{"id":"https://openalex.org/W3171579200","doi":"https://doi.org/10.1021/acs.jcim.1c00235","title":"3D Interaction Homology: Hydropathic Analyses of the \u201c\u03c0\u2013Cation\u201d and \u201c\u03c0\u2013\u03c0\u201d Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues","display_name":"3D Interaction Homology: Hydropathic Analyses of the \u201c\u03c0\u2013Cation\u201d and \u201c\u03c0\u2013\u03c0\u201d Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues","publication_year":2021,"publication_date":"2021-06-08","ids":{"openalex":"https://openalex.org/W3171579200","doi":"https://doi.org/10.1021/acs.jcim.1c00235","mag":"3171579200","pmid":"https://pubmed.ncbi.nlm.nih.gov/34101460"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c00235","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00235","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/A5015759399","display_name":"Mohammed H. AL Mughram","orcid":"https://orcid.org/0000-0002-7343-4083"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohammed H. AL Mughram","raw_affiliation_strings":["Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066092735","display_name":"Claudio Catalano","orcid":"https://orcid.org/0000-0002-2437-6235"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Claudio Catalano","raw_affiliation_strings":["Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068523426","display_name":"John P. Bowry","orcid":null},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John P. Bowry","raw_affiliation_strings":["Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028033960","display_name":"Martin K. Safo","orcid":"https://orcid.org/0000-0002-9536-1743"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin K. Safo","raw_affiliation_strings":["Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States","Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States"],"raw_orcid":"https://orcid.org/0000-0002-9536-1743","affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025444311","display_name":"J.N. Scarsdale","orcid":null},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Neel Scarsdale","raw_affiliation_strings":["Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States","Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007894073","display_name":"Glen E. Kellogg","orcid":"https://orcid.org/0000-0002-6282-6794"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Glen E. Kellogg","raw_affiliation_strings":["Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States","Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States","Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States"],"raw_orcid":"https://orcid.org/0000-0002-6282-6794","affiliations":[{"raw_affiliation_string":"Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States","institution_ids":["https://openalex.org/I184840846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5007894073"],"corresponding_institution_ids":["https://openalex.org/I184840846"],"apc_list":null,"apc_paid":null,"fwci":1.6513,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.83489214,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"61","issue":"6","first_page":"2937","last_page":"2956"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9977999925613403,"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"}},"topics":[{"id":"https://openalex.org/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9977999925613403,"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/T12748","display_name":"Molecular spectroscopy and chirality","score":0.9961000084877014,"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":0.9936000108718872,"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/phenylalanine","display_name":"Phenylalanine","score":0.7984656095504761},{"id":"https://openalex.org/keywords/tyrosine","display_name":"Tyrosine","score":0.7936098575592041},{"id":"https://openalex.org/keywords/tryptophan","display_name":"Tryptophan","score":0.7653355002403259},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5810741782188416},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.5344461798667908},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.4687986969947815},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.45265620946884155},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.26245588064193726}],"concepts":[{"id":"https://openalex.org/C2777431362","wikidata":"https://www.wikidata.org/wiki/Q170545","display_name":"Phenylalanine","level":3,"score":0.7984656095504761},{"id":"https://openalex.org/C2776165026","wikidata":"https://www.wikidata.org/wiki/Q188017","display_name":"Tyrosine","level":2,"score":0.7936098575592041},{"id":"https://openalex.org/C2776706248","wikidata":"https://www.wikidata.org/wiki/Q181003","display_name":"Tryptophan","level":3,"score":0.7653355002403259},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5810741782188416},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.5344461798667908},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.4687986969947815},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.45265620946884155},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.26245588064193726}],"mesh":[{"descriptor_ui":"D002412","descriptor_name":"Cations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002412","descriptor_name":"Cations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002412","descriptor_name":"Cations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010649","descriptor_name":"Phenylalanine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010649","descriptor_name":"Phenylalanine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010649","descriptor_name":"Phenylalanine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014364","descriptor_name":"Tryptophan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014364","descriptor_name":"Tryptophan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014364","descriptor_name":"Tryptophan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014443","descriptor_name":"Tyrosine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014443","descriptor_name":"Tyrosine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014443","descriptor_name":"Tyrosine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.1c00235","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00235","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:34101460","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34101460","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":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":78,"referenced_works":["https://openalex.org/W105839754","https://openalex.org/W1483942114","https://openalex.org/W1967524810","https://openalex.org/W1970170256","https://openalex.org/W1971526701","https://openalex.org/W1977556410","https://openalex.org/W1979858085","https://openalex.org/W1981212694","https://openalex.org/W1984493861","https://openalex.org/W1990122271","https://openalex.org/W2004224330","https://openalex.org/W2009158394","https://openalex.org/W2009593219","https://openalex.org/W2011087340","https://openalex.org/W2011658408","https://openalex.org/W2013059500","https://openalex.org/W2014050554","https://openalex.org/W2018441039","https://openalex.org/W2025102682","https://openalex.org/W2025524908","https://openalex.org/W2025786614","https://openalex.org/W2027189612","https://openalex.org/W2030686702","https://openalex.org/W2034126246","https://openalex.org/W2036248673","https://openalex.org/W2038780351","https://openalex.org/W2039388179","https://openalex.org/W2039735678","https://openalex.org/W2040608953","https://openalex.org/W2044672033","https://openalex.org/W2049902088","https://openalex.org/W2054525948","https://openalex.org/W2057267661","https://openalex.org/W2057309818","https://openalex.org/W2063223774","https://openalex.org/W2065473347","https://openalex.org/W2071466250","https://openalex.org/W2080796053","https://openalex.org/W2084165857","https://openalex.org/W2087826408","https://openalex.org/W2087884843","https://openalex.org/W2092062183","https://openalex.org/W2094186244","https://openalex.org/W2099057076","https://openalex.org/W2106648157","https://openalex.org/W2115967085","https://openalex.org/W2116893472","https://openalex.org/W2117569373","https://openalex.org/W2129305902","https://openalex.org/W2129455301","https://openalex.org/W2130479394","https://openalex.org/W2138701720","https://openalex.org/W2142347024","https://openalex.org/W2146298489","https://openalex.org/W2149240697","https://openalex.org/W2150155770","https://openalex.org/W2160721947","https://openalex.org/W2165232124","https://openalex.org/W2171546617","https://openalex.org/W2185259716","https://openalex.org/W2206846584","https://openalex.org/W2231783367","https://openalex.org/W2312506638","https://openalex.org/W2315189679","https://openalex.org/W2323743987","https://openalex.org/W2474139868","https://openalex.org/W2492958735","https://openalex.org/W2556222602","https://openalex.org/W2612329522","https://openalex.org/W2764301816","https://openalex.org/W2785579100","https://openalex.org/W2786469974","https://openalex.org/W2793852959","https://openalex.org/W2946122169","https://openalex.org/W2980789587","https://openalex.org/W2997234557","https://openalex.org/W2999044305","https://openalex.org/W3005306837"],"related_works":["https://openalex.org/W2052528157","https://openalex.org/W2057410200","https://openalex.org/W1513881935","https://openalex.org/W1980936780","https://openalex.org/W10138397","https://openalex.org/W2060862331","https://openalex.org/W2417569447","https://openalex.org/W2057155383","https://openalex.org/W2066530401","https://openalex.org/W2078780432"],"abstract_inverted_index":{"Three-dimensional":[0],"(3D)":[1],"maps":[2,88,272],"of":[3,7,15,51,93,131,158,165,170,205,229,240,243,247,262,281],"the":[4,32,39,63,70,106,132,144,148,154,159,171,206,230,268],"hydropathic":[5,270],"environments":[6],"protein":[8,45,64,282],"amino":[9],"acid":[10],"residues":[11,72,92,207],"are":[12,31,184],"information-rich":[13],"descriptors":[14],"preferred":[16],"conformations,":[17],"interaction":[18,278],"types":[19,96],"and":[20,22,38,42,75,77,83,103,115,151,215,245,285],"energetics,":[21],"solvent":[23],"accessibility.":[24],"The":[25,179],"interactions":[26,176,192,199,235,266],"made":[27],"by":[28,123,174],"each":[29,55,121,130],"residue":[30,56,134],"primary":[33],"factor":[34],"for":[35,54,89,197,233,276],"rotamer":[36],"selection":[37],"secondary,":[40],"tertiary,":[41],"even":[43,263],"quaternary":[44],"structure.":[46,65],"Our":[47],"evolving":[48],"basis":[49],"set":[50],"environmental":[52],"data":[53],"type":[57],"can":[58],"be":[59,188],"used":[60],"to":[61,101,187,226,257],"understand":[62],"This":[66,260],"work":[67],"focuses":[68],"on":[69,220,251],"aromatic":[71],"phenylalanine,":[73],"tyrosine,":[74],"tryptophan":[76,216],"their":[78,194],"structural":[79],"roles.":[80],"We":[81],"calculated":[82],"analyzed":[84],"side":[85,116,166,172,182],"chain-to-environment":[86],"3D":[87,124,269],"over":[90],"70,000":[91],"these":[94,264],"three":[95,133],"that":[97],"reveal,":[98],"with":[99,112,193],"respect":[100],"hydrophobic":[102,175],"polar":[104,191],"interactions,":[105],"environment":[107,271],"around":[108],"each.":[109],"After":[110],"binning":[111],"backbone":[113],"\u03d5/\u03c8":[114],"chain":[117,167,173],"\u03c71,":[118],"we":[119],"clustered":[120],"bin":[122],"similarities":[125],"between":[126],"map\u2013map":[127],"pairs.":[128],"For":[129,162],"types,":[135],"four":[136],"bins":[137],"were":[138],"examined":[139],"in":[140,143,147,153,190,202,238,267],"detail:":[141],"one":[142,152],"\u03b2-pleat,":[145],"two":[146],"right-hand":[149],"\u03b1-helix,":[150],"left-hand":[155],"\u03b1-helix":[156],"regions":[157],"Ramachandran":[160],"plot.":[161],"high":[163],"degrees":[164],"burial,":[168],"encapsulation":[169],"is":[177,273],"ubiquitous.":[178],"more":[180,185],"solvent-exposed":[181],"chains":[183],"likely":[186],"involved":[189],"environments.":[195],"Evidence":[196,232],"\u03c0\u2013\u03c0":[198],"was":[200,236],"observed":[201,237],"about":[203],"half":[204],"surveyed":[208],"[phenylalanine":[209],"(PHE):":[210],"53.3%,":[211],"tyrosine":[212],"(TYR):":[213],"34.1%,":[214],"(TRP):":[217],"55.7%],":[218],"but":[219,250],"an":[221,252],"energy":[222,253],"basis,":[223,254],"this":[224,255],"contributed":[225,256],"only":[227,258],"\u223c4%":[228],"total.":[231],"\u03c0\u2013cation":[234],"14.1%":[239],"PHE,":[241],"8.3%":[242],"TYR,":[244],"26.8%":[246],"TRP":[248],"residues,":[249],"\u223c1%.":[259],"recognition":[261],"subtle":[265],"key":[274],"support":[275],"our":[277],"homology":[279],"paradigm":[280],"structure":[283],"elucidation":[284],"possibly":[286],"prediction.":[287]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}