{"doi":"10.1093/bioinformatics/btaf606","title":"<i>COCOMAPS</i>\n                    2.0: a web server for identifying, analyzing, and visualizing atomic interactions at the interface of biomolecular complexes","abstract":"<jats:title>Abstract</jats:title>\n                  <jats:sec>\n                    <jats:title>Summary</jats:title>\n                    <jats:p>Herein, we present COCOMAPS 2.0, for the analysis, visualization, and comparison of the interface in protein–protein and protein–nucleic acid complexes. COCOMAPS 2.0 complements the residue-level and buried surface area analyses of the original COCOMAPS tool with a comprehensive and accurate atomic-level characterization of the interface, enabling detailed interpretation of molecular recognition. Furthermore, it provides a greatly enhanced flexibility, interactivity, and efficiency in graphical visualizations.</jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation</jats:title>\n                    <jats:p>COCOMAPS 2.0 is accessible as a public web tool at https://aocdweb.com/BioTools/cocomaps2 and as a standalone code at https://doi.org/10.5281/zenodo.17390665.</jats:p>\n                  </jats:sec>","journal":"Bioinformatics","year":2025,"id":597042,"datarank":0.4335557636844247,"base_score":2.8903717578961645,"endowment":2.8903717578961645,"self_citation_contribution":0.4335557636844247,"citation_network_contribution":0.0,"self_endowment_contribution":0.4335557636844247,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":17,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1529330,"name":"Utkarsh Kalra","orcid":null,"position":1,"is_corresponding":false},{"id":1529331,"name":"Andrea Petta","orcid":null,"position":2,"is_corresponding":false},{"id":663101,"name":"Suraj Sharma","orcid":"0000-0002-9826-8675","position":3,"is_corresponding":false},{"id":1529332,"name":"Abdul Rajjak Shaikh","orcid":null,"position":4,"is_corresponding":false},{"id":139701,"name":"Luigi Cavallo","orcid":"0000-0002-1398-338X","position":5,"is_corresponding":false},{"id":631835,"name":"Romina Oliva","orcid":"0000-0002-6156-6249","position":6,"is_corresponding":false},{"id":1022569,"name":"Mohit Chawla","orcid":"0000-0002-3332-3055","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"<i>COCOMAPS</i>\n                    2.0: a web server for identifying, analyzing, and visualizing atomic interactions at the interface of biomolecular complexes","abstract":"<jats:title>Abstract</jats:title>\n                  <jats:sec>\n                    <jats:title>Summary</jats:title>\n                    <jats:p>Herein, we present COCOMAPS 2.0, for the analysis, visualization, and comparison of the interface in protein–protein and protein–nucleic acid complexes. COCOMAPS 2.0 complements the residue-level and buried surface area analyses of the original COCOMAPS tool with a comprehensive and accurate atomic-level characterization of the interface, enabling detailed interpretation of molecular recognition. Furthermore, it provides a greatly enhanced flexibility, interactivity, and efficiency in graphical visualizations.</jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation</jats:title>\n                    <jats:p>COCOMAPS 2.0 is accessible as a public web tool at https://aocdweb.com/BioTools/cocomaps2 and as a standalone code at https://doi.org/10.5281/zenodo.17390665.</jats:p>\n                  </jats:sec>","is_dataset_classified":null,"base_score":2.833213344056216,"endowment":2.833213344056216,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"41335450","pmcid":"PMC12684709","openalex_id":"https://openalex.org/W4417033052","authors":[],"funders":[{"funder_name":"KAUST","grant_id":"URF/1/4384-01-01","title":null},{"funder_name":"KAUST","grant_id":"URF/1/4701-01-01","title":null},{"funder_name":"NextGeneration EU PRIN","grant_id":"2022HREZJT","title":null},{"funder_name":"Ministero dell'Università e della Ricerca, MUR","grant_id":"","title":null},{"funder_name":"Ministero dell’Università e della Ricerca, MUR","grant_id":"","title":null}],"total_grants":5,"fwci":12.226,"citation_percentile":0.98851302,"influential_citations":0,"citation_trend":[{"year":2025,"count":1},{"year":2026,"count":15}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.1093/bioinformatics/btaf606","host_type":"journal"},{"url":"https://doi.org/10.1093/bioinformatics/btaf606","host_type":"publisher"},{"url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf606/65728359/btaf606.pdf","host_type":"publisher"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/41/12/btaf606/65728359/btaf606.pdf","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/41335450","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12684709/","host_type":"repository"},{"url":"https://hdl.handle.net/11367/154439","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC12684709","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC12684709?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Computational Drug Discovery Methods","Protein Structure and Dynamics","Bioinformatics and Genomic Networks"],"mesh_terms":["Models, Molecular","Nucleic Acids","Protein Binding","Proteins","Software","Internet"],"keywords":["Interface (matter)","Web server","User interface","Software","Code (set theory)","Visualization","Source code","Web application"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"pdb"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-28T12:02:31.169519Z","pmid":null,"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":[]}