{"id":"https://openalex.org/W3006472092","doi":"https://doi.org/10.1021/acs.jcim.9b01066","title":"Quantitative Characterization of Binding Pockets and Binding Complementarity by Means of Zernike Descriptors","display_name":"Quantitative Characterization of Binding Pockets and Binding Complementarity by Means of Zernike Descriptors","publication_year":2020,"publication_date":"2020-02-12","ids":{"openalex":"https://openalex.org/W3006472092","doi":"https://doi.org/10.1021/acs.jcim.9b01066","mag":"3006472092","pmid":"https://pubmed.ncbi.nlm.nih.gov/32050068"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b01066","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01066","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b01066","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b01066","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004111266","display_name":"Lorenzo Di Rienzo","orcid":"https://orcid.org/0000-0003-4114-5049"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Lorenzo Di Rienzo","raw_affiliation_strings":["Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015294553","display_name":"Edoardo Milanetti","orcid":"https://orcid.org/0000-0002-3046-5170"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]},{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Edoardo Milanetti","raw_affiliation_strings":["Center for Life Nano Science@Sapienza, Italian Institute of Technology, Viale Regina Elena 291, 00161 Rome, Italy","Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Center for Life Nano Science@Sapienza, Italian Institute of Technology, Viale Regina Elena 291, 00161 Rome, Italy","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024933518","display_name":"Josephine Alba","orcid":"https://orcid.org/0000-0002-5467-4751"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Josephine Alba","raw_affiliation_strings":["Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064994528","display_name":"Marco D\u2019Abramo","orcid":"https://orcid.org/0000-0001-6020-8581"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Marco D\u2019Abramo","raw_affiliation_strings":["Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5064994528"],"corresponding_institution_ids":["https://openalex.org/I861853513"],"apc_list":null,"apc_paid":null,"fwci":2.3922,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.90957538,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"60","issue":"3","first_page":"1390","last_page":"1398"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.996999979019165,"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/T12748","display_name":"Molecular spectroscopy and chirality","score":0.9962000250816345,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/zernike-polynomials","display_name":"Zernike polynomials","score":0.7366504073143005},{"id":"https://openalex.org/keywords/complementarity","display_name":"Complementarity (molecular biology)","score":0.6662983298301697},{"id":"https://openalex.org/keywords/formalism","display_name":"Formalism (music)","score":0.6079191565513611},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5678930878639221},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.49604567885398865},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4629688262939453},{"id":"https://openalex.org/keywords/uncorrelated","display_name":"Uncorrelated","score":0.42555955052375793},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4109959006309509},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.38929641246795654},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3544418215751648},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.3516802191734314},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2555357813835144},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.21470540761947632},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2048799991607666},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17606690526008606},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.12192350625991821},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08453214168548584},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07748112082481384}],"concepts":[{"id":"https://openalex.org/C92423082","wikidata":"https://www.wikidata.org/wiki/Q132146","display_name":"Zernike polynomials","level":3,"score":0.7366504073143005},{"id":"https://openalex.org/C202269582","wikidata":"https://www.wikidata.org/wiki/Q2644277","display_name":"Complementarity (molecular biology)","level":2,"score":0.6662983298301697},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.6079191565513611},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5678930878639221},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.49604567885398865},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4629688262939453},{"id":"https://openalex.org/C169345407","wikidata":"https://www.wikidata.org/wiki/Q8216221","display_name":"Uncorrelated","level":2,"score":0.42555955052375793},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4109959006309509},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.38929641246795654},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3544418215751648},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3516802191734314},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2555357813835144},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.21470540761947632},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2048799991607666},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17606690526008606},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.12192350625991821},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08453214168548584},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07748112082481384},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C165699331","wikidata":"https://www.wikidata.org/wiki/Q461533","display_name":"Wavefront","level":2,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C558565934","wikidata":"https://www.wikidata.org/wiki/Q2743","display_name":"Musical","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.9b01066","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01066","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b01066","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:32050068","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32050068","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"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":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:iris.uniroma1.it:11573/1392370","is_oa":false,"landing_page_url":"http://hdl.handle.net/11573/1392370","pdf_url":null,"source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7997106","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7997106","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"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":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.9b01066","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01066","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b01066","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322510","display_name":"Sapienza Universit\u00e0 di Roma","ror":"https://ror.org/02be6w209"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3006472092.pdf","grobid_xml":"https://content.openalex.org/works/W3006472092.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W616457854","https://openalex.org/W1495469490","https://openalex.org/W1517566065","https://openalex.org/W1964396270","https://openalex.org/W1966305644","https://openalex.org/W1969370763","https://openalex.org/W1979414133","https://openalex.org/W1983036219","https://openalex.org/W1987947939","https://openalex.org/W1993976538","https://openalex.org/W2008697864","https://openalex.org/W2012378659","https://openalex.org/W2015115140","https://openalex.org/W2019951137","https://openalex.org/W2030088199","https://openalex.org/W2031194866","https://openalex.org/W2041735927","https://openalex.org/W2043556481","https://openalex.org/W2047399603","https://openalex.org/W2050136047","https://openalex.org/W2053275587","https://openalex.org/W2054881399","https://openalex.org/W2060079863","https://openalex.org/W2066143642","https://openalex.org/W2069158348","https://openalex.org/W2070741080","https://openalex.org/W2079953901","https://openalex.org/W2082390334","https://openalex.org/W2090794687","https://openalex.org/W2101980405","https://openalex.org/W2102535700","https://openalex.org/W2105902442","https://openalex.org/W2114459720","https://openalex.org/W2121106975","https://openalex.org/W2128402268","https://openalex.org/W2140407975","https://openalex.org/W2144714500","https://openalex.org/W2146940292","https://openalex.org/W2149434585","https://openalex.org/W2152443870","https://openalex.org/W2157255054","https://openalex.org/W2158076215","https://openalex.org/W2164485723","https://openalex.org/W2167459719","https://openalex.org/W2332278601","https://openalex.org/W2435221055","https://openalex.org/W2600993444","https://openalex.org/W2790162914","https://openalex.org/W2791988510","https://openalex.org/W2890515789","https://openalex.org/W2943906159","https://openalex.org/W2952198398","https://openalex.org/W6695871661"],"related_works":["https://openalex.org/W1997638723","https://openalex.org/W2547138831","https://openalex.org/W2061580049","https://openalex.org/W2067788074","https://openalex.org/W2183108721","https://openalex.org/W2073465494","https://openalex.org/W3160617640","https://openalex.org/W3141187597","https://openalex.org/W2369242147","https://openalex.org/W1969694079"],"abstract_inverted_index":{"In":[0],"this":[1],"work,":[2],"we":[3],"describe":[4,74],"the":[5,8,14,37,49],"application":[6],"of":[7,17,20,64],"Zernike":[9],"formalism":[10],"to":[11,29,35,52,57,73],"quantitatively":[12],"characterize":[13],"binding":[15,76],"pockets":[16],"two":[18],"sets":[19],"biologically":[21],"relevant":[22],"systems.":[23],"Such":[24],"an":[25],"approach,":[26],"when":[27],"applied":[28],"molecular":[30,43],"dynamics":[31],"trajectories,":[32],"is":[33,70],"able":[34],"pinpoint":[36],"subtle":[38],"differences":[39],"between":[40],"very":[41,71],"similar":[42],"regions":[44],"and":[45,78,84],"their":[46],"impact":[47],"on":[48],"local":[50],"propensity":[51],"ligand":[53],"binding,":[54],"allowing":[55],"us":[56],"quantify":[58],"such":[59],"differences.":[60],"The":[61],"statistical":[62],"robustness":[63],"our":[65],"procedure":[66],"suggests":[67],"that":[68],"it":[69],"suitable":[72],"protein":[75],"sites":[77],"protein-ligand":[79],"interactions":[80],"within":[81],"a":[82],"rigorous":[83],"well-defined":[85],"framework.":[86]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}