{"id":"https://openalex.org/W2028506726","doi":"https://doi.org/10.1021/ci200150p","title":"AcquaAlta: A Directional Approach to the Solvation of Ligand\u2013Protein Complexes","display_name":"AcquaAlta: A Directional Approach to the Solvation of Ligand\u2013Protein Complexes","publication_year":2011,"publication_date":"2011-06-29","ids":{"openalex":"https://openalex.org/W2028506726","doi":"https://doi.org/10.1021/ci200150p","mag":"2028506726","pmid":"https://pubmed.ncbi.nlm.nih.gov/21714532"},"language":"en","primary_location":{"id":"doi:10.1021/ci200150p","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200150p","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/A5086555565","display_name":"Gianluca Rossato","orcid":"https://orcid.org/0000-0001-9560-4437"},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Gianluca Rossato","raw_affiliation_strings":["Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015481785","display_name":"Beat Ernst","orcid":"https://orcid.org/0000-0001-5787-2297"},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Beat Ernst","raw_affiliation_strings":["Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland","Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel (Switzerland)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel (Switzerland)","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036750822","display_name":"Angelo Vedani","orcid":null},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Angelo Vedani","raw_affiliation_strings":["Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland","Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel (Switzerland)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel (Switzerland)","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058642572","display_name":"Martin Smie\u0161ko","orcid":"https://orcid.org/0000-0003-2758-2680"},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Martin Smie\u0161ko","raw_affiliation_strings":["Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland","Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel (Switzerland)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel (Switzerland)","institution_ids":["https://openalex.org/I1850255"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5058642572"],"corresponding_institution_ids":["https://openalex.org/I1850255"],"apc_list":null,"apc_paid":null,"fwci":2.0984,"has_fulltext":false,"cited_by_count":76,"citation_normalized_percentile":{"value":0.86871296,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"51","issue":"8","first_page":"1867","last_page":"1881"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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/T10044","display_name":"Protein Structure and Dynamics","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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9990000128746033,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9987000226974487,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.8583791255950928},{"id":"https://openalex.org/keywords/pharmacophore","display_name":"Pharmacophore","score":0.7299106121063232},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.7034485936164856},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6955527067184448},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.6054172515869141},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5746572613716125},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.5138850212097168},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.48013541102409363},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.4759870767593384},{"id":"https://openalex.org/keywords/searching-the-conformational-space-for-docking","display_name":"Searching the conformational space for docking","score":0.47577372193336487},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.45036882162094116},{"id":"https://openalex.org/keywords/implicit-solvation","display_name":"Implicit solvation","score":0.4206456243991852},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3916342854499817},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.36792874336242676},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.2876274883747101},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09667763113975525},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.08139243721961975}],"concepts":[{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.8583791255950928},{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.7299106121063232},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.7034485936164856},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6955527067184448},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6054172515869141},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5746572613716125},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.5138850212097168},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.48013541102409363},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.4759870767593384},{"id":"https://openalex.org/C44695244","wikidata":"https://www.wikidata.org/wiki/Q7441727","display_name":"Searching the conformational space for docking","level":3,"score":0.47577372193336487},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.45036882162094116},{"id":"https://openalex.org/C64147673","wikidata":"https://www.wikidata.org/wiki/Q6007318","display_name":"Implicit solvation","level":4,"score":0.4206456243991852},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3916342854499817},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.36792874336242676},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.2876274883747101},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09667763113975525},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.08139243721961975},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","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":"D008074","descriptor_name":"Lipoproteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D008074","descriptor_name":"Lipoproteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D008074","descriptor_name":"Lipoproteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D008074","descriptor_name":"Lipoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008074","descriptor_name":"Lipoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008074","descriptor_name":"Lipoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008074","descriptor_name":"Lipoproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008074","descriptor_name":"Lipoproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008074","descriptor_name":"Lipoproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009842","descriptor_name":"Oligopeptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D009842","descriptor_name":"Oligopeptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D009842","descriptor_name":"Oligopeptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D009842","descriptor_name":"Oligopeptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009842","descriptor_name":"Oligopeptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009842","descriptor_name":"Oligopeptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009842","descriptor_name":"Oligopeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009842","descriptor_name":"Oligopeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009842","descriptor_name":"Oligopeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D012995","descriptor_name":"Solubility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012995","descriptor_name":"Solubility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012995","descriptor_name":"Solubility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012996","descriptor_name":"Solutions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012996","descriptor_name":"Solutions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012996","descriptor_name":"Solutions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci200150p","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200150p","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:21714532","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21714532","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}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/6","score":0.8399999737739563,"display_name":"Clean water and sanitation"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":65,"referenced_works":["https://openalex.org/W590740985","https://openalex.org/W1484366044","https://openalex.org/W1529261901","https://openalex.org/W1966235871","https://openalex.org/W1967566074","https://openalex.org/W1967809254","https://openalex.org/W1967850897","https://openalex.org/W1971652848","https://openalex.org/W1972982314","https://openalex.org/W1973298136","https://openalex.org/W1974667766","https://openalex.org/W1979046104","https://openalex.org/W1980337077","https://openalex.org/W1983066351","https://openalex.org/W1983271674","https://openalex.org/W1984339363","https://openalex.org/W1984690321","https://openalex.org/W1992218453","https://openalex.org/W1992786240","https://openalex.org/W1997947637","https://openalex.org/W1998948060","https://openalex.org/W2005647584","https://openalex.org/W2015647379","https://openalex.org/W2015962659","https://openalex.org/W2032456809","https://openalex.org/W2032842297","https://openalex.org/W2037392720","https://openalex.org/W2037732343","https://openalex.org/W2039127550","https://openalex.org/W2040144549","https://openalex.org/W2044457930","https://openalex.org/W2044940178","https://openalex.org/W2047476073","https://openalex.org/W2052466177","https://openalex.org/W2052603520","https://openalex.org/W2058092508","https://openalex.org/W2062291001","https://openalex.org/W2062299665","https://openalex.org/W2063535987","https://openalex.org/W2065009334","https://openalex.org/W2065057333","https://openalex.org/W2066746009","https://openalex.org/W2071349077","https://openalex.org/W2080156380","https://openalex.org/W2082152087","https://openalex.org/W2087186478","https://openalex.org/W2088267861","https://openalex.org/W2088451388","https://openalex.org/W2089887872","https://openalex.org/W2091111431","https://openalex.org/W2091662140","https://openalex.org/W2102377211","https://openalex.org/W2109987750","https://openalex.org/W2110414140","https://openalex.org/W2121954997","https://openalex.org/W2124789466","https://openalex.org/W2126714395","https://openalex.org/W2132504067","https://openalex.org/W2135502041","https://openalex.org/W2146354085","https://openalex.org/W2148941593","https://openalex.org/W2151698347","https://openalex.org/W2166173217","https://openalex.org/W2171068265","https://openalex.org/W2206465552"],"related_works":["https://openalex.org/W1966793603","https://openalex.org/W2048341727","https://openalex.org/W2089507369","https://openalex.org/W2045242973","https://openalex.org/W1974433778","https://openalex.org/W2498829061","https://openalex.org/W4323037679","https://openalex.org/W2322826137","https://openalex.org/W2105465678","https://openalex.org/W2053689559"],"abstract_inverted_index":{"Water":[0],"molecules":[1,21,46,76,107,167],"mediating":[2],"polar":[3,78],"interactions":[4,43,79,111],"in":[5,22,31],"ligand-protein":[6],"complexes":[7],"can":[8],"substantially":[9],"contribute":[10],"to":[11,37,73,122,136,141,182],"binding":[12,145],"affinity":[13],"and":[14,49,82,93,101],"specificity.":[15],"To":[16],"account":[17],"for":[18],"such":[19],"water":[20,45,75,103,106,166],"computer-aided":[23],"drug":[24],"design,":[25],"we":[26,68],"performed":[27],"an":[28,70,157],"extensive":[29],"search":[30],"the":[32,39,57,113,117,130,137,142,153,162,171,174,178],"Cambridge":[33],"Structural":[34],"Database":[35],"(CSD)":[36],"identify":[38],"geometrical":[40],"criteria":[41],"defining":[42],"of":[44,59,97,139,159,161],"with":[47,53,89,112,177],"ligand":[48,60,81],"protein.":[50],"In":[51],"addition,":[52],"ab":[54],"initio":[55],"calculations":[56],"propensity":[58],"hydration":[61],"was":[62,87,133],"evaluated.":[63],"Based":[64],"on":[65,152,170],"this":[66],"information,":[67],"developed":[69],"algorithm":[71,132],"(AcquaAlta)":[72],"reproduce":[74],"bridging":[77],"between":[80,99],"protein":[83,114,146],"moieties.":[84],"This":[85],"approach":[86],"validated":[88],"20":[90],"crystal":[91,154],"structures":[92],"yielded":[94],"a":[95,126],"match":[96,118,176],"76%":[98],"experimental":[100,163,179],"calculated":[102,168],"positions.":[104],"When":[105],"establishing":[108],"only":[109],"weak":[110],"were":[115],"neglected,":[116],"could":[119],"be":[120],"improved":[121],"88%.":[123],"Supported":[124],"by":[125],"pharmacophore-based":[127],"alignment":[128],"tool,":[129],"solvation":[131],"then":[134],"applied":[135],"docking":[138],"oligopeptides":[140],"periplasmic":[143],"oligopeptide":[144],"A":[147],"(OppA).":[148],"Calculated":[149],"waters":[150,180],"based":[151,169],"poses":[155],"matched":[156],"average":[158,175],"66%":[160],"waters.":[164],"With":[165],"docked":[172],"ligands,":[173],"dropped":[181],"53%.":[183]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":4}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}