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

TL;DR

ProCaliper is an open-source Python tool that integrates protein structural, functional, and physico-chemical data for analysis and visualization, facilitating residue-level annotation and network construction.

Contribution

It introduces a comprehensive Python library that combines data retrieval, property computation, visualization, and network analysis of proteins in a unified framework.

Findings

Enables interactive visualization of protein properties and annotations.

Supports construction of residue-distance and functional site networks.

Provides open-source tools for integrated protein 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 physico-chemical properties, and structure visualization are separated. To address this, we introduce ProCaliper, an open-source Python library for computing and visualizing physico-chemical 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.