Skip to content

Protein structure alignment

Description

Protein structural alignment helps to identify and compare the three-dimensional spatial arrangement of atoms within different protein structures. This methodology allows to investigate the functional and evolutionary relationships between proteins by enabling the detection of conserved structural motifs.

This tool is built on top of the FATCAT

Methods

AlignProteins

Aligns two protein structures using FATCAT.

Equivalent to running:

$ FATCAT -p1 ref.pdb -p2 tgt.pdb

CleanupPDB

Converts raw PDB file into a ProteinStructure object. In addition, performs the following actions:

  • Removes residues that don't represent amino acids.
  • Removes residues that don't have a Ca atom.
  • Removes residues that have more than one Ca atom.

GetAffineTransformation

For the given alignment, calculates an affine transformation \(A\) that transforms blocks in the reference structure to the blocks in the target structure, i.e.

\[ x_{tgt} = Ax_{ref} \]

Models

Point3D

A point in a three-dimensional space.


Atom

Atom in a protein residue.


ProteinResidue

Protein residue.


ProteinChain

Protein chain


ProteinStructure

Protein structure.

Uses hierarchical structure, dissimilar to *.pdb file.


ProteinAlignment

Result of a protein alignment algorithm.