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

Summary: 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. Availability and implementation: 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.