# ProCaliper: functional and structural analysis, visualization, and annotation of proteins

## TL;DR

ProCaliper is a Python tool that helps researchers analyze and visualize protein structure and function by combining annotations and physicochemical data.

## Contribution

ProCaliper introduces an integrated open-source library for computing, visualizing, and analyzing residue-level protein properties and functional annotations.

## Key findings

- ProCaliper computes residue-level properties like charge and solvent accessibility.
- The tool visualizes computed data alongside user annotations and constructs residue interaction networks.
- ProCaliper integrates UniProt and AlphaFold data for functional and structural analysis.

## Abstract

Understanding protein function at the molecular level requires connecting residue-level annotations with physical and structural properties. This can be cumbersome and error-prone when functional annotation, computation of physicochemical properties, and structure visualization are separated. To address this, we introduce ProCaliper, an open-source Python library for computing and visualizing physicochemical properties of proteins. It can retrieve annotation and structure data from UniProt and AlphaFold databases, compute residue-level properties such as charge, solvent accessibility, and protonation state, and interactively visualize the results of these computations along with user-supplied residue-level data. Additionally, ProCaliper incorporates functional and structural information to construct and optionally sparsify networks that encode the distance between residues and/or annotated functional sites or regions.

The package ProCaliper and its source code, along with the code used to generate the figures in this manuscript, are freely available at https://github.com/PNNL-Predictive-Phenomics/ProCaliper.