{"id":"https://openalex.org/W2122144012","doi":"https://doi.org/10.1093/bioinformatics/btn108","title":"Visualization of unfavorable interactions in protein folds","display_name":"Visualization of unfavorable interactions in protein folds","publication_year":2008,"publication_date":"2008-03-29","ids":{"openalex":"https://openalex.org/W2122144012","doi":"https://doi.org/10.1093/bioinformatics/btn108","mag":"2122144012","pmid":"https://pubmed.ncbi.nlm.nih.gov/18375963"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn108","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn108","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5050449918","display_name":"Christian X. Weichenberger","orcid":"https://orcid.org/0000-0002-2176-0274"},"institutions":[{"id":"https://openalex.org/I11923345","display_name":"Wroc\u0142aw University of Science and Technology","ror":"https://ror.org/008fyn775","country_code":"PL","type":"education","lineage":["https://openalex.org/I11923345"]},{"id":"https://openalex.org/I182212641","display_name":"University of Salzburg","ror":"https://ror.org/05gs8cd61","country_code":"AT","type":"education","lineage":["https://openalex.org/I182212641"]}],"countries":["AT","PL"],"is_corresponding":false,"raw_author_name":"Christian X. Weichenberger","raw_affiliation_strings":["1 Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria and 2Institute of Physical and Theoretical Chemistry, Wroc\u0142aw University of Technology, Wybrze\u017ce Wyspia\u0144skiego 27, 50-370 Wroc\u0142aw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria and 2Institute of Physical and Theoretical Chemistry, Wroc\u0142aw University of Technology, Wybrze\u017ce Wyspia\u0144skiego 27, 50-370 Wroc\u0142aw, Poland","institution_ids":["https://openalex.org/I11923345","https://openalex.org/I182212641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069619095","display_name":"Piotr Byzia","orcid":null},"institutions":[{"id":"https://openalex.org/I11923345","display_name":"Wroc\u0142aw University of Science and Technology","ror":"https://ror.org/008fyn775","country_code":"PL","type":"education","lineage":["https://openalex.org/I11923345"]},{"id":"https://openalex.org/I182212641","display_name":"University of Salzburg","ror":"https://ror.org/05gs8cd61","country_code":"AT","type":"education","lineage":["https://openalex.org/I182212641"]}],"countries":["AT","PL"],"is_corresponding":false,"raw_author_name":"Piotr Byzia","raw_affiliation_strings":["1 Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria and 2Institute of Physical and Theoretical Chemistry, Wroc\u0142aw University of Technology, Wybrze\u017ce Wyspia\u0144skiego 27, 50-370 Wroc\u0142aw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria and 2Institute of Physical and Theoretical Chemistry, Wroc\u0142aw University of Technology, Wybrze\u017ce Wyspia\u0144skiego 27, 50-370 Wroc\u0142aw, Poland","institution_ids":["https://openalex.org/I11923345","https://openalex.org/I182212641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028301579","display_name":"Manfred J. Sippl","orcid":null},"institutions":[{"id":"https://openalex.org/I11923345","display_name":"Wroc\u0142aw University of Science and Technology","ror":"https://ror.org/008fyn775","country_code":"PL","type":"education","lineage":["https://openalex.org/I11923345"]},{"id":"https://openalex.org/I182212641","display_name":"University of Salzburg","ror":"https://ror.org/05gs8cd61","country_code":"AT","type":"education","lineage":["https://openalex.org/I182212641"]}],"countries":["AT","PL"],"is_corresponding":false,"raw_author_name":"Manfred J. Sippl","raw_affiliation_strings":["1 Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria and 2Institute of Physical and Theoretical Chemistry, Wroc\u0142aw University of Technology, Wybrze\u017ce Wyspia\u0144skiego 27, 50-370 Wroc\u0142aw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria and 2Institute of Physical and Theoretical Chemistry, Wroc\u0142aw University of Technology, Wybrze\u017ce Wyspia\u0144skiego 27, 50-370 Wroc\u0142aw, Poland","institution_ids":["https://openalex.org/I11923345","https://openalex.org/I182212641"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.531,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.66514367,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"24","issue":"9","first_page":"1206","last_page":"1207"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7006999850273132,"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":0.7006999850273132,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.21310000121593475,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":0.02290000021457672,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"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/visualization","display_name":"Visualization","score":0.7747701406478882},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6144303679466248},{"id":"https://openalex.org/keywords/asparagine","display_name":"Asparagine","score":0.5478605031967163},{"id":"https://openalex.org/keywords/service","display_name":"Service (business)","score":0.5305666923522949},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.5193070769309998},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3427335023880005},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.33453530073165894},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.29257795214653015},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2601882517337799},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.253775954246521},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1298782229423523},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.10547319054603577}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7747701406478882},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6144303679466248},{"id":"https://openalex.org/C2775895851","wikidata":"https://www.wikidata.org/wiki/Q185906","display_name":"Asparagine","level":3,"score":0.5478605031967163},{"id":"https://openalex.org/C2780378061","wikidata":"https://www.wikidata.org/wiki/Q25351891","display_name":"Service (business)","level":2,"score":0.5305666923522949},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.5193070769309998},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3427335023880005},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.33453530073165894},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.29257795214653015},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2601882517337799},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.253775954246521},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1298782229423523},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.10547319054603577},{"id":"https://openalex.org/C136264566","wikidata":"https://www.wikidata.org/wiki/Q159810","display_name":"Economy","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btn108","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn108","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18375963","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18375963","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.562.7665","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.562.7665","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2008/03/29/bioinformatics.btn108.full.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1589812083","https://openalex.org/W1974885083","https://openalex.org/W1992192767","https://openalex.org/W1993178653","https://openalex.org/W2024745990","https://openalex.org/W2075659901","https://openalex.org/W2083965528","https://openalex.org/W2088933990","https://openalex.org/W2106154817","https://openalex.org/W2112315056","https://openalex.org/W2122339645","https://openalex.org/W2130479394","https://openalex.org/W2156408001"],"related_works":["https://openalex.org/W3008054205","https://openalex.org/W2374232366","https://openalex.org/W2339524377","https://openalex.org/W2036849448","https://openalex.org/W2028917331","https://openalex.org/W2230290157","https://openalex.org/W107783397","https://openalex.org/W1560801995","https://openalex.org/W2070565582","https://openalex.org/W1994242752"],"abstract_inverted_index":{"UNLABELLED:":[0],"Three":[1],"dimensional":[2],"structures":[3],"of":[4,13,41,70],"proteins":[5],"contain":[6],"errors":[7,19],"which":[8],"often":[9],"originate":[10],"from":[11],"limitations":[12],"the":[14,37,47,55,68,84],"experimental":[15],"techniques":[16],"employed.":[17],"Such":[18],"frequently":[20],"result":[21],"in":[22,52,73],"unfavorable":[23],"atomic":[24],"interactions.":[25],"Here":[26],"we":[27,66],"present":[28],"a":[29],"new":[30],"web":[31,79],"service,":[32],"called":[33],"Interaction":[34,48],"Viewer,":[35],"for":[36],"visualization":[38],"and":[39,62,65,87],"correction":[40],"such":[42,75],"errors.":[43,76],"We":[44],"show":[45],"how":[46],"Viewer":[49],"is":[50,81],"used":[51],"combination":[53],"with":[54,83],"NQ-Flipper":[56,85],"service":[57,72,80,86],"to":[58],"spot":[59],"strained":[60],"asparagine":[61],"glutamine":[63],"rotamers":[64],"emphasize":[67],"convenience":[69],"this":[71],"correcting":[74],"AVAILABILITY:":[77],"The":[78],"integrated":[82],"accessible":[88],"at":[89],"http://flipper.services.came.sbg.ac.at":[90]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
