A new bioconcentration factor model based on SMILES and indices of presence of atoms
Indices of the presence of atoms (IPA) encode the presence or absence of atoms, such as nitrogen, oxygen, sulphur, phosphorus, fluorine, chlorine, and bromine in a molecule. They are calculated with the simplified molecular input line entry system (SMILES). Using the Monte Carlo method for correlati...
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| Veröffentlicht in: | European journal of medicinal chemistry 2010-09, Vol.45 (9), p.4399-4402 |
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| container_title | European journal of medicinal chemistry |
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| creator | Toropova, A.P. Toropov, A.A. Lombardo, A. Roncaglioni, A. Benfenati, E. Gini, G. |
| description | Indices of the presence of atoms (IPA) encode the presence or absence of atoms, such as nitrogen, oxygen, sulphur, phosphorus, fluorine, chlorine, and bromine in a molecule. They are calculated with the simplified molecular input line entry system (SMILES). Using the Monte Carlo method for correlation weights of these indices, one can improve the predictive ability of optimal SMILES-based descriptors in quantitative structure–activity relationships (QSAR) for bioconcentration factor. The model without IPA gave the following results:
n
=
503,
r
2
=
0.6803,
q
2
=
0.6781,
s
=
0.759,
F
=
1066 (subtraining set);
n
=
322,
r
2
=
0.8181,
r
pred
2
=
0.8159,
s
=
0.565,
F
=
1439 (calibration set);
n
=
105,
r
2
=
0.6703,
r
pred
2
=
0.6577,
R
m
2
=
0.6628,
s
=
0.728,
F
=
209 (test set);
n
=
106,
r
2
=
0.6624,
r
pred
2
=
0.6502,
R
m
2
=
0.6212,
s
=
0.757,
F
=
204 (validation set) The model with IPA gave:
n
=
503,
r
2
=
0.7082,
q
2
=
0.7062,
s
=
0.725,
F
=
1216 (subtraining set);
n
=
322,
r
2
=
0.8401,
r
pred
2
=
0.8383,
s
=
0.528,
F
=
1682 (calibration set);
n
=
105,
r
2
=
0.7489,
r
pred
2
=
0.7402,
R
m
2
=
0.7252,
s
=
0.637,
F
=
307 (test set);
n
=
106,
r
2
=
0.7306,
r
pred
2
=
0.7217,
R
m
2
=
0.7010,
s
=
0.680,
F
=
282 (validation set).
[Display omitted] |
| doi_str_mv | 10.1016/j.ejmech.2010.06.019 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_748956716</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0223523410004630</els_id><sourcerecordid>748956716</sourcerecordid><originalsourceid>FETCH-LOGICAL-c391t-bac57a141569b56c974cd2479cfb8f808322c41144c5890d66764b10f156df7c3</originalsourceid><addsrcrecordid>eNp9kE1vEzEQhi0EomnLP0DIF8RpU397fUGqqgKVUnFoe7a8Y1s42l0He9OKf4-jBLhxmtHoeWdGD0LvKVlTQtXVdh22U4Afa0baiKg1oeYVWlGt-o4zKV6jFWGMd5JxcYbOa90SQqQi5C06Y0Qaw4xeocdrPIcXPKQMeYYwL8UtKc84OlhywVP2YcSDq8HjNn24v9vcPmA3e5xmnyBUnCPelVBDCx96t-SpXqI30Y01vDvVC_T05fbx5lu3-f717uZ60wE3dOkGB1I7KqhUZpAKjBbgmdAG4tDHnvScMRCUCgGyN8QrpZUYKIkt4KMGfoE-HffuSv65D3WxU6oQxtHNIe-r1aI3UmmqGimOJJRcawnR7kqaXPllKbEHnXZrjzrtQaclyjadLfbhdGA_TMH_Df3x14CPJ8BVcGMsboZU_3Gcas41adznIxeajucUiq2QDs58KgEW63P6_ye_AePAkyg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>748956716</pqid></control><display><type>article</type><title>A new bioconcentration factor model based on SMILES and indices of presence of atoms</title><source>MEDLINE</source><source>Access via ScienceDirect (Elsevier)</source><creator>Toropova, A.P. ; Toropov, A.A. ; Lombardo, A. ; Roncaglioni, A. ; Benfenati, E. ; Gini, G.</creator><creatorcontrib>Toropova, A.P. ; Toropov, A.A. ; Lombardo, A. ; Roncaglioni, A. ; Benfenati, E. ; Gini, G.</creatorcontrib><description>Indices of the presence of atoms (IPA) encode the presence or absence of atoms, such as nitrogen, oxygen, sulphur, phosphorus, fluorine, chlorine, and bromine in a molecule. They are calculated with the simplified molecular input line entry system (SMILES). Using the Monte Carlo method for correlation weights of these indices, one can improve the predictive ability of optimal SMILES-based descriptors in quantitative structure–activity relationships (QSAR) for bioconcentration factor. The model without IPA gave the following results:
n
=
503,
r
2
=
0.6803,
q
2
=
0.6781,
s
=
0.759,
F
=
1066 (subtraining set);
n
=
322,
r
2
=
0.8181,
r
pred
2
=
0.8159,
s
=
0.565,
F
=
1439 (calibration set);
n
=
105,
r
2
=
0.6703,
r
pred
2
=
0.6577,
R
m
2
=
0.6628,
s
=
0.728,
F
=
209 (test set);
n
=
106,
r
2
=
0.6624,
r
pred
2
=
0.6502,
R
m
2
=
0.6212,
s
=
0.757,
F
=
204 (validation set) The model with IPA gave:
n
=
503,
r
2
=
0.7082,
q
2
=
0.7062,
s
=
0.725,
F
=
1216 (subtraining set);
n
=
322,
r
2
=
0.8401,
r
pred
2
=
0.8383,
s
=
0.528,
F
=
1682 (calibration set);
n
=
105,
r
2
=
0.7489,
r
pred
2
=
0.7402,
R
m
2
=
0.7252,
s
=
0.637,
F
=
307 (test set);
n
=
106,
r
2
=
0.7306,
r
pred
2
=
0.7217,
R
m
2
=
0.7010,
s
=
0.680,
F
=
282 (validation set).
[Display omitted]</description><identifier>ISSN: 0223-5234</identifier><identifier>EISSN: 1768-3254</identifier><identifier>DOI: 10.1016/j.ejmech.2010.06.019</identifier><identifier>PMID: 20599297</identifier><identifier>CODEN: EJMCA5</identifier><language>eng</language><publisher>Kidlington: Elsevier Masson SAS</publisher><subject>Balance of correlations ; Bioconcentration factor ; Biological and medical sciences ; General pharmacology ; Index of presence of atoms ; Medical sciences ; Models, Theoretical ; Pharmacology. Drug treatments ; Physicochemical properties. Structure-activity relationships ; QSAR ; Quantitative Structure-Activity Relationship ; SMILES</subject><ispartof>European journal of medicinal chemistry, 2010-09, Vol.45 (9), p.4399-4402</ispartof><rights>2010 Elsevier Masson SAS</rights><rights>2015 INIST-CNRS</rights><rights>2010 Elsevier Masson SAS. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c391t-bac57a141569b56c974cd2479cfb8f808322c41144c5890d66764b10f156df7c3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ejmech.2010.06.019$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23173370$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20599297$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Toropova, A.P.</creatorcontrib><creatorcontrib>Toropov, A.A.</creatorcontrib><creatorcontrib>Lombardo, A.</creatorcontrib><creatorcontrib>Roncaglioni, A.</creatorcontrib><creatorcontrib>Benfenati, E.</creatorcontrib><creatorcontrib>Gini, G.</creatorcontrib><title>A new bioconcentration factor model based on SMILES and indices of presence of atoms</title><title>European journal of medicinal chemistry</title><addtitle>Eur J Med Chem</addtitle><description>Indices of the presence of atoms (IPA) encode the presence or absence of atoms, such as nitrogen, oxygen, sulphur, phosphorus, fluorine, chlorine, and bromine in a molecule. They are calculated with the simplified molecular input line entry system (SMILES). Using the Monte Carlo method for correlation weights of these indices, one can improve the predictive ability of optimal SMILES-based descriptors in quantitative structure–activity relationships (QSAR) for bioconcentration factor. The model without IPA gave the following results:
n
=
503,
r
2
=
0.6803,
q
2
=
0.6781,
s
=
0.759,
F
=
1066 (subtraining set);
n
=
322,
r
2
=
0.8181,
r
pred
2
=
0.8159,
s
=
0.565,
F
=
1439 (calibration set);
n
=
105,
r
2
=
0.6703,
r
pred
2
=
0.6577,
R
m
2
=
0.6628,
s
=
0.728,
F
=
209 (test set);
n
=
106,
r
2
=
0.6624,
r
pred
2
=
0.6502,
R
m
2
=
0.6212,
s
=
0.757,
F
=
204 (validation set) The model with IPA gave:
n
=
503,
r
2
=
0.7082,
q
2
=
0.7062,
s
=
0.725,
F
=
1216 (subtraining set);
n
=
322,
r
2
=
0.8401,
r
pred
2
=
0.8383,
s
=
0.528,
F
=
1682 (calibration set);
n
=
105,
r
2
=
0.7489,
r
pred
2
=
0.7402,
R
m
2
=
0.7252,
s
=
0.637,
F
=
307 (test set);
n
=
106,
r
2
=
0.7306,
r
pred
2
=
0.7217,
R
m
2
=
0.7010,
s
=
0.680,
F
=
282 (validation set).
[Display omitted]</description><subject>Balance of correlations</subject><subject>Bioconcentration factor</subject><subject>Biological and medical sciences</subject><subject>General pharmacology</subject><subject>Index of presence of atoms</subject><subject>Medical sciences</subject><subject>Models, Theoretical</subject><subject>Pharmacology. Drug treatments</subject><subject>Physicochemical properties. Structure-activity relationships</subject><subject>QSAR</subject><subject>Quantitative Structure-Activity Relationship</subject><subject>SMILES</subject><issn>0223-5234</issn><issn>1768-3254</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kE1vEzEQhi0EomnLP0DIF8RpU397fUGqqgKVUnFoe7a8Y1s42l0He9OKf4-jBLhxmtHoeWdGD0LvKVlTQtXVdh22U4Afa0baiKg1oeYVWlGt-o4zKV6jFWGMd5JxcYbOa90SQqQi5C06Y0Qaw4xeocdrPIcXPKQMeYYwL8UtKc84OlhywVP2YcSDq8HjNn24v9vcPmA3e5xmnyBUnCPelVBDCx96t-SpXqI30Y01vDvVC_T05fbx5lu3-f717uZ60wE3dOkGB1I7KqhUZpAKjBbgmdAG4tDHnvScMRCUCgGyN8QrpZUYKIkt4KMGfoE-HffuSv65D3WxU6oQxtHNIe-r1aI3UmmqGimOJJRcawnR7kqaXPllKbEHnXZrjzrtQaclyjadLfbhdGA_TMH_Df3x14CPJ8BVcGMsboZU_3Gcas41adznIxeajucUiq2QDs58KgEW63P6_ye_AePAkyg</recordid><startdate>20100901</startdate><enddate>20100901</enddate><creator>Toropova, A.P.</creator><creator>Toropov, A.A.</creator><creator>Lombardo, A.</creator><creator>Roncaglioni, A.</creator><creator>Benfenati, E.</creator><creator>Gini, G.</creator><general>Elsevier Masson SAS</general><general>Elsevier</general><scope>IQODW</scope><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>20100901</creationdate><title>A new bioconcentration factor model based on SMILES and indices of presence of atoms</title><author>Toropova, A.P. ; Toropov, A.A. ; Lombardo, A. ; Roncaglioni, A. ; Benfenati, E. ; Gini, G.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c391t-bac57a141569b56c974cd2479cfb8f808322c41144c5890d66764b10f156df7c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Balance of correlations</topic><topic>Bioconcentration factor</topic><topic>Biological and medical sciences</topic><topic>General pharmacology</topic><topic>Index of presence of atoms</topic><topic>Medical sciences</topic><topic>Models, Theoretical</topic><topic>Pharmacology. Drug treatments</topic><topic>Physicochemical properties. Structure-activity relationships</topic><topic>QSAR</topic><topic>Quantitative Structure-Activity Relationship</topic><topic>SMILES</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Toropova, A.P.</creatorcontrib><creatorcontrib>Toropov, A.A.</creatorcontrib><creatorcontrib>Lombardo, A.</creatorcontrib><creatorcontrib>Roncaglioni, A.</creatorcontrib><creatorcontrib>Benfenati, E.</creatorcontrib><creatorcontrib>Gini, G.</creatorcontrib><collection>Pascal-Francis</collection><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>European journal of medicinal chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Toropova, A.P.</au><au>Toropov, A.A.</au><au>Lombardo, A.</au><au>Roncaglioni, A.</au><au>Benfenati, E.</au><au>Gini, G.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A new bioconcentration factor model based on SMILES and indices of presence of atoms</atitle><jtitle>European journal of medicinal chemistry</jtitle><addtitle>Eur J Med Chem</addtitle><date>2010-09-01</date><risdate>2010</risdate><volume>45</volume><issue>9</issue><spage>4399</spage><epage>4402</epage><pages>4399-4402</pages><issn>0223-5234</issn><eissn>1768-3254</eissn><coden>EJMCA5</coden><abstract>Indices of the presence of atoms (IPA) encode the presence or absence of atoms, such as nitrogen, oxygen, sulphur, phosphorus, fluorine, chlorine, and bromine in a molecule. They are calculated with the simplified molecular input line entry system (SMILES). Using the Monte Carlo method for correlation weights of these indices, one can improve the predictive ability of optimal SMILES-based descriptors in quantitative structure–activity relationships (QSAR) for bioconcentration factor. The model without IPA gave the following results:
n
=
503,
r
2
=
0.6803,
q
2
=
0.6781,
s
=
0.759,
F
=
1066 (subtraining set);
n
=
322,
r
2
=
0.8181,
r
pred
2
=
0.8159,
s
=
0.565,
F
=
1439 (calibration set);
n
=
105,
r
2
=
0.6703,
r
pred
2
=
0.6577,
R
m
2
=
0.6628,
s
=
0.728,
F
=
209 (test set);
n
=
106,
r
2
=
0.6624,
r
pred
2
=
0.6502,
R
m
2
=
0.6212,
s
=
0.757,
F
=
204 (validation set) The model with IPA gave:
n
=
503,
r
2
=
0.7082,
q
2
=
0.7062,
s
=
0.725,
F
=
1216 (subtraining set);
n
=
322,
r
2
=
0.8401,
r
pred
2
=
0.8383,
s
=
0.528,
F
=
1682 (calibration set);
n
=
105,
r
2
=
0.7489,
r
pred
2
=
0.7402,
R
m
2
=
0.7252,
s
=
0.637,
F
=
307 (test set);
n
=
106,
r
2
=
0.7306,
r
pred
2
=
0.7217,
R
m
2
=
0.7010,
s
=
0.680,
F
=
282 (validation set).
[Display omitted]</abstract><cop>Kidlington</cop><pub>Elsevier Masson SAS</pub><pmid>20599297</pmid><doi>10.1016/j.ejmech.2010.06.019</doi><tpages>4</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0223-5234 |
| ispartof | European journal of medicinal chemistry, 2010-09, Vol.45 (9), p.4399-4402 |
| issn | 0223-5234 1768-3254 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_748956716 |
| source | MEDLINE; Access via ScienceDirect (Elsevier) |
| subjects | Balance of correlations Bioconcentration factor Biological and medical sciences General pharmacology Index of presence of atoms Medical sciences Models, Theoretical Pharmacology. Drug treatments Physicochemical properties. Structure-activity relationships QSAR Quantitative Structure-Activity Relationship SMILES |
| title | A new bioconcentration factor model based on SMILES and indices of presence of atoms |
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