{"id":"https://openalex.org/W2207471390","doi":"https://doi.org/10.1109/bibm.2015.7359854","title":"Visualizing the topology and re-analyzing the causes of small-world property of amino acid network","display_name":"Visualizing the topology and re-analyzing the causes of small-world property of amino acid network","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2207471390","doi":"https://doi.org/10.1109/bibm.2015.7359854","mag":"2207471390"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2015.7359854","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359854","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5033688848","display_name":"Yongpan Hua","orcid":null},"institutions":[{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]},{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yongpan Hua","raw_affiliation_strings":["College of Computer Science, Sichuan University, Chengdu, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I4210125143","https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101891598","display_name":"Xiuchan Xiao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]},{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiuchan Xiao","raw_affiliation_strings":["College of Computer Science, Sichuan University, Chengdu, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I4210125143","https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050314106","display_name":"Min Zhu","orcid":"https://orcid.org/0000-0002-5664-1558"},"institutions":[{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]},{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Min Zhu","raw_affiliation_strings":["College of Computer Science, Sichuan University, Chengdu, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I4210125143","https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008767990","display_name":"Yangxu Wang","orcid":"https://orcid.org/0009-0004-6529-8052"},"institutions":[{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]},{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yangxu Wang","raw_affiliation_strings":["College of Computer Science, Sichuan University, Chengdu, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I4210125143","https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100703866","display_name":"Menglong Li","orcid":"https://orcid.org/0000-0001-7365-0344"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Menglong Li","raw_affiliation_strings":["College of Chemistry, Sichuan University, Chengdu, China"],"affiliations":[{"raw_affiliation_string":"College of Chemistry, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5033688848"],"corresponding_institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210125143"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07145081,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1209","last_page":"1215"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9988999962806702,"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":0.9988999962806702,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9984999895095825,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.9891999959945679,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.6461109519004822},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.6032979488372803},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5929529666900635},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5293287038803101},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.5032936930656433},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.48985955119132996},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.45700135827064514},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.4515692889690399},{"id":"https://openalex.org/keywords/network-structure","display_name":"Network structure","score":0.44370895624160767},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.42210492491722107},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35479235649108887},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3363625407218933},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3230615556240082},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23835191130638123},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.20325449109077454},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1833454668521881},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11403179168701172},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.08248031139373779}],"concepts":[{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.6461109519004822},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.6032979488372803},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5929529666900635},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5293287038803101},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5032936930656433},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.48985955119132996},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.45700135827064514},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.4515692889690399},{"id":"https://openalex.org/C2988224531","wikidata":"https://www.wikidata.org/wiki/Q20830730","display_name":"Network structure","level":2,"score":0.44370895624160767},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.42210492491722107},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35479235649108887},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3363625407218933},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3230615556240082},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23835191130638123},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.20325449109077454},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1833454668521881},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11403179168701172},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.08248031139373779},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2015.7359854","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359854","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W88407908","https://openalex.org/W229097380","https://openalex.org/W1540530720","https://openalex.org/W1819481941","https://openalex.org/W1964439982","https://openalex.org/W1965817297","https://openalex.org/W1965894900","https://openalex.org/W1973394305","https://openalex.org/W1973897761","https://openalex.org/W1980934601","https://openalex.org/W1987958688","https://openalex.org/W2006356944","https://openalex.org/W2007268492","https://openalex.org/W2008708467","https://openalex.org/W2014415120","https://openalex.org/W2039883288","https://openalex.org/W2040956707","https://openalex.org/W2042547992","https://openalex.org/W2044483297","https://openalex.org/W2049277949","https://openalex.org/W2073660699","https://openalex.org/W2097944242","https://openalex.org/W2101414808","https://openalex.org/W2107498970","https://openalex.org/W2108101947","https://openalex.org/W2111697874","https://openalex.org/W2112090702","https://openalex.org/W2121029982","https://openalex.org/W2124663041","https://openalex.org/W2125910575","https://openalex.org/W2128044898","https://openalex.org/W2132022337","https://openalex.org/W2139447922","https://openalex.org/W2141366228","https://openalex.org/W2142001247","https://openalex.org/W2148768886","https://openalex.org/W2153953580","https://openalex.org/W2155142785","https://openalex.org/W2158346543","https://openalex.org/W2160257187","https://openalex.org/W2160784118","https://openalex.org/W2164243919","https://openalex.org/W2166468869","https://openalex.org/W2168708922","https://openalex.org/W2168904132","https://openalex.org/W2184417913","https://openalex.org/W2469279958","https://openalex.org/W4298884898","https://openalex.org/W6608852248","https://openalex.org/W6668826556"],"related_works":["https://openalex.org/W4206825711","https://openalex.org/W2400206922","https://openalex.org/W2036623301","https://openalex.org/W2728406523","https://openalex.org/W2117898316","https://openalex.org/W1999214538","https://openalex.org/W2157750263","https://openalex.org/W2343724234","https://openalex.org/W2270029940","https://openalex.org/W1588073457"],"abstract_inverted_index":{"Amino":[0],"acid":[1,39,92,137,146,195,199],"network":[2,18,93,147,189,200,231],"is":[3,148,201],"the":[4,12,31,69,73,96,151,162,166,173,182],"reduced":[5],"representation":[6],"of":[7,14,27,75,85,90,98,132,142,165,168,176,213],"protein":[8,15,28,52,57,76,86,143,169,228],"structure,":[9],"which":[10,215],"benefits":[11],"investigation":[13],"structure.":[16],"And":[17,197],"paradigm":[19],"offers":[20],"an":[21,64],"insight":[22],"into":[23],"viewing":[24],"global":[25],"connectivity":[26],"and":[29,72,94,109,111,150,171,178,181,206],"studying":[30],"interaction":[32,183],"between":[33,184],"secondary":[34,99,125,140,185],"structures":[35,53,122,126,170,180],"by":[36,203,230],"visualizing":[37],"amino":[38,91,136,145,194,198],"networks.":[40,196],"However,":[41],"there":[42],"exists":[43],"some":[44],"disadvantages":[45],"in":[46,130,135,144,158],"current":[47,79],"research.":[48],"Much":[49],"research":[50,80],"about":[51],"are":[54],"based":[55],"on":[56],"contact":[58],"map,":[59],"but":[60,123],"it":[61],"cannot":[62],"provide":[63],"easy":[65],"way":[66],"to":[67,160,192,209,226],"present":[68,105],"local":[70],"regularity":[71,153],"topology":[74,167],"structures.":[77,100],"Until":[78],"recently":[81],"consider":[82],"primary":[83,121],"structure":[84,141,229],"cause":[87],"small-world":[88,133,155],"property":[89,134],"neglect":[95],"effects":[97],"In":[101],"this":[102],"paper,":[103],"we":[104,187],"two":[106],"algorithms":[107],"RandomSS":[108],"RandomSC,":[110],"compare":[112],"them":[113],"with":[114],"RandomNN":[115],"algorithm.":[116],"We":[117],"find":[118],"not":[119],"only":[120],"also":[124,221],"play":[127],"key":[128],"roles":[129],"emergence":[131],"network.":[138],"The":[139],"regular,":[149],"inherent":[152],"reinforces":[154],"property.":[156],"Moreover,":[157],"order":[159],"reveal":[161],"characteristic":[163],"patterns":[164],"visualize":[172],"regular":[174],"layout":[175],"Helix":[177],"Sheet":[179],"structures,":[186],"use":[188],"visualization":[190],"methods":[191],"show":[193,210],"visualized":[202],"macroscopic":[204],"view":[205,208,225],"microscopic":[207],"different":[211],"regions":[212],"protein,":[214],"own":[216],"various":[217],"roles.":[218],"This":[219],"paper":[220],"provides":[222],"a":[223],"new":[224],"study":[227],"paradigm.":[232]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
