{"doi":"10.1007/s10969-012-9126-6","title":"Structure- and sequence-based function prediction for non-homologous proteins","abstract":null,"journal":"Journal of Structural and Functional Genomics","year":2012,"id":67970,"datarank":1.20474719833543,"base_score":3.5553480614894135,"endowment":3.5553480614894135,"self_citation_contribution":0.5333022092234121,"citation_network_contribution":0.671444989112018,"self_endowment_contribution":0.5333022092234121,"citer_contribution":0.671444989112018,"corpus_percentile":null,"corpus_rank":null,"citation_count":34,"citer_count":26,"citers_with_citation_signal":19,"citers_with_endowment":19,"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":360512,"name":"Meghana Chitale","orcid":null,"position":1,"is_corresponding":false},{"id":122308,"name":"Daisuke Kihara","orcid":null,"position":2,"is_corresponding":false},{"id":360511,"name":"Lee Sael","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Structure- and sequence-based function prediction for non-homologous proteins","abstract":"The structural genomics projects have been accumulating an increasing number of protein structures, many of which remain functionally unknown. In parallel effort to experimental methods, computational methods are expected to make a significant contribution for functional elucidation of such proteins. However, conventional computational methods that transfer functions from homologous proteins do not help much for these uncharacterized protein structures because they do not have apparent structural or sequence similarity with the known proteins. Here, we briefly review two avenues of computational function prediction methods, i.e. structure-based methods and sequence-based methods. The focus is on our recent developments of local structure-based and sequence-based methods, which can effectively extract function information from distantly related proteins. Two structure-based methods, Pocket-Surfer and Patch-Surfer, identify similar known ligand binding sites for pocket regions in a query protein without using global protein fold similarity information. Two sequence-based methods, protein function prediction and extended similarity group, make use of weakly similar sequences that are conventionally discarded in homology based function annotation. Combined together with experimental methods we hope that computational methods will make leading contribution in functional elucidation of the protein structures.","is_dataset_classified":null,"base_score":3.5553480614894135,"endowment":3.5553480614894135,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"22270458","pmcid":"PMC3375349","openalex_id":"https://openalex.org/W2149355317","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"R01GM097528","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM075004","title":null},{"funder_name":"National Institutes of Health","grant_id":"5R01GM075004-04","title":"Surface Shape Based Screening of Large Protein Databases"},{"funder_name":"National Science Foundation","grant_id":"0915801","title":"III: Small: Quality Assessment of Computational Protein Models"},{"funder_name":"National Science Foundation","grant_id":"0850009","title":"Template-Based Protein Structure Prediction Beyond Sequence Homology"},{"funder_name":"National Institutes of Health","grant_id":"5R01GM097528-02","title":"Identification of protein-metabolite interactome."},{"funder_name":"National Science Foundation","grant_id":"0800568","title":"Information Transfer in Biological Systems"}],"total_grants":7,"fwci":2.3836,"citation_percentile":0.89185458,"influential_citations":1,"citation_trend":[{"year":2012,"count":4},{"year":2013,"count":6},{"year":2014,"count":4},{"year":2015,"count":4},{"year":2016,"count":1},{"year":2017,"count":2},{"year":2018,"count":3},{"year":2020,"count":3},{"year":2022,"count":4},{"year":2024,"count":2},{"year":2026,"count":1}],"oa_status":"closed","license":"Springer TDM","oa_locations":[{"url":"https://europepmc.org/articles/pmc3375349?pdf=render","host_type":"GREEN"},{"url":"http://link.springer.com/content/pdf/10.1007/s10969-012-9126-6.pdf","host_type":"publisher"},{"url":"http://link.springer.com/article/10.1007/s10969-012-9126-6/fulltext.html","host_type":"publisher"},{"url":"http://link.springer.com/content/pdf/10.1007/s10969-012-9126-6","host_type":"publisher"},{"url":"https://doi.org/10.1007/s10969-012-9126-6","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/22270458","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3375349","host_type":"repository"},{"url":"https://dx.doi.org/10.1007/s10969-012-9126-6","host_type":""}],"fields_of_study":["Protein Structure and Dynamics","Computational Drug Discovery Methods","Machine Learning in Bioinformatics","Biology","Medicine","Computer Science","0301 basic medicine","0303 health sciences","03 medical and health sciences","Algorithms","Binding Sites","Computational Biology","Databases, Protein","Internet","Molecular Sequence Annotation","Protein Conformation","Proteins","Reproducibility of Results","Sequence Analysis, Protein","Sequence Homology, Amino Acid","Software","Structure-Activity Relationship"],"mesh_terms":["Algorithms","Binding Sites","Protein Conformation","Proteins","Software","Structure-Activity Relationship","Reproducibility of Results","Sequence Homology, Amino Acid","Computational Biology","Internet","Sequence Analysis, Protein","Databases, Protein","Molecular Sequence Annotation"],"keywords":["Structural genomics","Computational biology","Protein function prediction","Protein structure database","Protein superfamily","Sequence (biology)","Homology modeling","Similarity (geometry)","Sequence alignment","Structural alignment","Function (biology)","Protein structure","Protein sequencing","Threading (protein sequence)","Structural similarity","Homology (biology)","Biology","Computer science","Peptide sequence","Protein function","Genetics","Artificial intelligence","Sequence database","Gene","Biochemistry","Image (mathematics)","Internet","Binding Sites","Sequence Homology, Amino Acid","Protein Conformation","Proteins","Reproducibility of Results","Molecular Sequence Annotation","Structure-Activity Relationship","Sequence Analysis, Protein","Databases, Protein","Algorithms","Software"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"go"},{"name":"uniprot"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-18T21:28:47.275070Z","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":[]}