{"doi":"10.1007/978-1-0716-4662-5_6","title":"A Survey of Current Status in AI-Based Topology Prediction of Transmembrane Proteins","abstract":null,"journal":"Methods in Molecular Biology","year":2025,"id":651698,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"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":1051928,"name":"Richa Mishra","orcid":"0000-0002-1173-8962","position":1,"is_corresponding":false},{"id":901737,"name":"Shandar Ahmad","orcid":"0000-0002-7287-305X","position":2,"is_corresponding":false},{"id":1699764,"name":"Divyangana Bathla","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"A Survey of Current Status in AI-Based Topology Prediction of Transmembrane Proteins","abstract":"Most of the sequence-based structure prediction and experimental structure determination research have been focused on soluble proteins, with relatively less attention paid to the transmembrane proteins. With the availability of high-quality methods for the structure prediction of the soluble proteins, there is a need to fill the gaps for the prediction of transmembrane proteins, motivated by the fact that they are the primary targets of many drug design efforts. We provide a systematic survey of machine learning methods that predict various aspects of topological properties of transmembrane proteins, including helical and beta-barrel proteins. We reveal that despite a smaller number of unique solved structures for this group of proteins, a battery of corresponding algorithms has been developed. These algorithms offer various degrees of accuracy which needs further improvements. We present a case study to illustrate a typical predictive scenario that shows that the available prediction methods may produce somewhat different results and we discuss how to deal with situations like this.","is_dataset_classified":null,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"40728610","pmcid":null,"openalex_id":"https://openalex.org/W4412708798","authors":[],"funders":[],"total_grants":0,"fwci":7.6301,"citation_percentile":0.97035195,"influential_citations":0,"citation_trend":[{"year":2026,"count":2}],"oa_status":"closed","license":null,"oa_locations":[{"url":"https://doi.org/10.1007/978-1-0716-4662-5_6","host_type":"book series"},{"url":"https://pubmed.ncbi.nlm.nih.gov/40728610","host_type":"repository"}],"fields_of_study":["Machine Learning in Bioinformatics","Protein Structure and Dynamics","RNA and protein synthesis mechanisms"],"mesh_terms":["Machine Learning","Algorithms","Humans","Membrane Proteins","Models, Molecular","Protein Conformation","Computational Biology","Databases, Protein"],"keywords":["Current (fluid)","Topology (electrical circuits)","Membrane topology","Transmembrane protein","Computer science","Mathematics","Biology","Engineering","Electrical engineering","Genetics","Combinatorics","Machine Learning","Transmembrane Proteins","Topology Prediction","Helical Membrane Proteins","Beta-barrel Membrane Proteins","Sequence-based Predictions"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-10T10:25:17.419858Z","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":[]}