{"id":"https://openalex.org/W2319292461","doi":"https://doi.org/10.1021/acs.jcim.5b00702","title":"Deciphering the Complexity of Ligand\u2013Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations","display_name":"Deciphering the Complexity of Ligand\u2013Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations","publication_year":2016,"publication_date":"2016-03-28","ids":{"openalex":"https://openalex.org/W2319292461","doi":"https://doi.org/10.1021/acs.jcim.5b00702","mag":"2319292461","pmid":"https://pubmed.ncbi.nlm.nih.gov/27019343"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5b00702","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00702","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049972475","display_name":"Alberto Cuzzolin","orcid":null},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Alberto Cuzzolin","raw_affiliation_strings":["Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090674819","display_name":"Mattia Sturlese","orcid":"https://orcid.org/0000-0003-3944-0313"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mattia Sturlese","raw_affiliation_strings":["Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039639796","display_name":"Giuseppe Deganutti","orcid":"https://orcid.org/0000-0001-8780-2986"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giuseppe Deganutti","raw_affiliation_strings":["Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021413221","display_name":"Veronica Salmaso","orcid":"https://orcid.org/0000-0001-5305-8351"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Veronica Salmaso","raw_affiliation_strings":["Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069374388","display_name":"Davide Sabbadin","orcid":"https://orcid.org/0000-0003-1510-0904"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Davide Sabbadin","raw_affiliation_strings":["Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064432337","display_name":"Antonella Ciancetta","orcid":"https://orcid.org/0000-0002-7612-2050"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Antonella Ciancetta","raw_affiliation_strings":["Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008583952","display_name":"Stefano Moro","orcid":"https://orcid.org/0000-0002-7514-3802"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefano Moro","raw_affiliation_strings":["Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Molecular\rModeling Section\r(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5049972475"],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":null,"apc_paid":null,"fwci":6.6692,"has_fulltext":false,"cited_by_count":98,"citation_normalized_percentile":{"value":0.97259059,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"56","issue":"4","first_page":"687","last_page":"705"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9998000264167786,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9998000264167786,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9995999932289124,"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":0.9994000196456909,"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/computer-science","display_name":"Computer science","score":0.619016170501709},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5241836905479431},{"id":"https://openalex.org/keywords/g-protein-coupled-receptor","display_name":"G protein-coupled receptor","score":0.5079475045204163},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4789317548274994},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.4598771631717682},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45700183510780334},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4354555606842041},{"id":"https://openalex.org/keywords/molecular-recognition","display_name":"Molecular recognition","score":0.43232598900794983},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.42644989490509033},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40496331453323364},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.356631338596344},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3433983027935028},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32584643363952637},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.29775503277778625},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.21213829517364502},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16689324378967285},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13417595624923706},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1140587329864502},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09327822923660278},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.08260935544967651}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.619016170501709},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5241836905479431},{"id":"https://openalex.org/C135285700","wikidata":"https://www.wikidata.org/wiki/Q38173","display_name":"G protein-coupled receptor","level":3,"score":0.5079475045204163},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4789317548274994},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.4598771631717682},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45700183510780334},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4354555606842041},{"id":"https://openalex.org/C179303850","wikidata":"https://www.wikidata.org/wiki/Q4300362","display_name":"Molecular recognition","level":3,"score":0.43232598900794983},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.42644989490509033},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40496331453323364},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.356631338596344},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3433983027935028},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32584643363952637},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.29775503277778625},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.21213829517364502},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16689324378967285},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13417595624923706},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1140587329864502},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09327822923660278},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.08260935544967651},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.5b00702","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00702","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:27019343","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27019343","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.unife.it:11392/2466550","is_oa":false,"landing_page_url":"http://hdl.handle.net/11392/2466550","pdf_url":null,"source":{"id":"https://openalex.org/S4306400369","display_name":"Institutional Research Information System University of Ferrara (University of Ferrara)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I201324441","host_organization_name":"University of Ferrara","host_organization_lineage":["https://openalex.org/I201324441"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:www.research.unipd.it:11577/3220108","is_oa":false,"landing_page_url":"http://hdl.handle.net/11577/3220108","pdf_url":null,"source":{"id":"https://openalex.org/S4306402547","display_name":"Padua Research Archive (University of Padova)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"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"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2547899626","display_name":null,"funder_award_id":"20103W4779_002","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"}],"funders":[{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W23685639","https://openalex.org/W590740985","https://openalex.org/W982389493","https://openalex.org/W1135792216","https://openalex.org/W1672217021","https://openalex.org/W1917347435","https://openalex.org/W1974667766","https://openalex.org/W1975732928","https://openalex.org/W1976499671","https://openalex.org/W1985598247","https://openalex.org/W1986719264","https://openalex.org/W1986915643","https://openalex.org/W1988284264","https://openalex.org/W1988636074","https://openalex.org/W1994941561","https://openalex.org/W1997772366","https://openalex.org/W2009001257","https://openalex.org/W2017016317","https://openalex.org/W2023287483","https://openalex.org/W2027408247","https://openalex.org/W2029667189","https://openalex.org/W2032143666","https://openalex.org/W2034992941","https://openalex.org/W2035266068","https://openalex.org/W2035687084","https://openalex.org/W2047218153","https://openalex.org/W2051809420","https://openalex.org/W2060433756","https://openalex.org/W2069505357","https://openalex.org/W2081838152","https://openalex.org/W2082586732","https://openalex.org/W2084290194","https://openalex.org/W2091616887","https://openalex.org/W2095145098","https://openalex.org/W2096242757","https://openalex.org/W2097775366","https://openalex.org/W2100561975","https://openalex.org/W2102513649","https://openalex.org/W2111917512","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2133620840","https://openalex.org/W2136572246","https://openalex.org/W2144288821","https://openalex.org/W2147993766","https://openalex.org/W2157623058","https://openalex.org/W2158127851","https://openalex.org/W2160907977","https://openalex.org/W2201429615","https://openalex.org/W2263409063","https://openalex.org/W2523003005"],"related_works":["https://openalex.org/W2609050007","https://openalex.org/W1981292198","https://openalex.org/W4224216382","https://openalex.org/W3195483439","https://openalex.org/W1135792216","https://openalex.org/W2177786495","https://openalex.org/W2164210098","https://openalex.org/W2108339230","https://openalex.org/W2011432577","https://openalex.org/W2098622919"],"abstract_inverted_index":{"Molecular":[0],"recognition":[1,138,199],"is":[2,29],"a":[3,31,41,51],"crucial":[4],"issue":[5],"when":[6],"aiming":[7],"to":[8,19,57,79,167],"interpret":[9],"the":[10,26,86,94,100,117,136,159,169,172,175,181,184,195],"mechanism":[11],"of":[12,88,99,116,124,140,174,183,197],"known":[13],"active":[14,22],"substances":[15],"as":[16,18,188,190],"well":[17,189],"develop":[20],"novel":[21],"candidates.":[23],"Unfortunately,":[24],"simulating":[25],"binding":[27,90,107],"process":[28],"still":[30],"challenging":[32],"task":[33],"because":[34],"it":[35,78],"requires":[36],"classical":[37],"MD":[38,68],"experiments":[39],"in":[40,126,171,193],"long":[42],"microsecond":[43],"time":[44],"scale":[45],"that":[46,145,162],"are":[47],"affordable":[48],"only":[49],"with":[50,128],"high-level":[52],"computational":[53],"capacity.":[54],"In":[55,109,130],"order":[56],"overcome":[58],"this":[59,110],"limiting":[60],"factor,":[61],"we":[62,112,132,146,157,163,179],"have":[63,133,164],"recently":[64],"implemented":[65,166],"an":[66,114],"alternative":[67],"approach,":[69],"named":[70],"supervised":[71],"molecular":[72],"dynamics":[73],"(SuMD),":[74],"and":[75,102,153],"successfully":[76],"applied":[77],"G":[80],"protein-coupled":[81],"receptors":[82],"(GPCRs).":[83],"SuMD":[84,118,176,185],"enables":[85],"investigation":[87],"ligand-receptor":[89],"events":[91],"independently":[92],"from":[93,104],"starting":[95],"position,":[96],"chemical":[97],"structure":[98],"ligand,":[101],"also":[103],"its":[105,191],"receptor":[106],"affinity.":[108],"article,":[111],"present":[113],"extension":[115],"application":[119],"domain":[120,187],"including":[121],"different":[122,142,150],"types":[123],"proteins":[125],"comparison":[127],"GPCRs.":[129],"particular,":[131],"deeply":[134],"analyzed":[135],"ligand-protein":[137,198],"pathways":[139],"six":[141],"case":[143],"studies":[144],"grouped":[147],"into":[148],"two":[149],"classes:":[151],"globular":[152],"membrane":[154],"proteins.":[155],"Moreover,":[156],"introduce":[158],"SuMD-Analyzer":[160],"tool":[161],"specifically":[165],"help":[168],"user":[170],"analysis":[173],"trajectories.":[177],"Finally,":[178],"emphasize":[180],"limit":[182],"applicability":[186],"strengths":[192],"analyzing":[194],"complexity":[196],"pathways.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":19},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":9}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}