{"doi":"10.1016/j.drudis.2025.104466","title":"Recent advances in computational strategies for allosteric site prediction: Machine learning, molecular dynamics, and network-based approaches","abstract":null,"journal":"Drug Discovery Today","year":2025,"id":612446,"datarank":0.38474240361923057,"base_score":2.5649493574615367,"endowment":2.5649493574615367,"self_citation_contribution":0.38474240361923057,"citation_network_contribution":0.0,"self_endowment_contribution":0.38474240361923057,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":12,"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":1576906,"name":"Guo Tang","orcid":null,"position":1,"is_corresponding":false},{"id":356007,"name":"Ning Liu","orcid":"0000-0001-5499-5849","position":2,"is_corresponding":false},{"id":669773,"name":"Xiaolong Li","orcid":"0000-0002-8396-2912","position":3,"is_corresponding":false},{"id":701027,"name":"Shaoyong Lu","orcid":"0000-0002-1334-6292","position":4,"is_corresponding":false},{"id":1576905,"name":"Jianxiang Huang","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Recent advances in computational strategies for allosteric site prediction: Machine learning, molecular dynamics, and network-based approaches","abstract":"The landscape of allosteric drug discovery is undergoing a transformative shift, driven by the integration of three computational approaches: machine learning (ML), molecular dynamics (MD) simulations, and network theory. ML identifies potential allosteric sites from multidimensional biological datasets; MD simulations, empowered by enhanced sampling algorithms, reveal transient conformational states; and network analyses uncover communication pathways, further aiding in site identification. Their synergy enables rational allosteric modulator design. However, challenges like high computational costs, limited datasets, and model generalizability persist. Future strategies will leverage ML-accelerated MD, open-science data platforms, and advanced ML techniques, including transfer learning with models like AlphaFold and ESM-2. This multidisciplinary approach holds great promise to enhance allosteric drug discovery, driving therapeutic breakthroughs in the post-structural genomics era.","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"40914553","pmcid":null,"openalex_id":null,"authors":[],"funders":[{"funder_name":"National Key Research and Development Program of China","grant_id":"2023YFC3404700","title":null},{"funder_name":"National Major Science and Technology Projects of China","grant_id":"2024ZD0531200","title":null}],"total_grants":2,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"closed","license":"https://doi.org/10.15223/policy-004","oa_locations":[{"url":"https://api.elsevier.com/content/article/PII:S1359644625001795?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S1359644625001795?httpAccept=text/plain","host_type":"publisher"}],"fields_of_study":["Medicine","Computer Science","Chemistry"],"mesh_terms":["Humans","Allosteric Regulation","Allosteric Site","Drug Discovery","Molecular Dynamics Simulation","Machine Learning"],"keywords":["drug discovery","Machine Learning","Molecular Dynamics Simulations","Allosteric Sites","Allosteric Communication"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-02T03:29:31.966744Z","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":[]}