see "3cmp" in the example).

2. Submitting a structure as a file

Submitted file should follow PDB format (see instructions). Positions and substitutions of interest can be provided in the box. If none are provided, all possible subsitutions in all positions would be analysed.


The output of the program is a table of analysed substitutions with identification if the clash would form or not and structural visualisation of the protein structure and subsitutions. If an e-mail address is provided, the link with the output is sent to the user.