ProCaliper: functional and structural analysis, visualization, and annotation of proteins
Fuente:
arXiv
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866916810609131520 |
|---|---|
| author | Rozum, Jordan C. Ufford, Hunter Im, Alexandria K. Zhang, Tong Pollock, David D. Kim, Doo Nam Feng, Song |
| author_facet | Rozum, Jordan C. Ufford, Hunter Im, Alexandria K. Zhang, Tong Pollock, David D. Kim, Doo Nam Feng, Song |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2506_19961 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | ProCaliper: functional and structural analysis, visualization, and annotation of proteins Rozum, Jordan C. Ufford, Hunter Im, Alexandria K. Zhang, Tong Pollock, David D. Kim, Doo Nam Feng, Song Biomolecules Molecular Networks 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. |
| title | ProCaliper: functional and structural analysis, visualization, and annotation of proteins |
| topic | Biomolecules Molecular Networks |
| url | https://arxiv.org/abs/2506.19961 |