Publication Information

{'id': 'https://openalex.org/W2158338599', 'doi': 'https://doi.org/10.1093/bioinformatics/btg237', 'title': 'Characterizing proteolytic cleavage site activity using bio-basis function neural networks', 'display_name': 'Characterizing proteolytic cleavage site activity using bio-basis function neural networks', 'publication_year': 2003, 'publication_date': '2003-09-22', 'ids': {'openalex': 'https://openalex.org/W2158338599', 'doi': 'https://doi.org/10.1093/bioinformatics/btg237', 'mag': '2158338599', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/14512344'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/btg237', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/19/14/1741/679282/btg237.pdf', 'source': {'id': 'https://openalex.org/S52395412', 'display_name': 'Bioinformatics', 'issn_l': '1367-4803', 'issn': ['1367-4803', '1367-4811'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'type': 'article', 'type_crossref': 'journal-article', 'indexed_in': ['crossref', 'pubmed'], 'open_access': {'is_oa': True, 'oa_status': 'bronze', 'oa_url': 'https://academic.oup.com/bioinformatics/article-pdf/19/14/1741/679282/btg237.pdf', 'any_repository_has_fulltext': False}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5007464420', 'display_name': 'Rebecca Thomson', 'orcid': None}, 'institutions': [{'id': 'https://openalex.org/I40120149', 'display_name': 'University of Oxford', 'ror': 'https://ror.org/052gg0110', 'country_code': 'GB', 'type': 'education', 'lineage': ['https://openalex.org/I40120149']}], 'countries': ['GB'], 'is_corresponding': False, 'raw_author_name': 'Rebecca Thomson', 'raw_affiliation_strings': ['Department of Structure Biology, Oxford University, UK.'], 'affiliations': [{'raw_affiliation_string': 'Department of Structure Biology, Oxford University, UK.', 'institution_ids': ['https://openalex.org/I40120149']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5051248114', 'display_name': 'Charlie Hodgman', 'orcid': 'https://orcid.org/0000-0001-5862-8296'}, 'institutions': [], 'countries': [], 'is_corresponding': False, 'raw_author_name': 'T. Charles Hodgman', 'raw_affiliation_strings': [], 'affiliations': []}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5101837304', 'display_name': 'Zheng Rong Yang', 'orcid': 'https://orcid.org/0000-0002-6733-7893'}, 'institutions': [{'id': 'https://openalex.org/I23923803', 'display_name': 'University of Exeter', 'ror': 'https://ror.org/03yghzc09', 'country_code': 'GB', 'type': 'education', 'lineage': ['https://openalex.org/I23923803']}], 'countries': ['GB'], 'is_corresponding': False, 'raw_author_name': 'Zheng Rong Yang', 'raw_affiliation_strings': ['University of Exeter;'], 'affiliations': [{'raw_affiliation_string': 'University of Exeter;', 'institution_ids': ['https://openalex.org/I23923803']}]}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5071446829', 'display_name': 'Austin K. Doyle', 'orcid': None}, 'institutions': [], 'countries': [], 'is_corresponding': False, 'raw_author_name': 'Austin K. Doyle', 'raw_affiliation_strings': [], 'affiliations': []}], 'institution_assertions': [], 'countries_distinct_count': 1, 'institutions_distinct_count': 2, 'corresponding_author_ids': [], 'corresponding_institution_ids': [], 'apc_list': {'value': 3618, 'currency': 'USD', 'value_usd': 3618, 'provenance': 'doaj'}, 'apc_paid': None, 'fwci': 3.97, 'has_fulltext': True, 'fulltext_origin': 'ngrams', 'cited_by_count': 86, 'citation_normalized_percentile': {'value': 0.722178, 'is_in_top_1_percent': False, 'is_in_top_10_percent': False}, 'cited_by_percentile_year': {'min': 95, 'max': 96}, 'biblio': {'volume': '19', 'issue': '14', 'first_page': '1741', 'last_page': '1747'}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T12254', 'display_name': 'Machine Learning in Bioinformatics', 'score': 0.9993, 'subfield': {'id': 'https://openalex.org/subfields/1312', 'display_name': 'Molecular Biology'}, 'field': {'id': 'https://openalex.org/fields/13', 'display_name': 'Biochemistry, Genetics and Molecular Biology'}, 'domain': {'id': 'https://openalex.org/domains/1', 'display_name': 'Life Sciences'}}, 'topics': [{'id': 'https://openalex.org/T12254', 'display_name': 'Machine Learning in Bioinformatics', 'score': 0.9993, 'subfield': {'id': 'https://openalex.org/subfields/1312', 'display_name': 'Molecular Biology'}, 'field': {'id': 'https://openalex.org/fields/13', 'display_name': 'Biochemistry, Genetics and Molecular Biology'}, 'domain': {'id': 'https://openalex.org/domains/1', 'display_name': 'Life Sciences'}}, {'id': 'https://openalex.org/T10519', 'display_name': 'Advanced Proteomics Techniques and Applications', 'score': 0.9926, 'subfield': {'id': 'https://openalex.org/subfields/1607', 'display_name': 'Spectroscopy'}, 'field': {'id': 'https://openalex.org/fields/16', 'display_name': 'Chemistry'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}, {'id': 'https://openalex.org/T10044', 'display_name': 'Protein Structure and Dynamics', 'score': 0.9809, 'subfield': {'id': 'https://openalex.org/subfields/1312', 'display_name': 'Molecular Biology'}, 'field': {'id': 'https://openalex.org/fields/13', 'display_name': 'Biochemistry, Genetics and Molecular Biology'}, 'domain': {'id': 'https://openalex.org/domains/1', 'display_name': 'Life Sciences'}}], 'keywords': [{'id': 'https://openalex.org/keywords/cleavage', 'display_name': 'Cleavage (geology)', 'score': 0.7781985}, {'id': 'https://openalex.org/keywords/robustness', 'display_name': 'Robustness', 'score': 0.4990282}], 'concepts': [{'id': 'https://openalex.org/C175156509', 'wikidata': 'https://www.wikidata.org/wiki/Q1990218', 'display_name': 'Cleavage (geology)', 'level': 3, 'score': 0.7781985}, {'id': 'https://openalex.org/C2776714187', 'wikidata': 'https://www.wikidata.org/wiki/Q212410', 'display_name': 'Protease', 'level': 3, 'score': 0.6137076}, {'id': 'https://openalex.org/C50644808', 'wikidata': 'https://www.wikidata.org/wiki/Q192776', 'display_name': 'Artificial neural network', 'level': 2, 'score': 0.56532663}, {'id': 'https://openalex.org/C63479239', 'wikidata': 'https://www.wikidata.org/wiki/Q7353546', 'display_name': 'Robustness (evolution)', 'level': 3, 'score': 0.4990282}, {'id': 'https://openalex.org/C70721500', 'wikidata': 'https://www.wikidata.org/wiki/Q177005', 'display_name': 'Computational biology', 'level': 1, 'score': 0.48724833}, {'id': 'https://openalex.org/C41008148', 'wikidata': 'https://www.wikidata.org/wiki/Q21198', 'display_name': 'Computer science', 'level': 0, 'score': 0.48154905}, {'id': 'https://openalex.org/C2780340462', 'wikidata': 'https://www.wikidata.org/wiki/Q127450', 'display_name': 'Trypsin', 'level': 3, 'score': 0.43107542}, {'id': 'https://openalex.org/C154945302', 'wikidata': 'https://www.wikidata.org/wiki/Q11660', 'display_name': 'Artificial intelligence', 'level': 1, 'score': 0.389811}, {'id': 'https://openalex.org/C185592680', 'wikidata': 'https://www.wikidata.org/wiki/Q2329', 'display_name': 'Chemistry', 'level': 0, 'score': 0.35358122}, {'id': 'https://openalex.org/C186060115', 'wikidata': 'https://www.wikidata.org/wiki/Q30336093', 'display_name': 'Biological system', 'level': 1, 'score': 0.3424468}, {'id': 'https://openalex.org/C119857082', 'wikidata': 'https://www.wikidata.org/wiki/Q2539', 'display_name': 'Machine learning', 'level': 1, 'score': 0.34140837}, {'id': 'https://openalex.org/C55493867', 'wikidata': 'https://www.wikidata.org/wiki/Q7094', 'display_name': 'Biochemistry', 'level': 1, 'score': 0.28794086}, {'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.2847916}, {'id': 'https://openalex.org/C181199279', 'wikidata': 'https://www.wikidata.org/wiki/Q8047', 'display_name': 'Enzyme', 'level': 2, 'score': 0.15265119}, {'id': 'https://openalex.org/C151730666', 'wikidata': 'https://www.wikidata.org/wiki/Q7205', 'display_name': 'Paleontology', 'level': 1, 'score': 0.0}, {'id': 'https://openalex.org/C43369102', 'wikidata': 'https://www.wikidata.org/wiki/Q2307625', 'display_name': 'Fracture (geology)', 'level': 2, 'score': 0.0}, {'id': 'https://openalex.org/C104317684', 'wikidata': 'https://www.wikidata.org/wiki/Q7187', 'display_name': 'Gene', 'level': 2, 'score': 0.0}], 'mesh': [{'descriptor_ui': 'D009415', 'descriptor_name': 'Nerve Net', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D010446', 'descriptor_name': 'Peptide Fragments', 'qualifier_ui': 'Q000737', 'qualifier_name': 'chemistry', 'is_major_topic': True}, {'descriptor_ui': 'D010447', 'descriptor_name': 'Peptide Hydrolases', 'qualifier_ui': 'Q000145', 'qualifier_name': 'classification', 'is_major_topic': True}, {'descriptor_ui': 'D010447', 'descriptor_name': 'Peptide Hydrolases', 'qualifier_ui': 'Q000737', 'qualifier_name': 'chemistry', 'is_major_topic': True}, {'descriptor_ui': 'D016415', 'descriptor_name': 'Sequence Alignment', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D020539', 'descriptor_name': 'Sequence Analysis, Protein', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D000595', 'descriptor_name': 'Amino Acid Sequence', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D001665', 'descriptor_name': 'Binding Sites', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D016000', 'descriptor_name': 'Cluster Analysis', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D030562', 'descriptor_name': 'Databases, Protein', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D004789', 'descriptor_name': 'Enzyme Activation', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D016333', 'descriptor_name': 'HIV Protease', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D016333', 'descriptor_name': 'HIV Protease', 'qualifier_ui': 'Q000737', 'qualifier_name': 'chemistry', 'is_major_topic': False}, {'descriptor_ui': 'D006868', 'descriptor_name': 'Hydrolysis', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D008969', 'descriptor_name': 'Molecular Sequence Data', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D010363', 'descriptor_name': 'Pattern Recognition, Automated', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D010446', 'descriptor_name': 'Peptide Fragments', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D010447', 'descriptor_name': 'Peptide Hydrolases', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D015203', 'descriptor_name': 'Reproducibility of Results', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D012680', 'descriptor_name': 'Sensitivity and Specificity', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D016415', 'descriptor_name': 'Sequence Alignment', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D020539', 'descriptor_name': 'Sequence Analysis, Protein', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D014357', 'descriptor_name': 'Trypsin', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D014357', 'descriptor_name': 'Trypsin', 'qualifier_ui': 'Q000737', 'qualifier_name': 'chemistry', 'is_major_topic': False}], 'locations_count': 2, 'locations': [{'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/btg237', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/19/14/1741/679282/btg237.pdf', 'source': {'id': 'https://openalex.org/S52395412', 'display_name': 'Bioinformatics', 'issn_l': '1367-4803', 'issn': ['1367-4803', '1367-4811'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/14512344', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S4306525036', 'display_name': 'PubMed', 'issn_l': None, 'issn': None, 'is_oa': False, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1299303238', 'host_organization_name': 'National Institutes of Health', 'host_organization_lineage': ['https://openalex.org/I1299303238'], 'host_organization_lineage_names': ['National Institutes of Health'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': None, 'is_accepted': False, 'is_published': False}], 'best_oa_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/btg237', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/19/14/1741/679282/btg237.pdf', 'source': {'id': 'https://openalex.org/S52395412', 'display_name': 'Bioinformatics', 'issn_l': '1367-4803', 'issn': ['1367-4803', '1367-4811'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'sustainable_development_goals': [{'score': 0.77, 'display_name': 'Good health and well-being', 'id': 'https://metadata.un.org/sdg/3'}], 'grants': [], 'datasets': [], 'versions': [], 'referenced_works_count': 24, 'referenced_works': ['https://openalex.org/W1485790693', 'https://openalex.org/W1514209943', 'https://openalex.org/W1567730256', 'https://openalex.org/W1981555301', 'https://openalex.org/W1985917720', 'https://openalex.org/W1986962105', 'https://openalex.org/W1987713050', 'https://openalex.org/W1990376815', 'https://openalex.org/W1991848143', 'https://openalex.org/W2013710989', 'https://openalex.org/W2030636556', 'https://openalex.org/W2043551626', 'https://openalex.org/W2045722009', 'https://openalex.org/W2053702224', 'https://openalex.org/W2064684862', 'https://openalex.org/W2073040712', 'https://openalex.org/W2087946919', 'https://openalex.org/W2119423166', 'https://openalex.org/W2122642866', 'https://openalex.org/W2140701212', 'https://openalex.org/W2156798505', 'https://openalex.org/W2158461363', 'https://openalex.org/W3017143921', 'https://openalex.org/W569561726'], 'related_works': ['https://openalex.org/W3189975923', 'https://openalex.org/W2466016252', 'https://openalex.org/W2318999255', 'https://openalex.org/W2156260160', 'https://openalex.org/W2088359450', 'https://openalex.org/W2025544676', 'https://openalex.org/W2021163071', 'https://openalex.org/W2011561549', 'https://openalex.org/W1971704222', 'https://openalex.org/W1586031216'], 'abstract_inverted_index': {'Abstract': [0], 'Motivation:': [1], 'In': [2], 'protein': [3, 19], 'chemistry,': [4], 'proteomics': [5], 'and': [6, 78, 108, 131, 137, 149, 160], 'biopharmaceutical': [7], 'development,': [8], 'there': [9], 'is': [10, 20, 122], 'a': [11, 18, 23], 'desire': [12], 'to': [13, 128, 155], 'know': [14], 'not': [15, 52], 'only': [16], 'where': [17], 'cleaved': [21], 'by': [22], 'protease,': [24], 'but': [25], 'also': [26], 'the': [27, 79, 94, 104, 110, 129, 138], 'susceptibility': [28], 'of': [29, 81, 96, 133, 140], 'its': [30], 'cleavage': [31, 38, 64, 135, 143], 'sites.': [32, 144], 'The': [33, 91, 100], 'current': [34], 'tools': [35], 'for': [36, 61, 87, 113, 147], 'proteolytic': [37, 63, 98], 'prediction': [39, 77, 107, 121, 130, 139], 'have': [40], 'often': [41], 'relied': [42], 'purely': [43], 'on': [44], 'regular': [45], 'expressions,': [46], 'or': [47], 'involve': [48], 'models': [49], 'that': [50, 118], 'do': [51], 'represent': [53], 'biological': [54], 'data': [55, 150], 'well.': [56], 'Results:': [57], 'A': [58], 'novel': [59], 'methodology': [60, 127], 'characterizing': [62], 'site': [65], 'activities': [66], 'has': [67], 'been': [68], 'developed,': [69], 'which': [70], 'incorporates': [71], 'two': [72], 'fundamental': [73], 'features:': [74], 'activity': [75, 119], 'class': [76, 120], 'use': [80], 'an': [82], 'amino': [83], 'acid': [84], 'similarity': [85], 'matrix': [86], '(non-parametric)': [88], 'neural': [89], 'learning.': [90, 114], 'first': [92], 'solved': [93], 'problem': [95], 'predicting': [97], 'efficiency.': [99], 'second': [101], 'significantly': [102], 'improved': [103], 'robustness': [105], 'in': [106], 'reduced': [109], 'time': [111], 'complexity': [112], 'This': [115], 'study': [116], 'shows': [117], 'successful': [123], 'when': [124], 'applying': [125], 'this': [126], 'characterization': [132], 'Trypsin': [134], 'sites': [136], 'HIV': [141], 'protease': [142], 'Availability:': [145], 'Requests': [146], 'software': [148], 'should': [151], 'be': [152], 'made': [153], 'respectively': [154], 'Dr': [156], 'Zheng': [157], 'Rong': [158], 'Yang': [159], 'Miss': [161], 'Rebecca': [162], 'Thomson.': [163]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2158338599', 'counts_by_year': [{'year': 2021, 'cited_by_count': 3}, {'year': 2020, 'cited_by_count': 1}, {'year': 2019, 'cited_by_count': 1}, {'year': 2014, 'cited_by_count': 7}, {'year': 2013, 'cited_by_count': 1}, {'year': 2012, 'cited_by_count': 3}], 'updated_date': '2024-12-13T16:33:18.438075', 'created_date': '2016-06-24'}