A β-Shape from the Voronoi Diagram of Atoms for Protein Structure Analysis
In this paper, we present a β-shape and a β-complex for a set of atoms with arbitrary sizes for a faster response to the topological queries among atoms. These concepts are the generalizations of the well-known α-shape and α-complex (and their weighted counterparts as well). To compute a β-shape, we...
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| creator | Seo, Jeongyeon Kim, Donguk Cho, Cheol-Hyung Kim, Deok-Soo |
| description | In this paper, we present a β-shape and a β-complex for a set of atoms with arbitrary sizes for a faster response to the topological queries among atoms. These concepts are the generalizations of the well-known α-shape and α-complex (and their weighted counterparts as well). To compute a β-shape, we first compute the Voronoi diagram of atoms and then transform the Voronoi diagram to a quasi-triangulation which is the topological dual of the Voronoi diagram. Then, we compute a β-complex from the quasi-triangulation by analyzing the valid intervals for each simplex in the quasi-triangulation. It is shown that a β-complex can be computed in O(m) time in the worst case from the Voronoi diagram of atoms, where m is the number of simplices in the quasi-triangulation. Then, a β-shape for a particular β consisting of k simplices can be located in O(log m + k) time in the worst case from the simplicies in the β-complex sorted according to the interval values. |
| doi_str_mv | 10.1007/11751540_12 |
| format | Conference Proceeding |
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J. Kenneth ; Mun, Youngsong</contributor><creatorcontrib>Seo, Jeongyeon ; Kim, Donguk ; Cho, Cheol-Hyung ; Kim, Deok-Soo ; Choo, Hyunseung ; Gervasi, Osvaldo ; Taniar, David ; Gavrilova, Marina ; Laganá, Antonio ; Kumar, Vipin ; Tan, C. J. Kenneth ; Mun, Youngsong</creatorcontrib><description>In this paper, we present a β-shape and a β-complex for a set of atoms with arbitrary sizes for a faster response to the topological queries among atoms. These concepts are the generalizations of the well-known α-shape and α-complex (and their weighted counterparts as well). To compute a β-shape, we first compute the Voronoi diagram of atoms and then transform the Voronoi diagram to a quasi-triangulation which is the topological dual of the Voronoi diagram. Then, we compute a β-complex from the quasi-triangulation by analyzing the valid intervals for each simplex in the quasi-triangulation. It is shown that a β-complex can be computed in O(m) time in the worst case from the Voronoi diagram of atoms, where m is the number of simplices in the quasi-triangulation. Then, a β-shape for a particular β consisting of k simplices can be located in O(log m + k) time in the worst case from the simplicies in the β-complex sorted according to the interval values.</description><identifier>ISSN: 0302-9743</identifier><identifier>ISBN: 354034070X</identifier><identifier>ISBN: 9783540340706</identifier><identifier>EISSN: 1611-3349</identifier><identifier>EISBN: 3540340718</identifier><identifier>EISBN: 9783540340713</identifier><identifier>DOI: 10.1007/11751540_12</identifier><language>eng</language><publisher>Berlin, Heidelberg: Springer Berlin Heidelberg</publisher><subject>Algorithmics. Computability. Computer arithmetics ; Applied sciences ; complex ; Computer science; control theory; systems ; Exact sciences and technology ; Information systems. Data bases ; Memory organisation. Data processing ; shape ; Software ; Theoretical computing ; Voronoi diagram of spheres</subject><ispartof>Computational Science and Its Applications - ICCSA 2006, 2006, p.101-110</ispartof><rights>Springer-Verlag Berlin Heidelberg 2006</rights><rights>2008 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c261t-11e6141aeddcbff966d84423d3aea20d296dee81798fa0405b8eb8eb928eeeee3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/11751540_12$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/11751540_12$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>309,310,775,776,780,785,786,789,4036,4037,27902,38232,41418,42487</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=19968219$$DView record in Pascal Francis$$Hfree_for_read</backlink></links><search><contributor>Choo, Hyunseung</contributor><contributor>Gervasi, Osvaldo</contributor><contributor>Taniar, David</contributor><contributor>Gavrilova, Marina</contributor><contributor>Laganá, Antonio</contributor><contributor>Kumar, Vipin</contributor><contributor>Tan, C. J. Kenneth</contributor><contributor>Mun, Youngsong</contributor><creatorcontrib>Seo, Jeongyeon</creatorcontrib><creatorcontrib>Kim, Donguk</creatorcontrib><creatorcontrib>Cho, Cheol-Hyung</creatorcontrib><creatorcontrib>Kim, Deok-Soo</creatorcontrib><title>A β-Shape from the Voronoi Diagram of Atoms for Protein Structure Analysis</title><title>Computational Science and Its Applications - ICCSA 2006</title><description>In this paper, we present a β-shape and a β-complex for a set of atoms with arbitrary sizes for a faster response to the topological queries among atoms. These concepts are the generalizations of the well-known α-shape and α-complex (and their weighted counterparts as well). To compute a β-shape, we first compute the Voronoi diagram of atoms and then transform the Voronoi diagram to a quasi-triangulation which is the topological dual of the Voronoi diagram. Then, we compute a β-complex from the quasi-triangulation by analyzing the valid intervals for each simplex in the quasi-triangulation. It is shown that a β-complex can be computed in O(m) time in the worst case from the Voronoi diagram of atoms, where m is the number of simplices in the quasi-triangulation. Then, a β-shape for a particular β consisting of k simplices can be located in O(log m + k) time in the worst case from the simplicies in the β-complex sorted according to the interval values.</description><subject>Algorithmics. Computability. Computer arithmetics</subject><subject>Applied sciences</subject><subject>complex</subject><subject>Computer science; control theory; systems</subject><subject>Exact sciences and technology</subject><subject>Information systems. Data bases</subject><subject>Memory organisation. Data processing</subject><subject>shape</subject><subject>Software</subject><subject>Theoretical computing</subject><subject>Voronoi diagram of spheres</subject><issn>0302-9743</issn><issn>1611-3349</issn><isbn>354034070X</isbn><isbn>9783540340706</isbn><isbn>3540340718</isbn><isbn>9783540340713</isbn><fulltext>true</fulltext><rsrctype>conference_proceeding</rsrctype><creationdate>2006</creationdate><recordtype>conference_proceeding</recordtype><recordid>eNpNkM1OwzAQhM2fRCg98QK-cOAQ8NquYx-j8isqgVRA3KJtYreBJq7s9NDX4kF4JlIVCUYrzUozmsNHyBmwS2AsuwLIRjCSrAC-R05E_wnJMtD7JAEFkAohzcFfwN4PScIE46nJpDgmwxg_WC8BSguVkMecfn-l0wWuLHXBN7RbWPrmg299Ta9rnAdsqHc073wTqfOBPgff2bql0y6sy24dLM1bXG5iHU_JkcNltMNfH5DX25uX8X06ebp7GOeTtOQKuhTAKpCAtqrKmXNGqUpLyUUl0CJnFTeqslZDZrRDJtlopu32DNd2KzEg57vdFcYSly5gW9axWIW6wbApwBilOZi-d7HrxT5q5zYUM-8_YwE9vB5l8Q-l-AHIamGa</recordid><startdate>2006</startdate><enddate>2006</enddate><creator>Seo, Jeongyeon</creator><creator>Kim, Donguk</creator><creator>Cho, Cheol-Hyung</creator><creator>Kim, Deok-Soo</creator><general>Springer Berlin Heidelberg</general><general>Springer</general><scope>IQODW</scope></search><sort><creationdate>2006</creationdate><title>A β-Shape from the Voronoi Diagram of Atoms for Protein Structure Analysis</title><author>Seo, Jeongyeon ; Kim, Donguk ; Cho, Cheol-Hyung ; Kim, Deok-Soo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c261t-11e6141aeddcbff966d84423d3aea20d296dee81798fa0405b8eb8eb928eeeee3</frbrgroupid><rsrctype>conference_proceedings</rsrctype><prefilter>conference_proceedings</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Algorithmics. Computability. Computer arithmetics</topic><topic>Applied sciences</topic><topic>complex</topic><topic>Computer science; control theory; systems</topic><topic>Exact sciences and technology</topic><topic>Information systems. Data bases</topic><topic>Memory organisation. Data processing</topic><topic>shape</topic><topic>Software</topic><topic>Theoretical computing</topic><topic>Voronoi diagram of spheres</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Seo, Jeongyeon</creatorcontrib><creatorcontrib>Kim, Donguk</creatorcontrib><creatorcontrib>Cho, Cheol-Hyung</creatorcontrib><creatorcontrib>Kim, Deok-Soo</creatorcontrib><collection>Pascal-Francis</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Seo, Jeongyeon</au><au>Kim, Donguk</au><au>Cho, Cheol-Hyung</au><au>Kim, Deok-Soo</au><au>Choo, Hyunseung</au><au>Gervasi, Osvaldo</au><au>Taniar, David</au><au>Gavrilova, Marina</au><au>Laganá, Antonio</au><au>Kumar, Vipin</au><au>Tan, C. J. Kenneth</au><au>Mun, Youngsong</au><format>book</format><genre>proceeding</genre><ristype>CONF</ristype><atitle>A β-Shape from the Voronoi Diagram of Atoms for Protein Structure Analysis</atitle><btitle>Computational Science and Its Applications - ICCSA 2006</btitle><date>2006</date><risdate>2006</risdate><spage>101</spage><epage>110</epage><pages>101-110</pages><issn>0302-9743</issn><eissn>1611-3349</eissn><isbn>354034070X</isbn><isbn>9783540340706</isbn><eisbn>3540340718</eisbn><eisbn>9783540340713</eisbn><abstract>In this paper, we present a β-shape and a β-complex for a set of atoms with arbitrary sizes for a faster response to the topological queries among atoms. These concepts are the generalizations of the well-known α-shape and α-complex (and their weighted counterparts as well). To compute a β-shape, we first compute the Voronoi diagram of atoms and then transform the Voronoi diagram to a quasi-triangulation which is the topological dual of the Voronoi diagram. Then, we compute a β-complex from the quasi-triangulation by analyzing the valid intervals for each simplex in the quasi-triangulation. It is shown that a β-complex can be computed in O(m) time in the worst case from the Voronoi diagram of atoms, where m is the number of simplices in the quasi-triangulation. Then, a β-shape for a particular β consisting of k simplices can be located in O(log m + k) time in the worst case from the simplicies in the β-complex sorted according to the interval values.</abstract><cop>Berlin, Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1007/11751540_12</doi><tpages>10</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0302-9743 |
| ispartof | Computational Science and Its Applications - ICCSA 2006, 2006, p.101-110 |
| issn | 0302-9743 1611-3349 |
| language | eng |
| recordid | cdi_pascalfrancis_primary_19968219 |
| source | Springer Books |
| subjects | Algorithmics. Computability. Computer arithmetics Applied sciences complex Computer science control theory systems Exact sciences and technology Information systems. Data bases Memory organisation. Data processing shape Software Theoretical computing Voronoi diagram of spheres |
| title | A β-Shape from the Voronoi Diagram of Atoms for Protein Structure Analysis |
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