WatCon : A Python Tool for Analysis of Conserved Water Networks Across Protein Families
Brownless, Alfie Louise R. ; Harrison-Rawn, Travis and Kamerlin, Shina C.L. LU
(2025)
In JACS Au
5(12).
p.6379-6395
- Abstract
Water structure is crucially important to protein function and catalysis and can be conserved throughout related proteins despite differences in sequence. The complex hydrogen-bonding networks formed by water molecules and protein residues have been studied extensively, and graph-theory-based methods have frequently been used to describe these networks. Although there exist a number of tools which can be used to track water positions and networks, corresponding methods for easily analyzing complex water network structure across related proteins are limited. To address this challenge, we present here a new tool, WatCon, an open-source Python package which can be used to analyze water positions and water network structure across protein... (More)
Water structure is crucially important to protein function and catalysis and can be conserved throughout related proteins despite differences in sequence. The complex hydrogen-bonding networks formed by water molecules and protein residues have been studied extensively, and graph-theory-based methods have frequently been used to describe these networks. Although there exist a number of tools which can be used to track water positions and networks, corresponding methods for easily analyzing complex water network structure across related proteins are limited. To address this challenge, we present here a new tool, WatCon, an open-source Python package which can be used to analyze water positions and water network structure across protein families using both dynamic and static structural information. Importantly, WatCon can be used to classify conservation of water networks, characterize water networks across structures, and project subsequent results for easy visual interpretation. To illustrate WatCon usage, we provide five example applications illustrating WatCon analyses of static structures, dynamic trajectories, and cross-family analysis. This in turn showcases the utility of WatCon for enhancing our understanding of biochemical systems, predicting water hotspots of potential relevance to protein engineering and predicting pathogenic mutations. WatCon can be downloaded at https://github.com/kamerlinlab/WatCon and is available under the GNU General Public License v3.0.
(Less)
- author
- Brownless, Alfie Louise R.
; Harrison-Rawn, Travis
and Kamerlin, Shina C.L.
LU
- organization
- publishing date
- 2025-12-22
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Graph Theory, Protein Structure, Protein Tyrosine Phosphatases, Water Conservation, Water Networks
- in
- JACS Au
- volume
- 5
- issue
- 12
- pages
- 17 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- pmid:41450622
- scopus:105025246732
- ISSN
- 2691-3704
- DOI
- 10.1021/jacsau.5c00447
- language
- English
- LU publication?
- yes
- additional info
- Publisher Copyright: © 2025 The Authors. Published by American Chemical Society
- id
- 75885fd4-a470-4255-87cf-d5df405969fb
- date added to LUP
- 2026-02-10 16:30:34
- date last changed
- 2026-02-11 03:54:44
@article{75885fd4-a470-4255-87cf-d5df405969fb,
abstract = {{<p>Water structure is crucially important to protein function and catalysis and can be conserved throughout related proteins despite differences in sequence. The complex hydrogen-bonding networks formed by water molecules and protein residues have been studied extensively, and graph-theory-based methods have frequently been used to describe these networks. Although there exist a number of tools which can be used to track water positions and networks, corresponding methods for easily analyzing complex water network structure across related proteins are limited. To address this challenge, we present here a new tool, WatCon, an open-source Python package which can be used to analyze water positions and water network structure across protein families using both dynamic and static structural information. Importantly, WatCon can be used to classify conservation of water networks, characterize water networks across structures, and project subsequent results for easy visual interpretation. To illustrate WatCon usage, we provide five example applications illustrating WatCon analyses of static structures, dynamic trajectories, and cross-family analysis. This in turn showcases the utility of WatCon for enhancing our understanding of biochemical systems, predicting water hotspots of potential relevance to protein engineering and predicting pathogenic mutations. WatCon can be downloaded at https://github.com/kamerlinlab/WatCon and is available under the GNU General Public License v3.0.</p>}},
author = {{Brownless, Alfie Louise R. and Harrison-Rawn, Travis and Kamerlin, Shina C.L.}},
issn = {{2691-3704}},
keywords = {{Graph Theory; Protein Structure; Protein Tyrosine Phosphatases; Water Conservation; Water Networks}},
language = {{eng}},
month = {{12}},
number = {{12}},
pages = {{6379--6395}},
publisher = {{The American Chemical Society (ACS)}},
series = {{JACS Au}},
title = {{WatCon : A Python Tool for Analysis of Conserved Water Networks Across Protein Families}},
url = {{http://dx.doi.org/10.1021/jacsau.5c00447}},
doi = {{10.1021/jacsau.5c00447}},
volume = {{5}},
year = {{2025}},
}