{"doi":"10.1093/bioinformatics/btae516","title":"<i>WatFinder</i>: a <i>ProDy</i> tool for protein–water interactions","abstract":"SUMMARY: We introduce WatFinder, a tool designed to identify and visualize protein-water interactions (water bridges, water-mediated associations, or water channels, fluxes, and clusters) relevant to protein stability, dynamics, and function. WatFinder is integrated into ProDy, a Python API broadly used for structure-based prediction of protein dynamics. WatFinder provides a suite of functions for generating raw data as well as outputs from statistical analyses. The ProDy framework facilitates comprehensive automation and efficient analysis of the ensembles of structures resolved for a given protein or the time-evolved conformations from simulations in explicit water, as illustrated in five case studies presented in the Supplementary Material. AVAILABILITY AND IMPLEMENTATION: ProDy is open-source and freely available under MIT License from https://github.com/ProDy/ProDy.","journal":"Bioinformatics","year":2024,"id":447314,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9572,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1265396,"name":"Frane Doljanin","orcid":null,"position":1,"is_corresponding":false},{"id":366890,"name":"Anthony T. Bogetti","orcid":"0000-0003-0610-2879","position":2,"is_corresponding":false},{"id":1264901,"name":"Feng Zhang","orcid":"0000-0003-4902-8955","position":3,"is_corresponding":false},{"id":1071716,"name":"Thiliban Manivarma","orcid":"0000-0002-4092-9119","position":4,"is_corresponding":false},{"id":110068,"name":"İvet Bahar","orcid":"0000-0001-9959-4176","position":5,"is_corresponding":false},{"id":110053,"name":"Karolina Mikulska‐Ruminska","orcid":"0000-0001-7227-5503","position":6,"is_corresponding":false},{"id":363832,"name":"James Krieger","orcid":"0000-0001-6194-6244","position":0,"is_corresponding":true}],"reference_count":15,"raw_metadata":null,"created_at":"2026-07-19T02:01:59.101070Z","pmid":"39152994","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}