DOI: 10.5061/dryad.c59zw3rj5
title: CAIRA: Catalytic associated irregular residue analyser

description: For the semi-automated identification of potential cleavage
 specificity-modulating SNVs we developed a program, called CAIRA
 (Catalytic Associated Irregular Residue Analyser). Entering the UniProt ID
 of a protease, CAIRA takes the predicted AlphaFold structure, generates a
 user-definable radius (e.g. 20 Å) around the active site and filters the
 COSMIC database for cancer-associated SNVs within this radius, which might
 have cleavage specificity-modulating effects. CAIRA can be used with all
 types of proteases (metallo, serine, aspartyl and cysteine proteases). To
 further assess their potential impact, SNV-affected amino acids are
 labelled in the protein structure of a downloadable pdb-file.
description: CAIRA<strong> </strong>was programmed using python.
 Protein structures were obtained from AlphaFold. Cleavage specificity
 logos were generated as described above using cleavage site specificity
 data from MEROPS the Peptidase Database. Cancer-associated SNVs data was
 taken from the COSMIC database (cancer.sanger.ac.uk;). Catalytically
 important amino acid residue(s) within the active site were extracted from
 UniProt annotation  and are used as the centre of the sphere. For
 proteases with more than one catalytically important amino acid residue
 within the active site (aspartyl, serine and cysteine proteases) CAIRA
 uses the middle between the relevant residues as the centre of the sphere.
 In the beta version, the ‘use binding cavity (beta)’ button can also be
 additionally used to switch to a version in which the binding cavity is
 imitated and SNVs can be output within it. For this purpose, cylinders of
 adjustable size are placed around the chemical bonds of the backbone of
 the protease's propeptide and amino acids of the protease that lie
 with at least one atom within these cylinders are filtered out and checked
 for annotated SNVs. The logo of CAIRA was designed with the help of Adobe
 Firefly.
description: # CAIRA: Catalytic associated irregular residue analyser
 [https://doi.org/10.5061/dryad.c59zw3rj5](https://doi.org/10.5061/dryad.c59zw3rj5) ## Description of the data and file structure For the semi-automated identification of potential cleavage specificity-modulating SNVs we developed a program, called **CAIRA (C**atalytic **A**ssociated **I**rregular **R**esidue **A**nalyser). Entering the UniProt ID of a protease, CAIRA takes the predicted AlphaFold structure, generates a user-definable radius (e.g. 20 Å) around the active site and filters the COSMIC database for cancer-associated SNVs within this radius, which might have cleavage specificity-modulating effects. CAIRA can be used with all types of proteases (metallo, serine, aspartyl and cysteine proteases). To further assess their potential impact, SNV-affected amino acids are labelled in the protein structure of a downloadable pdb-file. ### Files and variables #### File: logo.ico **Description:** logo of CAIRA 3.0 (is included in CAIRA3.0.exe). The logo of CAIRA was designed with the help of Adobe Firefly. #### File: merops\_dictionary.json **Description:** Cleavage specificity logos within CAIRA3.0.exe are generated using cleavage site specificity data from MEROPS the Peptidase Database (Rawlings, N.D., Waller, M., Barrett, A.J. & Bateman, A. (2014) MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 42, D503-D509). Cleavage specificity data obtained used for this from MEROPS data base is included in merops_dictionary.json. #### File: logo.jpg **Description:**  logo of CAIRA 3.0 (is included in CAIRA3.0.exe). The logo of CAIRA was designed with the help of Adobe Firefly. ## Code/software The CAIRA program can be run from CAIRA3.0.exe (this is a one file version). The underlying python script is included in CAIRA3.0.py.  AAS_in_tube2.py contains functions that are imported into CAIRA 3.0. **C**atalytic **a**ssociated **i**rregular **r**esidue **a**nalyser (CAIRA) was programmed using python 3.12.5 in IDLE environment. Used packages: requests csv pandas subprocess os matplotlib.pyplot numpy matplotlib.backends.backend_tkagg Bio sys io json shutil PyQt5 PyQt5.QtWidgets PyQt5.QtCore PyQt5.QtGui OpenGL.GL OpenGL.GLU OpenGL.GLUT matplotlib.backends.backend_qt5agg FigureCanvasQTAgg re math sys ## Access information Data was derived from the following sources: * merops_dictionsry.json includes cleavage specificity data obtained from MEROPS data base (Rawlings, N.D., Waller, M., Barrett, A.J. & Bateman, A. (2014) MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 42, D503-D509). [http://merops.sanger.ac.uk/](http://merops.sanger.ac.uk/). Licence: The *MEROPS* database is is provided under the terms of the [GNU Library General Public License](http://www.gnu.org/copyleft/lgpl.html) and the complete content of the database is referred to as the 'Library'.