{"id":"https://openalex.org/W2120508443","doi":"https://doi.org/10.1093/bioinformatics/btr348","title":"Xwalk: computing and visualizing distances in cross-linking experiments","display_name":"Xwalk: computing and visualizing distances in cross-linking experiments","publication_year":2011,"publication_date":"2011-06-11","ids":{"openalex":"https://openalex.org/W2120508443","doi":"https://doi.org/10.1093/bioinformatics/btr348","mag":"2120508443","pmid":"https://pubmed.ncbi.nlm.nih.gov/21666267"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr348","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr348","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/15/2163/48865208/bioinformatics_27_15_2163.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/15/2163/48865208/bioinformatics_27_15_2163.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031852359","display_name":"Abdullah Kahraman","orcid":"https://orcid.org/0000-0003-3523-4467"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Abdullah Kahraman","raw_affiliation_strings":["Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH Zurich), CH-8093 Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH Zurich), CH-8093 Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088","https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089221737","display_name":"Lars Malmstr\u00f6m","orcid":"https://orcid.org/0000-0001-9885-9312"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Lars Malmstr\u00f6m","raw_affiliation_strings":["Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH Zurich), CH-8093 Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH Zurich), CH-8093 Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088","https://openalex.org/I5124864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053361384","display_name":"Ruedi Aebersold","orcid":"https://orcid.org/0000-0002-9576-3267"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Ruedi Aebersold","raw_affiliation_strings":["Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH Zurich), CH-8093 Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH Zurich), CH-8093 Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088","https://openalex.org/I5124864"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5031852359","https://openalex.org/A5053361384"],"corresponding_institution_ids":["https://openalex.org/I35440088","https://openalex.org/I5124864"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.0668,"has_fulltext":true,"cited_by_count":163,"citation_normalized_percentile":{"value":0.87152966,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"27","issue":"15","first_page":"2163","last_page":"2164"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5476999878883362,"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":0.5476999878883362,"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":0.1137000024318695,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.047600001096725464,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5854673385620117},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.574527382850647},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5592164397239685},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5282365679740906},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.48124170303344727},{"id":"https://openalex.org/keywords/linker","display_name":"Linker","score":0.4397678077220917},{"id":"https://openalex.org/keywords/shortest-path-problem","display_name":"Shortest path problem","score":0.4129032492637634},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.41045302152633667},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.4055193364620209},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3272245526313782},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.32652539014816284},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22413721680641174},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.198386549949646},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1643444001674652},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.10844776034355164},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.0837583839893341},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.07762092351913452}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5854673385620117},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.574527382850647},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5592164397239685},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5282365679740906},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.48124170303344727},{"id":"https://openalex.org/C2780557392","wikidata":"https://www.wikidata.org/wiki/Q523796","display_name":"Linker","level":2,"score":0.4397678077220917},{"id":"https://openalex.org/C22590252","wikidata":"https://www.wikidata.org/wiki/Q1058754","display_name":"Shortest path problem","level":3,"score":0.4129032492637634},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.41045302152633667},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.4055193364620209},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3272245526313782},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.32652539014816284},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22413721680641174},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.198386549949646},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1643444001674652},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10844776034355164},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0837583839893341},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.07762092351913452}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/bioinformatics/btr348","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr348","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/15/2163/48865208/bioinformatics_27_15_2163.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21666267","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21666267","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":null},{"id":"pmh:oai:doc.rero.ch:291956","is_oa":false,"landing_page_url":"http://doc.rero.ch/record/291956/files/btr348.pdf","pdf_url":"http://doc.rero.ch/record/291956/files/btr348.pdf","source":{"id":"https://openalex.org/S4306400148","display_name":"reroDoc Digital Library","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/38734","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/38734","pdf_url":"http://hdl.handle.net/20.500.11850/38734","source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 27 (15)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3137222","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3137222","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.896.2025","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.896.2025","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/2011/06/11/bioinformatics.btr348.full.pdf","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:27/15/2163","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/15/2163","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"doi:10.3929/ethz-b-000038734","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000038734","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Other"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr348","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr348","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/15/2163/48865208/bioinformatics_27_15_2163.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321652","display_name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich","ror":"https://ror.org/05a28rw58"},{"id":"https://openalex.org/F4320327577","display_name":"SystemsX.ch","ror":"https://ror.org/02s09gf16"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2120508443.pdf","grobid_xml":"https://content.openalex.org/works/W2120508443.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1990536986","https://openalex.org/W2026507477","https://openalex.org/W2026826116","https://openalex.org/W2035503835","https://openalex.org/W2085277871","https://openalex.org/W2092717237","https://openalex.org/W2096739999","https://openalex.org/W2108067237","https://openalex.org/W2164886036","https://openalex.org/W6657103972"],"related_works":["https://openalex.org/W2075996317","https://openalex.org/W2027377285","https://openalex.org/W4247375799","https://openalex.org/W2372005294","https://openalex.org/W2065110017","https://openalex.org/W2048490996","https://openalex.org/W2073620476","https://openalex.org/W2080971378","https://openalex.org/W3144105522","https://openalex.org/W2116772258"],"abstract_inverted_index":{"MOTIVATION:":[0],"Chemical":[1],"cross-linking":[2],"of":[3,13,70,85],"proteins":[4],"or":[5,115],"protein":[6,48,62,104],"complexes":[7],"and":[8,42,52,68],"the":[9,14,30,37,66,83,86,94,103],"mass":[10],"spectrometry-based":[11],"localization":[12],"cross-linked":[15,58],"amino":[16,59,91],"acids":[17,60],"in":[18],"peptide":[19],"sequences":[20],"is":[21,108],"a":[22,75,112],"powerful":[23],"method":[24],"for":[25,40],"generating":[26],"distance":[27],"restraints":[28],"on":[29,46,61],"substrate's":[31],"topology.":[32],"RESULTS:":[33],"Here,":[34],"we":[35],"introduce":[36],"algorithm":[38],"Xwalk":[39,50,107],"predicting":[41],"validating":[43],"these":[44],"cross-links":[45],"existing":[47],"structures.":[49],"calculates":[51],"displays":[53],"non-linear":[54],"distances":[55],"between":[56,89],"chemically":[57],"surfaces,":[63],"while":[64],"mimicking":[65],"flexibility":[67],"non-linearity":[69],"cross-linker":[71],"molecules.":[72],"It":[73],"returns":[74],"'solvent":[76],"accessible":[77],"surface":[78],"distance',":[79],"which":[80],"corresponds":[81],"to":[82],"length":[84],"shortest":[87],"path":[88,95],"two":[90],"acids,":[92],"where":[93],"leads":[96],"through":[97],"solvent":[98],"occupied":[99],"space":[100],"without":[101],"penetrating":[102],"surface.":[105],"AVAILABILITY:":[106],"freely":[109],"available":[110],"as":[111],"web":[113],"server":[114],"stand-alone":[116],"JAVA":[117],"application":[118],"at":[119],"http://www.xwalk.org.":[120]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":13},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":5}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
