Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies
To test and validate the Automated force field Topology Builder and Repository (ATB; http://compbio.biosci.uq.edu.au/atb/ ) the hydration free enthalpies for a set of 214 drug-like molecules, including 47 molecules that form part of the SAMPL4 challenge have been estimated using thermodynamic integr...
Gespeichert in:
| Veröffentlicht in: | Journal of computer-aided molecular design 2014-03, Vol.28 (3), p.221-233 |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 233 |
|---|---|
| container_issue | 3 |
| container_start_page | 221 |
| container_title | Journal of computer-aided molecular design |
| container_volume | 28 |
| creator | Koziara, Katarzyna B. Stroet, Martin Malde, Alpeshkumar K. Mark, Alan E. |
| description | To test and validate the Automated force field Topology Builder and Repository (ATB;
http://compbio.biosci.uq.edu.au/atb/
) the hydration free enthalpies for a set of 214 drug-like molecules, including 47 molecules that form part of the SAMPL4 challenge have been estimated using thermodynamic integration and compared to experiment. The calculations were performed using a fully automated protocol that incorporated a dynamic analysis of the convergence and integration error in the selection of intermediate points. The system has been designed and implemented such that hydration free enthalpies can be obtained without manual intervention following the submission of a molecule to the ATB. The overall average unsigned error (AUE) using ATB 2.0 topologies for the complete set of 214 molecules was 6.7 kJ/mol and for molecules within the SAMPL4 7.5 kJ/mol. The root mean square error (RMSE) was 9.5 and 10.0 kJ/mol respectively. However, for molecules containing functional groups that form part of the main GROMOS force field the AUE was 3.4 kJ/mol and the RMSE was 4.0 kJ/mol. This suggests it will be possible to further refine the parameters provided by the ATB based on hydration free enthalpies. |
| doi_str_mv | 10.1007/s10822-014-9713-7 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1671605233</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1671605233</sourcerecordid><originalsourceid>FETCH-LOGICAL-c405t-b069ba95e0dd868b156d28b244a68f62ead7a66e2913299e0a87ff4303055dc43</originalsourceid><addsrcrecordid>eNqFkc1q3DAURkVpaSbTPkA3RdBNsnByJVmS1d0k9A8C3UygOyFb1zMOHsuV7MC8fTU4KaVQutJC5_ukew8h7xhcMQB9nRhUnBfAysJoJgr9gqyY1KIojWQvyQoMh0LJ8scZOU_pAXLGKHhNznhZaq2NWZG0xTR1w466wdNH13feTV0YaGjptEe6madwcBN6ug1j6MPuSG_mrvcY6cVme3NJHzGmE8-v4CMdI_quec7vjz4uZW1EpDhMe9ePHaY35FXr-oRvn841uf_8aXv7tbj7_uXb7eauaEqQU1GDMrUzEsH7SlU1k8rzqs5_d6pqFUfntVMKuWGCG4PgKt22pQABUvqmFGtysfSOMfyc85z20KUG-94NGOZkmdJMgeRC_B-VHBhjPG95TT78hT6EOQ55kEwxU1YGhMoUW6gmhpQitnaM3cHFo2VgT_LsIs9mefYkz-qcef_UPNcH9L8Tz7YywBcg5athh_GPp__Z-gvzQaLq</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1519489036</pqid></control><display><type>article</type><title>Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies</title><source>MEDLINE</source><source>SpringerLink Journals - AutoHoldings</source><creator>Koziara, Katarzyna B. ; Stroet, Martin ; Malde, Alpeshkumar K. ; Mark, Alan E.</creator><creatorcontrib>Koziara, Katarzyna B. ; Stroet, Martin ; Malde, Alpeshkumar K. ; Mark, Alan E.</creatorcontrib><description>To test and validate the Automated force field Topology Builder and Repository (ATB;
http://compbio.biosci.uq.edu.au/atb/
) the hydration free enthalpies for a set of 214 drug-like molecules, including 47 molecules that form part of the SAMPL4 challenge have been estimated using thermodynamic integration and compared to experiment. The calculations were performed using a fully automated protocol that incorporated a dynamic analysis of the convergence and integration error in the selection of intermediate points. The system has been designed and implemented such that hydration free enthalpies can be obtained without manual intervention following the submission of a molecule to the ATB. The overall average unsigned error (AUE) using ATB 2.0 topologies for the complete set of 214 molecules was 6.7 kJ/mol and for molecules within the SAMPL4 7.5 kJ/mol. The root mean square error (RMSE) was 9.5 and 10.0 kJ/mol respectively. However, for molecules containing functional groups that form part of the main GROMOS force field the AUE was 3.4 kJ/mol and the RMSE was 4.0 kJ/mol. This suggests it will be possible to further refine the parameters provided by the ATB based on hydration free enthalpies.</description><identifier>ISSN: 0920-654X</identifier><identifier>EISSN: 1573-4951</identifier><identifier>DOI: 10.1007/s10822-014-9713-7</identifier><identifier>PMID: 24477799</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Algorithms ; Animal Anatomy ; Automated ; Chemical compounds ; Chemistry ; Chemistry and Materials Science ; Computer Applications in Chemistry ; Computer Simulation ; Construction ; Dissolution ; Dynamical systems ; Dynamics ; Enthalpy ; Errors ; Histology ; Hydration ; Models, Chemical ; Molecular structure ; Morphology ; Pharmaceutical Preparations - chemistry ; Physical Chemistry ; Solvents ; Thermodynamics ; Topology ; Water - chemistry</subject><ispartof>Journal of computer-aided molecular design, 2014-03, Vol.28 (3), p.221-233</ispartof><rights>Springer International Publishing Switzerland 2014</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c405t-b069ba95e0dd868b156d28b244a68f62ead7a66e2913299e0a87ff4303055dc43</citedby><cites>FETCH-LOGICAL-c405t-b069ba95e0dd868b156d28b244a68f62ead7a66e2913299e0a87ff4303055dc43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10822-014-9713-7$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10822-014-9713-7$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27923,27924,41487,42556,51318</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24477799$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Koziara, Katarzyna B.</creatorcontrib><creatorcontrib>Stroet, Martin</creatorcontrib><creatorcontrib>Malde, Alpeshkumar K.</creatorcontrib><creatorcontrib>Mark, Alan E.</creatorcontrib><title>Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies</title><title>Journal of computer-aided molecular design</title><addtitle>J Comput Aided Mol Des</addtitle><addtitle>J Comput Aided Mol Des</addtitle><description>To test and validate the Automated force field Topology Builder and Repository (ATB;
http://compbio.biosci.uq.edu.au/atb/
) the hydration free enthalpies for a set of 214 drug-like molecules, including 47 molecules that form part of the SAMPL4 challenge have been estimated using thermodynamic integration and compared to experiment. The calculations were performed using a fully automated protocol that incorporated a dynamic analysis of the convergence and integration error in the selection of intermediate points. The system has been designed and implemented such that hydration free enthalpies can be obtained without manual intervention following the submission of a molecule to the ATB. The overall average unsigned error (AUE) using ATB 2.0 topologies for the complete set of 214 molecules was 6.7 kJ/mol and for molecules within the SAMPL4 7.5 kJ/mol. The root mean square error (RMSE) was 9.5 and 10.0 kJ/mol respectively. However, for molecules containing functional groups that form part of the main GROMOS force field the AUE was 3.4 kJ/mol and the RMSE was 4.0 kJ/mol. This suggests it will be possible to further refine the parameters provided by the ATB based on hydration free enthalpies.</description><subject>Algorithms</subject><subject>Animal Anatomy</subject><subject>Automated</subject><subject>Chemical compounds</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Computer Applications in Chemistry</subject><subject>Computer Simulation</subject><subject>Construction</subject><subject>Dissolution</subject><subject>Dynamical systems</subject><subject>Dynamics</subject><subject>Enthalpy</subject><subject>Errors</subject><subject>Histology</subject><subject>Hydration</subject><subject>Models, Chemical</subject><subject>Molecular structure</subject><subject>Morphology</subject><subject>Pharmaceutical Preparations - chemistry</subject><subject>Physical Chemistry</subject><subject>Solvents</subject><subject>Thermodynamics</subject><subject>Topology</subject><subject>Water - chemistry</subject><issn>0920-654X</issn><issn>1573-4951</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkc1q3DAURkVpaSbTPkA3RdBNsnByJVmS1d0k9A8C3UygOyFb1zMOHsuV7MC8fTU4KaVQutJC5_ukew8h7xhcMQB9nRhUnBfAysJoJgr9gqyY1KIojWQvyQoMh0LJ8scZOU_pAXLGKHhNznhZaq2NWZG0xTR1w466wdNH13feTV0YaGjptEe6madwcBN6ug1j6MPuSG_mrvcY6cVme3NJHzGmE8-v4CMdI_quec7vjz4uZW1EpDhMe9ePHaY35FXr-oRvn841uf_8aXv7tbj7_uXb7eauaEqQU1GDMrUzEsH7SlU1k8rzqs5_d6pqFUfntVMKuWGCG4PgKt22pQABUvqmFGtysfSOMfyc85z20KUG-94NGOZkmdJMgeRC_B-VHBhjPG95TT78hT6EOQ55kEwxU1YGhMoUW6gmhpQitnaM3cHFo2VgT_LsIs9mefYkz-qcef_UPNcH9L8Tz7YywBcg5athh_GPp__Z-gvzQaLq</recordid><startdate>20140301</startdate><enddate>20140301</enddate><creator>Koziara, Katarzyna B.</creator><creator>Stroet, Martin</creator><creator>Malde, Alpeshkumar K.</creator><creator>Mark, Alan E.</creator><general>Springer International Publishing</general><general>Springer Nature B.V</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>3V.</scope><scope>7SC</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>88I</scope><scope>8AL</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>JQ2</scope><scope>K7-</scope><scope>K9.</scope><scope>KB.</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>M0N</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>P5Z</scope><scope>P62</scope><scope>PCBAR</scope><scope>PDBOC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>7U5</scope></search><sort><creationdate>20140301</creationdate><title>Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies</title><author>Koziara, Katarzyna B. ; Stroet, Martin ; Malde, Alpeshkumar K. ; Mark, Alan E.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c405t-b069ba95e0dd868b156d28b244a68f62ead7a66e2913299e0a87ff4303055dc43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Algorithms</topic><topic>Animal Anatomy</topic><topic>Automated</topic><topic>Chemical compounds</topic><topic>Chemistry</topic><topic>Chemistry and Materials Science</topic><topic>Computer Applications in Chemistry</topic><topic>Computer Simulation</topic><topic>Construction</topic><topic>Dissolution</topic><topic>Dynamical systems</topic><topic>Dynamics</topic><topic>Enthalpy</topic><topic>Errors</topic><topic>Histology</topic><topic>Hydration</topic><topic>Models, Chemical</topic><topic>Molecular structure</topic><topic>Morphology</topic><topic>Pharmaceutical Preparations - chemistry</topic><topic>Physical Chemistry</topic><topic>Solvents</topic><topic>Thermodynamics</topic><topic>Topology</topic><topic>Water - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Koziara, Katarzyna B.</creatorcontrib><creatorcontrib>Stroet, Martin</creatorcontrib><creatorcontrib>Malde, Alpeshkumar K.</creatorcontrib><creatorcontrib>Mark, Alan E.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Computer and Information Systems Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>Computing Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection (ProQuest)</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Computer Science Collection</collection><collection>Computer Science Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Computing Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>Materials Science Collection</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>Solid State and Superconductivity Abstracts</collection><jtitle>Journal of computer-aided molecular design</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Koziara, Katarzyna B.</au><au>Stroet, Martin</au><au>Malde, Alpeshkumar K.</au><au>Mark, Alan E.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies</atitle><jtitle>Journal of computer-aided molecular design</jtitle><stitle>J Comput Aided Mol Des</stitle><addtitle>J Comput Aided Mol Des</addtitle><date>2014-03-01</date><risdate>2014</risdate><volume>28</volume><issue>3</issue><spage>221</spage><epage>233</epage><pages>221-233</pages><issn>0920-654X</issn><eissn>1573-4951</eissn><abstract>To test and validate the Automated force field Topology Builder and Repository (ATB;
http://compbio.biosci.uq.edu.au/atb/
) the hydration free enthalpies for a set of 214 drug-like molecules, including 47 molecules that form part of the SAMPL4 challenge have been estimated using thermodynamic integration and compared to experiment. The calculations were performed using a fully automated protocol that incorporated a dynamic analysis of the convergence and integration error in the selection of intermediate points. The system has been designed and implemented such that hydration free enthalpies can be obtained without manual intervention following the submission of a molecule to the ATB. The overall average unsigned error (AUE) using ATB 2.0 topologies for the complete set of 214 molecules was 6.7 kJ/mol and for molecules within the SAMPL4 7.5 kJ/mol. The root mean square error (RMSE) was 9.5 and 10.0 kJ/mol respectively. However, for molecules containing functional groups that form part of the main GROMOS force field the AUE was 3.4 kJ/mol and the RMSE was 4.0 kJ/mol. This suggests it will be possible to further refine the parameters provided by the ATB based on hydration free enthalpies.</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><pmid>24477799</pmid><doi>10.1007/s10822-014-9713-7</doi><tpages>13</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0920-654X |
| ispartof | Journal of computer-aided molecular design, 2014-03, Vol.28 (3), p.221-233 |
| issn | 0920-654X 1573-4951 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_1671605233 |
| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Algorithms Animal Anatomy Automated Chemical compounds Chemistry Chemistry and Materials Science Computer Applications in Chemistry Computer Simulation Construction Dissolution Dynamical systems Dynamics Enthalpy Errors Histology Hydration Models, Chemical Molecular structure Morphology Pharmaceutical Preparations - chemistry Physical Chemistry Solvents Thermodynamics Topology Water - chemistry |
| title | Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-13T01%3A51%3A18IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Testing%20and%20validation%20of%20the%20Automated%20Topology%20Builder%20(ATB)%20version%202.0:%20prediction%20of%20hydration%20free%20enthalpies&rft.jtitle=Journal%20of%20computer-aided%20molecular%20design&rft.au=Koziara,%20Katarzyna%20B.&rft.date=2014-03-01&rft.volume=28&rft.issue=3&rft.spage=221&rft.epage=233&rft.pages=221-233&rft.issn=0920-654X&rft.eissn=1573-4951&rft_id=info:doi/10.1007/s10822-014-9713-7&rft_dat=%3Cproquest_cross%3E1671605233%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1519489036&rft_id=info:pmid/24477799&rfr_iscdi=true |