A comparison of the Low Mode and Monte Carlo conformational search methods
The Low Mode (LM) and Monte Carlo (MC) conformational search methods were compared on three diverse molecular systems; (4 R, 5 S, 6 S, 7 R)-hexahydro-5,6-dihydroxy-1,3,4,7-tetrakis(phenylmethyl)-2H-1,3-diazapin-2-one ( 1), 2-methoxy-2-phenyl-2-triflouromethyl- N-α-methyl benzyl propanamide ( 2) and...
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| Veröffentlicht in: | Journal of molecular graphics & modelling 2002-10, Vol.21 (2), p.129-150 |
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| container_title | Journal of molecular graphics & modelling |
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| creator | Parish, Carol Lombardi, Rosina Sinclair, Kent Smith, Emelyn Goldberg, Alla Rappleye, Melissa Dure, Myrianne |
| description | The Low Mode (LM) and Monte Carlo (MC) conformational search methods were compared on three diverse molecular systems; (4
R, 5
S, 6
S, 7
R)-hexahydro-5,6-dihydroxy-1,3,4,7-tetrakis(phenylmethyl)-2H-1,3-diazapin-2-one (
1), 2-methoxy-2-phenyl-2-triflouromethyl-
N-α-methyl benzyl propanamide (
2) and a trimeric 39-membered polyazamacrolide (
3). We find that either method, or a combination of the methods, is equally efficient at searching the conformational space of the smaller molecular systems while a 50:50 hybrid of Low Mode and Monte Carlo is most efficient at searching the space of the larger molecular system. |
| doi_str_mv | 10.1016/S1093-3263(02)00144-4 |
| format | Article |
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R, 5
S, 6
S, 7
R)-hexahydro-5,6-dihydroxy-1,3,4,7-tetrakis(phenylmethyl)-2H-1,3-diazapin-2-one (
1), 2-methoxy-2-phenyl-2-triflouromethyl-
N-α-methyl benzyl propanamide (
2) and a trimeric 39-membered polyazamacrolide (
3). We find that either method, or a combination of the methods, is equally efficient at searching the conformational space of the smaller molecular systems while a 50:50 hybrid of Low Mode and Monte Carlo is most efficient at searching the space of the larger molecular system.</description><identifier>ISSN: 1093-3263</identifier><identifier>EISSN: 1873-4243</identifier><identifier>DOI: 10.1016/S1093-3263(02)00144-4</identifier><identifier>PMID: 12398344</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Algorithms ; Amides - chemistry ; Conformational analysis ; Cyclic urea ; Fluorobenzenes - chemistry ; Heterocyclic Compounds, 1-Ring - chemistry ; Hydrogen Bonding ; Low Mode ; Macrolides - chemistry ; Models, Molecular ; Molecular Conformation ; Molecular flexibility ; Molecular Structure ; Monte Carlo ; Monte Carlo Method ; Mosher amide ; Polyazamacrolide ; Software ; Urea - chemistry</subject><ispartof>Journal of molecular graphics & modelling, 2002-10, Vol.21 (2), p.129-150</ispartof><rights>2002 Elsevier Science Inc.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c413t-d0f6c0b16779d5cb1fe39754976754d7cb202f78a40eb0b7b7ca4ccba4c4c1d43</citedby><cites>FETCH-LOGICAL-c413t-d0f6c0b16779d5cb1fe39754976754d7cb202f78a40eb0b7b7ca4ccba4c4c1d43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/S1093-3263(02)00144-4$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3548,27923,27924,45994</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/12398344$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Parish, Carol</creatorcontrib><creatorcontrib>Lombardi, Rosina</creatorcontrib><creatorcontrib>Sinclair, Kent</creatorcontrib><creatorcontrib>Smith, Emelyn</creatorcontrib><creatorcontrib>Goldberg, Alla</creatorcontrib><creatorcontrib>Rappleye, Melissa</creatorcontrib><creatorcontrib>Dure, Myrianne</creatorcontrib><title>A comparison of the Low Mode and Monte Carlo conformational search methods</title><title>Journal of molecular graphics & modelling</title><addtitle>J Mol Graph Model</addtitle><description>The Low Mode (LM) and Monte Carlo (MC) conformational search methods were compared on three diverse molecular systems; (4
R, 5
S, 6
S, 7
R)-hexahydro-5,6-dihydroxy-1,3,4,7-tetrakis(phenylmethyl)-2H-1,3-diazapin-2-one (
1), 2-methoxy-2-phenyl-2-triflouromethyl-
N-α-methyl benzyl propanamide (
2) and a trimeric 39-membered polyazamacrolide (
3). We find that either method, or a combination of the methods, is equally efficient at searching the conformational space of the smaller molecular systems while a 50:50 hybrid of Low Mode and Monte Carlo is most efficient at searching the space of the larger molecular system.</description><subject>Algorithms</subject><subject>Amides - chemistry</subject><subject>Conformational analysis</subject><subject>Cyclic urea</subject><subject>Fluorobenzenes - chemistry</subject><subject>Heterocyclic Compounds, 1-Ring - chemistry</subject><subject>Hydrogen Bonding</subject><subject>Low Mode</subject><subject>Macrolides - chemistry</subject><subject>Models, Molecular</subject><subject>Molecular Conformation</subject><subject>Molecular flexibility</subject><subject>Molecular Structure</subject><subject>Monte Carlo</subject><subject>Monte Carlo Method</subject><subject>Mosher amide</subject><subject>Polyazamacrolide</subject><subject>Software</subject><subject>Urea - chemistry</subject><issn>1093-3263</issn><issn>1873-4243</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2002</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkE1PwzAMhiMEYjD4CaCcEBwKTpM16wlNE58a4gCcozRxtaC2GUkH4t-TfSCOXGwfHvuVH0JOGFwyYMXVC4OSZzwv-DnkFwBMiEzskAM2ljwTueC7af5FBuQwxncA4GOQ-2TAcl6OuRAH5HFCjW8XOrjoO-pr2s-RzvwXffIWqe5sGroe6VSHxie0q31ode98pxsaUQczpy32c2_jEdmrdRPxeNuH5O325nV6n82e7x6mk1lmBON9ZqEuDFSskLK0I1OxGnkpR6KURapWmiqHvJZjLQArqGQljRbGVKkIw6zgQ3K2ubsI_mOJsVetiwabRnfol1HJ9HCyUCRwtAFN8DEGrNUiuFaHb8VArSSqtUS1MqQgV2uJahVwug1YVi3av62ttQRcbwBMb346DCoah51B6wKaXlnv_on4ATGKgMw</recordid><startdate>20021001</startdate><enddate>20021001</enddate><creator>Parish, Carol</creator><creator>Lombardi, Rosina</creator><creator>Sinclair, Kent</creator><creator>Smith, Emelyn</creator><creator>Goldberg, Alla</creator><creator>Rappleye, Melissa</creator><creator>Dure, Myrianne</creator><general>Elsevier Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20021001</creationdate><title>A comparison of the Low Mode and Monte Carlo conformational search methods</title><author>Parish, Carol ; Lombardi, Rosina ; Sinclair, Kent ; Smith, Emelyn ; Goldberg, Alla ; Rappleye, Melissa ; Dure, Myrianne</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c413t-d0f6c0b16779d5cb1fe39754976754d7cb202f78a40eb0b7b7ca4ccba4c4c1d43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2002</creationdate><topic>Algorithms</topic><topic>Amides - chemistry</topic><topic>Conformational analysis</topic><topic>Cyclic urea</topic><topic>Fluorobenzenes - chemistry</topic><topic>Heterocyclic Compounds, 1-Ring - chemistry</topic><topic>Hydrogen Bonding</topic><topic>Low Mode</topic><topic>Macrolides - chemistry</topic><topic>Models, Molecular</topic><topic>Molecular Conformation</topic><topic>Molecular flexibility</topic><topic>Molecular Structure</topic><topic>Monte Carlo</topic><topic>Monte Carlo Method</topic><topic>Mosher amide</topic><topic>Polyazamacrolide</topic><topic>Software</topic><topic>Urea - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Parish, Carol</creatorcontrib><creatorcontrib>Lombardi, Rosina</creatorcontrib><creatorcontrib>Sinclair, Kent</creatorcontrib><creatorcontrib>Smith, Emelyn</creatorcontrib><creatorcontrib>Goldberg, Alla</creatorcontrib><creatorcontrib>Rappleye, Melissa</creatorcontrib><creatorcontrib>Dure, Myrianne</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of molecular graphics & modelling</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Parish, Carol</au><au>Lombardi, Rosina</au><au>Sinclair, Kent</au><au>Smith, Emelyn</au><au>Goldberg, Alla</au><au>Rappleye, Melissa</au><au>Dure, Myrianne</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A comparison of the Low Mode and Monte Carlo conformational search methods</atitle><jtitle>Journal of molecular graphics & modelling</jtitle><addtitle>J Mol Graph Model</addtitle><date>2002-10-01</date><risdate>2002</risdate><volume>21</volume><issue>2</issue><spage>129</spage><epage>150</epage><pages>129-150</pages><issn>1093-3263</issn><eissn>1873-4243</eissn><abstract>The Low Mode (LM) and Monte Carlo (MC) conformational search methods were compared on three diverse molecular systems; (4
R, 5
S, 6
S, 7
R)-hexahydro-5,6-dihydroxy-1,3,4,7-tetrakis(phenylmethyl)-2H-1,3-diazapin-2-one (
1), 2-methoxy-2-phenyl-2-triflouromethyl-
N-α-methyl benzyl propanamide (
2) and a trimeric 39-membered polyazamacrolide (
3). We find that either method, or a combination of the methods, is equally efficient at searching the conformational space of the smaller molecular systems while a 50:50 hybrid of Low Mode and Monte Carlo is most efficient at searching the space of the larger molecular system.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>12398344</pmid><doi>10.1016/S1093-3263(02)00144-4</doi><tpages>22</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1093-3263 |
| ispartof | Journal of molecular graphics & modelling, 2002-10, Vol.21 (2), p.129-150 |
| issn | 1093-3263 1873-4243 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_72631876 |
| source | MEDLINE; ScienceDirect Journals (5 years ago - present) |
| subjects | Algorithms Amides - chemistry Conformational analysis Cyclic urea Fluorobenzenes - chemistry Heterocyclic Compounds, 1-Ring - chemistry Hydrogen Bonding Low Mode Macrolides - chemistry Models, Molecular Molecular Conformation Molecular flexibility Molecular Structure Monte Carlo Monte Carlo Method Mosher amide Polyazamacrolide Software Urea - chemistry |
| title | A comparison of the Low Mode and Monte Carlo conformational search methods |
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