Get quick answers to your questions about the article from our AI researcher chatbot
{'id': 'https://openalex.org/W2162797705', 'doi': 'https://doi.org/10.1186/1471-2105-12-170', 'title': 'Objective identification of residue ranges for the superposition of protein structures', 'display_name': 'Objective identification of residue ranges for the superposition of protein structures', 'publication_year': 2011, 'publication_date': '2011-05-18', 'ids': {'openalex': 'https://openalex.org/W2162797705', 'doi': 'https://doi.org/10.1186/1471-2105-12-170', 'mag': '2162797705', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/21592348', 'pmcid': 'https://www.ncbi.nlm.nih.gov/pmc/articles/3120703'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1186/1471-2105-12-170', 'pdf_url': 'https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-170', 'source': {'id': 'https://openalex.org/S19032547', 'display_name': 'BMC Bioinformatics', 'issn_l': '1471-2105', 'issn': ['1471-2105'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310320256', 'host_organization_name': 'BioMed Central', 'host_organization_lineage': ['https://openalex.org/P4310319965', 'https://openalex.org/P4310320256'], 'host_organization_lineage_names': ['Springer Nature', 'BioMed Central'], 'type': 'journal'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'type': 'article', 'type_crossref': 'journal-article', 'indexed_in': ['crossref', 'doaj', 'pubmed'], 'open_access': {'is_oa': True, 'oa_status': 'gold', 'oa_url': 'https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-170', 'any_repository_has_fulltext': True}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5090106428', 'display_name': 'Donata K. Kirchner', 'orcid': None}, 'institutions': [{'id': 'https://openalex.org/I114090438', 'display_name': 'Goethe University Frankfurt', 'ror': 'https://ror.org/04cvxnb49', 'country_code': 'DE', 'type': 'education', 'lineage': ['https://openalex.org/I114090438']}, {'id': 'https://openalex.org/I2801628138', 'display_name': 'Frankfurt Institute for Advanced Studies', 'ror': 'https://ror.org/05vmv8m79', 'country_code': 'DE', 'type': 'facility', 'lineage': ['https://openalex.org/I2801628138']}], 'countries': ['DE'], 'is_corresponding': False, 'raw_author_name': 'Donata K Kirchner', 'raw_affiliation_strings': ['Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany'], 'affiliations': [{'raw_affiliation_string': 'Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany', 'institution_ids': ['https://openalex.org/I114090438', 'https://openalex.org/I2801628138']}]}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5059078778', 'display_name': 'Peter Güntert', 'orcid': 'https://orcid.org/0000-0002-2911-7574'}, 'institutions': [{'id': 'https://openalex.org/I2801628138', 'display_name': 'Frankfurt Institute for Advanced Studies', 'ror': 'https://ror.org/05vmv8m79', 'country_code': 'DE', 'type': 'facility', 'lineage': ['https://openalex.org/I2801628138']}, {'id': 'https://openalex.org/I114090438', 'display_name': 'Goethe University Frankfurt', 'ror': 'https://ror.org/04cvxnb49', 'country_code': 'DE', 'type': 'education', 'lineage': ['https://openalex.org/I114090438']}], 'countries': ['DE'], 'is_corresponding': False, 'raw_author_name': 'Peter Güntert', 'raw_affiliation_strings': ['Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany'], 'affiliations': [{'raw_affiliation_string': 'Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany', 'institution_ids': ['https://openalex.org/I2801628138', 'https://openalex.org/I114090438']}]}], 'institution_assertions': [], 'countries_distinct_count': 1, 'institutions_distinct_count': 2, 'corresponding_author_ids': [], 'corresponding_institution_ids': [], 'apc_list': {'value': 1690, 'currency': 'GBP', 'value_usd': 2072, 'provenance': 'doaj'}, 'apc_paid': {'value': 1690, 'currency': 'GBP', 'value_usd': 2072, 'provenance': 'doaj'}, 'fwci': 1.428, 'has_fulltext': True, 'fulltext_origin': 'ngrams', 'cited_by_count': 58, 'citation_normalized_percentile': {'value': 0.836714, 'is_in_top_1_percent': False, 'is_in_top_10_percent': False}, 'cited_by_percentile_year': {'min': 95, 'max': 96}, 'biblio': {'volume': '12', 'issue': '1', 'first_page': None, 'last_page': None}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T10044', 'display_name': 'Protein Structure and Dynamics', 'score': 0.9998, '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/T10044', 'display_name': 'Protein Structure and Dynamics', 'score': 0.9998, '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/T11162', 'display_name': 'Enzyme Structure and Function', 'score': 0.9989, 'subfield': {'id': 'https://openalex.org/subfields/2505', 'display_name': 'Materials Chemistry'}, 'field': {'id': 'https://openalex.org/fields/25', 'display_name': 'Materials Science'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}, {'id': 'https://openalex.org/T10932', 'display_name': 'Microbial Metabolic Engineering and Bioproduction', 'score': 0.9793, '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/residue', 'display_name': 'Residue (chemistry)', 'score': 0.7660476}], 'concepts': [{'id': 'https://openalex.org/C2781338088', 'wikidata': 'https://www.wikidata.org/wiki/Q903495', 'display_name': 'Residue (chemistry)', 'level': 2, 'score': 0.7660476}, {'id': 'https://openalex.org/C47701112', 'wikidata': 'https://www.wikidata.org/wiki/Q735188', 'display_name': 'Protein structure', 'level': 2, 'score': 0.58081764}, {'id': 'https://openalex.org/C186060115', 'wikidata': 'https://www.wikidata.org/wiki/Q30336093', 'display_name': 'Biological system', 'level': 1, 'score': 0.5583084}, {'id': 'https://openalex.org/C2994376932', 'wikidata': 'https://www.wikidata.org/wiki/Q735188', 'display_name': 'Amino acid residue', 'level': 4, 'score': 0.55710256}, {'id': 'https://openalex.org/C27753989', 'wikidata': 'https://www.wikidata.org/wiki/Q284885', 'display_name': 'Superposition principle', 'level': 2, 'score': 0.53108466}, {'id': 'https://openalex.org/C185592680', 'wikidata': 'https://www.wikidata.org/wiki/Q2329', 'display_name': 'Chemistry', 'level': 0, 'score': 0.40115643}, {'id': 'https://openalex.org/C11413529', 'wikidata': 'https://www.wikidata.org/wiki/Q8366', 'display_name': 'Algorithm', 'level': 1, 'score': 0.34383965}, {'id': 'https://openalex.org/C33923547', 'wikidata': 'https://www.wikidata.org/wiki/Q395', 'display_name': 'Mathematics', 'level': 0, 'score': 0.32135788}, {'id': 'https://openalex.org/C167625842', 'wikidata': 'https://www.wikidata.org/wiki/Q899763', 'display_name': 'Peptide sequence', 'level': 3, 'score': 0.2262286}, {'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.18939924}, {'id': 'https://openalex.org/C55493867', 'wikidata': 'https://www.wikidata.org/wiki/Q7094', 'display_name': 'Biochemistry', 'level': 1, 'score': 0.16103065}, {'id': 'https://openalex.org/C134306372', 'wikidata': 'https://www.wikidata.org/wiki/Q7754', 'display_name': 'Mathematical analysis', 'level': 1, 'score': 0.08210719}, {'id': 'https://openalex.org/C104317684', 'wikidata': 'https://www.wikidata.org/wiki/Q7187', 'display_name': 'Gene', 'level': 2, 'score': 0.0}], 'mesh': [{'descriptor_ui': 'D000465', 'descriptor_name': 'Algorithms', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D011506', 'descriptor_name': 'Proteins', 'qualifier_ui': 'Q000737', 'qualifier_name': 'chemistry', 'is_major_topic': True}, {'descriptor_ui': 'D040681', 'descriptor_name': 'Structural Homology, Protein', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D000818', 'descriptor_name': 'Animals', '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': 'D006801', 'descriptor_name': 'Humans', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D008958', 'descriptor_name': 'Models, Molecular', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D019906', 'descriptor_name': 'Nuclear Magnetic Resonance, Biomolecular', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D017434', 'descriptor_name': 'Protein Structure, Tertiary', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D011506', 'descriptor_name': 'Proteins', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}], 'locations_count': 4, 'locations': [{'is_oa': True, 'landing_page_url': 'https://doi.org/10.1186/1471-2105-12-170', 'pdf_url': 'https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-170', 'source': {'id': 'https://openalex.org/S19032547', 'display_name': 'BMC Bioinformatics', 'issn_l': '1471-2105', 'issn': ['1471-2105'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310320256', 'host_organization_name': 'BioMed Central', 'host_organization_lineage': ['https://openalex.org/P4310319965', 'https://openalex.org/P4310320256'], 'host_organization_lineage_names': ['Springer Nature', 'BioMed Central'], 'type': 'journal'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': False, 'landing_page_url': 'https://doaj.org/article/f0a5d3b73d214f22affef2c10ce80f02', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S4306401280', 'display_name': 'DOAJ (DOAJ: Directory of Open Access Journals)', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': None, 'host_organization_name': None, 'host_organization_lineage': [], 'host_organization_lineage_names': [], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': None, 'is_accepted': False, 'is_published': False}, {'is_oa': True, 'landing_page_url': 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120703', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S2764455111', 'display_name': 'PubMed Central', 'issn_l': None, 'issn': None, 'is_oa': True, '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': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/21592348', '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/10.1186/1471-2105-12-170', 'pdf_url': 'https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-170', 'source': {'id': 'https://openalex.org/S19032547', 'display_name': 'BMC Bioinformatics', 'issn_l': '1471-2105', 'issn': ['1471-2105'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310320256', 'host_organization_name': 'BioMed Central', 'host_organization_lineage': ['https://openalex.org/P4310319965', 'https://openalex.org/P4310320256'], 'host_organization_lineage_names': ['Springer Nature', 'BioMed Central'], 'type': 'journal'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'sustainable_development_goals': [], 'grants': [], 'datasets': [], 'versions': [], 'referenced_works_count': 39, 'referenced_works': ['https://openalex.org/W1520784216', 'https://openalex.org/W1975459052', 'https://openalex.org/W1976132022', 'https://openalex.org/W1980017556', 'https://openalex.org/W1982819689', 'https://openalex.org/W1991285104', 'https://openalex.org/W1991518782', 'https://openalex.org/W1997262127', 'https://openalex.org/W1998512003', 'https://openalex.org/W2002195659', 'https://openalex.org/W2005008560', 'https://openalex.org/W2014418975', 'https://openalex.org/W2039665187', 'https://openalex.org/W2040045256', 'https://openalex.org/W2052933818', 'https://openalex.org/W2066637007', 'https://openalex.org/W2077743314', 'https://openalex.org/W2087500715', 'https://openalex.org/W2088347357', 'https://openalex.org/W2088933990', 'https://openalex.org/W2089043814', 'https://openalex.org/W2098164044', 'https://openalex.org/W2098613471', 'https://openalex.org/W2099324237', 'https://openalex.org/W2099646325', 'https://openalex.org/W2110483430', 'https://openalex.org/W2113301165', 'https://openalex.org/W2115295332', 'https://openalex.org/W2122339645', 'https://openalex.org/W2125760879', 'https://openalex.org/W2130479394', 'https://openalex.org/W2130696395', 'https://openalex.org/W2133283923', 'https://openalex.org/W2134358906', 'https://openalex.org/W2143189872', 'https://openalex.org/W2148439328', 'https://openalex.org/W2158749319', 'https://openalex.org/W2248142141', 'https://openalex.org/W2409784569'], 'related_works': ['https://openalex.org/W4252717782', 'https://openalex.org/W2465762825', 'https://openalex.org/W2395372183', 'https://openalex.org/W2256296280', 'https://openalex.org/W2254984054', 'https://openalex.org/W2088383935', 'https://openalex.org/W2081626841', 'https://openalex.org/W2068251981', 'https://openalex.org/W1989778206', 'https://openalex.org/W1984061674'], 'abstract_inverted_index': {'The': [0, 84, 247, 271], 'automation': [1], 'of': [2, 42, 48, 71, 126, 169, 181, 192, 219, 226, 252, 260, 268, 290, 306, 321, 347, 353], 'objectively': [3], 'selecting': [4], 'amino': [5, 62], 'acid': [6, 63], 'residue': [7, 31, 43, 64, 99, 196, 236, 255, 284, 309, 348], 'ranges': [8, 32, 44, 65, 100, 118, 145, 197, 237, 256, 285, 300, 310, 349], 'for': [9, 14, 28, 33, 60, 66, 76, 163, 189, 216, 238, 257, 264, 343, 350], 'structure': [10, 19, 77, 82, 108, 230, 262, 278], 'superpositions': [11, 279], 'is': [12, 24, 86, 205, 250], 'important': [13], 'meaningful': [15], 'and': [16, 57, 69, 114, 160, 222, 293, 316, 340], 'consistent': [17], 'protein': [18, 36, 72, 115, 128, 229, 261, 269, 354], 'analyses.': [20], 'So': [21], 'far': [22], 'there': [23], 'no': [25], 'widely-used': [26], 'standard': [27], 'choosing': [29], 'these': [30], 'experimentally': [34], 'determined': [35, 147], 'structures,': [37, 73], 'where': [38], 'the': [39, 46, 67, 141, 156, 166, 178, 182, 190, 243, 258, 282, 291, 298, 304, 308, 322, 332, 345, 351], 'manual': [40], 'selection': [41], 'or': [45], 'use': [47], 'suboptimal': [49], 'criteria': [50], 'remain': [51], 'commonplace.': [52], 'We': [53, 233], 'present': [54], 'an': [55, 89, 338], 'automated': [56], 'objective': [58, 339], 'method': [59, 85, 249, 272, 342], 'finding': [61], 'superposition': [68, 259, 352], 'analysis': [70], 'in': [74, 88, 101, 140, 198, 242], 'particular': [75], 'bundles': [78, 263], 'resulting': [79], 'from': [80, 311, 326], 'NMR': [81, 240], 'calculations.': [83], 'implemented': [87], 'algorithm,': [90], 'CYRANGE,': [91], 'that': [92, 130, 204], 'yields,': [93], 'without': [94, 329], 'protein-specific': [95], 'parameter': [96], 'adjustment,': [97], 'appropriate': [98], 'most': [102], 'commonly': [103, 227], 'occurring': [104], 'situations,': [105], 'including': [106], 'low-precision': [107], 'bundles,': [109], 'multi-domain': [110], 'proteins,': [111], 'symmetric': [112], 'multimers,': [113], 'complexes.': [116], 'Residue': [117, 144], 'are': [119, 146, 214, 301], 'chosen': [120], 'to': [121, 136, 200], 'comprise': [122], 'as': [123, 206, 208], 'many': [124], 'residues': [125, 151, 170, 173], 'a': [127, 137, 202, 217, 265, 287], 'domain': [129, 165], 'increasing': [131, 331], 'their': [132], 'number': [133], 'would': [134], 'lead': [135], 'steep': [138], 'rise': [139], 'RMSD': [142, 183, 333], 'value.': [143], 'by': [148, 171, 175], 'first': [149], 'clustering': [150], 'into': [152], 'domains': [153], 'based': [154, 280], 'on': [155, 281], 'distance': [157], 'variance': [158], 'matrix,': [159], 'then': [161], 'refining': [162], 'each': [164], 'initial': [167], 'choice': [168, 346], 'excluding': [172], 'one': [174, 176], 'until': [177], 'relative': [179], 'decrease': [180], 'value': [184], 'becomes': [185], 'insignificant.': [186], 'A': [187], 'penalty': [188], 'opening': [191], 'gaps': [193, 296, 315], 'favours': [194], 'contiguous': [195], 'order': [199], 'obtain': [201], 'result': [203], 'simple': [207], 'possible,': [209], 'but': [210], 'not': [211], 'simpler.': [212], 'Results': [213], 'given': [215], 'set': [218], '37': [220], 'proteins': [221], 'compared': [223], 'with': [224], 'those': [225, 325], 'used': [228], 'validation': [231], 'packages.': [232], 'also': [234], 'provide': [235], '6351': [239], 'structures': [241], 'Protein': [244], 'Data': [245], 'Bank.': [246], 'CYRANGE': [248, 283, 312, 335], 'capable': [251], 'automatically': [253], 'determining': [254], 'large': [266], 'variety': [267], 'structures.': [270, 355], 'correctly': [273], 'identifies': [274], 'ordered': [275], 'regions.': [276], 'Global': [277], 'allow': [286], 'clear': [288], 'presentation': [289], 'structure,': [292], 'unnecessary': [294], 'small': [295], 'within': [297], 'selected': [299], 'absent.': [302], 'In': [303], 'majority': [305], 'cases,': [307], 'contain': [313], 'fewer': [314], 'cover': [317], 'considerably': [318], 'larger': [319], 'parts': [320], 'sequence': [323], 'than': [324], 'other': [327], 'methods': [328], 'significantly': [330], 'values.': [334], 'thus': [336], 'provides': [337], 'automatic': [341], 'standardizing': [344]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2162797705', 'counts_by_year': [{'year': 2024, 'cited_by_count': 3}, {'year': 2023, 'cited_by_count': 8}, {'year': 2022, 'cited_by_count': 7}, {'year': 2021, 'cited_by_count': 5}, {'year': 2020, 'cited_by_count': 1}, {'year': 2019, 'cited_by_count': 3}, {'year': 2017, 'cited_by_count': 8}, {'year': 2016, 'cited_by_count': 2}, {'year': 2015, 'cited_by_count': 10}, {'year': 2014, 'cited_by_count': 3}, {'year': 2013, 'cited_by_count': 5}, {'year': 2012, 'cited_by_count': 2}], 'updated_date': '2025-01-16T16:37:53.413083', 'created_date': '2016-06-24'}