Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach
ABACUS [Grishaev et al. (2005) Proteins 61:36-43] is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence se...
Gespeichert in:
| Veröffentlicht in: | Journal of biomolecular NMR 2008-05, Vol.41 (1), p.29-41 |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 41 |
|---|---|
| container_issue | 1 |
| container_start_page | 29 |
| container_title | Journal of biomolecular NMR |
| container_volume | 41 |
| creator | Lemak, Alexander Steren, Carlos A Arrowsmith, Cheryl H Llinás, Miguel |
| description | ABACUS [Grishaev et al. (2005) Proteins 61:36-43] is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic search. Here, we report further development of the two main algorithms that increase the flexibility and robustness of the method. Performance of the BACUS [Grishaev and Llinás (2004) J Biomol NMR 28:1-101] algorithm was significantly improved through use of sequential connectivities available from through-bond correlated 3D-NMR experiments, and a new set of likelihood probabilities derived from a database of 56 ultra high resolution X-ray structures. A Multicanonical Monte Carlo procedure, Fragment Monte Carlo (FMC), was developed for sequence-specific assignment of spin-systems. It relies on an enhanced assignment sampling and provides the uncertainty of assignments in a quantitative manner. The efficiency of the protocol was validated on data from four proteins of between 68-116 residues, yielding 100% accuracy in sequence specific assignment of backbone and side chain resonances. |
| doi_str_mv | 10.1007/s10858-008-9238-2 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_70743968</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>70743968</sourcerecordid><originalsourceid>FETCH-LOGICAL-c393t-cb14d0a82a835753e5df3299ca04b319f13aa1bb27878e2dc09bb2ff1d0aa0ad3</originalsourceid><addsrcrecordid>eNp9kUGPFCEQhYnRuLOrP8CLEg_eWgtoBjiOE11NduNhnDOppulZNj0wQreJ_14mPckmHrxAoL73iuIR8obBRwagPhUGWuoGQDeGC93wZ2TFpBKNBGDPyQoMlw1XQl-R61IeAcBovn5Jrphupda8XRG_879mH52n5eRdGIKj2ZcU8XyFpYRDPPo40d8B6f08TsFhTLGuI71PcfJ0i3lMtHjM7oHOJcQDxUg3nzfb_Y7i6ZQTuodX5MWAY_GvL_sN2X_98nP7rbn7cft9u7lrnDBialzH2h5Qc9RCKim87AfBjXEIbSeYGZhAZF3HlVba896BqYdhYFWEgL24IR8W39q2jlUmewzF-XHE6NNcrALVCrPWFXz_D_iY5hzr26zWTCjNjawQWyCXUynZD_aUwxHzH8vAngOwSwC2BmDPAVheNW8vxnN39P2T4vLjFeALUGopHnx-6vw_13eLaMBk8ZBDsfsdByYqY9ayNeIvCtGaSg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>881378295</pqid></control><display><type>article</type><title>Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach</title><source>MEDLINE</source><source>SpringerLink Journals - AutoHoldings</source><creator>Lemak, Alexander ; Steren, Carlos A ; Arrowsmith, Cheryl H ; Llinás, Miguel</creator><creatorcontrib>Lemak, Alexander ; Steren, Carlos A ; Arrowsmith, Cheryl H ; Llinás, Miguel</creatorcontrib><description>ABACUS [Grishaev et al. (2005) Proteins 61:36-43] is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic search. Here, we report further development of the two main algorithms that increase the flexibility and robustness of the method. Performance of the BACUS [Grishaev and Llinás (2004) J Biomol NMR 28:1-101] algorithm was significantly improved through use of sequential connectivities available from through-bond correlated 3D-NMR experiments, and a new set of likelihood probabilities derived from a database of 56 ultra high resolution X-ray structures. A Multicanonical Monte Carlo procedure, Fragment Monte Carlo (FMC), was developed for sequence-specific assignment of spin-systems. It relies on an enhanced assignment sampling and provides the uncertainty of assignments in a quantitative manner. The efficiency of the protocol was validated on data from four proteins of between 68-116 residues, yielding 100% accuracy in sequence specific assignment of backbone and side chain resonances.</description><identifier>ISSN: 0925-2738</identifier><identifier>EISSN: 1573-5001</identifier><identifier>DOI: 10.1007/s10858-008-9238-2</identifier><identifier>PMID: 18458824</identifier><language>eng</language><publisher>Dordrecht: Dordrecht : Springer Netherlands</publisher><subject>Algorithms ; Amino Acid Sequence ; BACUS ; Biochemistry ; Biological and Medical Physics ; Biophysics ; Fragment Monte Carlo ; Monte Carlo Method ; NOE identification ; Nuclear Magnetic Resonance, Biomolecular ; Physics ; Physics and Astronomy ; Proteins - chemistry ; Resonance assignment ; Spectroscopy/Spectrometry ; Studies</subject><ispartof>Journal of biomolecular NMR, 2008-05, Vol.41 (1), p.29-41</ispartof><rights>Springer Science+Business Media B.V. 2008</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c393t-cb14d0a82a835753e5df3299ca04b319f13aa1bb27878e2dc09bb2ff1d0aa0ad3</citedby><cites>FETCH-LOGICAL-c393t-cb14d0a82a835753e5df3299ca04b319f13aa1bb27878e2dc09bb2ff1d0aa0ad3</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/s10858-008-9238-2$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10858-008-9238-2$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18458824$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lemak, Alexander</creatorcontrib><creatorcontrib>Steren, Carlos A</creatorcontrib><creatorcontrib>Arrowsmith, Cheryl H</creatorcontrib><creatorcontrib>Llinás, Miguel</creatorcontrib><title>Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach</title><title>Journal of biomolecular NMR</title><addtitle>J Biomol NMR</addtitle><addtitle>J Biomol NMR</addtitle><description>ABACUS [Grishaev et al. (2005) Proteins 61:36-43] is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic search. Here, we report further development of the two main algorithms that increase the flexibility and robustness of the method. Performance of the BACUS [Grishaev and Llinás (2004) J Biomol NMR 28:1-101] algorithm was significantly improved through use of sequential connectivities available from through-bond correlated 3D-NMR experiments, and a new set of likelihood probabilities derived from a database of 56 ultra high resolution X-ray structures. A Multicanonical Monte Carlo procedure, Fragment Monte Carlo (FMC), was developed for sequence-specific assignment of spin-systems. It relies on an enhanced assignment sampling and provides the uncertainty of assignments in a quantitative manner. The efficiency of the protocol was validated on data from four proteins of between 68-116 residues, yielding 100% accuracy in sequence specific assignment of backbone and side chain resonances.</description><subject>Algorithms</subject><subject>Amino Acid Sequence</subject><subject>BACUS</subject><subject>Biochemistry</subject><subject>Biological and Medical Physics</subject><subject>Biophysics</subject><subject>Fragment Monte Carlo</subject><subject>Monte Carlo Method</subject><subject>NOE identification</subject><subject>Nuclear Magnetic Resonance, Biomolecular</subject><subject>Physics</subject><subject>Physics and Astronomy</subject><subject>Proteins - chemistry</subject><subject>Resonance assignment</subject><subject>Spectroscopy/Spectrometry</subject><subject>Studies</subject><issn>0925-2738</issn><issn>1573-5001</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</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>eNp9kUGPFCEQhYnRuLOrP8CLEg_eWgtoBjiOE11NduNhnDOppulZNj0wQreJ_14mPckmHrxAoL73iuIR8obBRwagPhUGWuoGQDeGC93wZ2TFpBKNBGDPyQoMlw1XQl-R61IeAcBovn5Jrphupda8XRG_879mH52n5eRdGIKj2ZcU8XyFpYRDPPo40d8B6f08TsFhTLGuI71PcfJ0i3lMtHjM7oHOJcQDxUg3nzfb_Y7i6ZQTuodX5MWAY_GvL_sN2X_98nP7rbn7cft9u7lrnDBialzH2h5Qc9RCKim87AfBjXEIbSeYGZhAZF3HlVba896BqYdhYFWEgL24IR8W39q2jlUmewzF-XHE6NNcrALVCrPWFXz_D_iY5hzr26zWTCjNjawQWyCXUynZD_aUwxHzH8vAngOwSwC2BmDPAVheNW8vxnN39P2T4vLjFeALUGopHnx-6vw_13eLaMBk8ZBDsfsdByYqY9ayNeIvCtGaSg</recordid><startdate>20080501</startdate><enddate>20080501</enddate><creator>Lemak, Alexander</creator><creator>Steren, Carlos A</creator><creator>Arrowsmith, Cheryl H</creator><creator>Llinás, Miguel</creator><general>Dordrecht : Springer Netherlands</general><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>FBQ</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>3V.</scope><scope>7QL</scope><scope>7QO</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope></search><sort><creationdate>20080501</creationdate><title>Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach</title><author>Lemak, Alexander ; Steren, Carlos A ; Arrowsmith, Cheryl H ; Llinás, Miguel</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c393t-cb14d0a82a835753e5df3299ca04b319f13aa1bb27878e2dc09bb2ff1d0aa0ad3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Algorithms</topic><topic>Amino Acid Sequence</topic><topic>BACUS</topic><topic>Biochemistry</topic><topic>Biological and Medical Physics</topic><topic>Biophysics</topic><topic>Fragment Monte Carlo</topic><topic>Monte Carlo Method</topic><topic>NOE identification</topic><topic>Nuclear Magnetic Resonance, Biomolecular</topic><topic>Physics</topic><topic>Physics and Astronomy</topic><topic>Proteins - chemistry</topic><topic>Resonance assignment</topic><topic>Spectroscopy/Spectrometry</topic><topic>Studies</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lemak, Alexander</creatorcontrib><creatorcontrib>Steren, Carlos A</creatorcontrib><creatorcontrib>Arrowsmith, Cheryl H</creatorcontrib><creatorcontrib>Llinás, Miguel</creatorcontrib><collection>AGRIS</collection><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>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical 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>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of biomolecular NMR</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lemak, Alexander</au><au>Steren, Carlos A</au><au>Arrowsmith, Cheryl H</au><au>Llinás, Miguel</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach</atitle><jtitle>Journal of biomolecular NMR</jtitle><stitle>J Biomol NMR</stitle><addtitle>J Biomol NMR</addtitle><date>2008-05-01</date><risdate>2008</risdate><volume>41</volume><issue>1</issue><spage>29</spage><epage>41</epage><pages>29-41</pages><issn>0925-2738</issn><eissn>1573-5001</eissn><abstract>ABACUS [Grishaev et al. (2005) Proteins 61:36-43] is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic search. Here, we report further development of the two main algorithms that increase the flexibility and robustness of the method. Performance of the BACUS [Grishaev and Llinás (2004) J Biomol NMR 28:1-101] algorithm was significantly improved through use of sequential connectivities available from through-bond correlated 3D-NMR experiments, and a new set of likelihood probabilities derived from a database of 56 ultra high resolution X-ray structures. A Multicanonical Monte Carlo procedure, Fragment Monte Carlo (FMC), was developed for sequence-specific assignment of spin-systems. It relies on an enhanced assignment sampling and provides the uncertainty of assignments in a quantitative manner. The efficiency of the protocol was validated on data from four proteins of between 68-116 residues, yielding 100% accuracy in sequence specific assignment of backbone and side chain resonances.</abstract><cop>Dordrecht</cop><pub>Dordrecht : Springer Netherlands</pub><pmid>18458824</pmid><doi>10.1007/s10858-008-9238-2</doi><tpages>13</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0925-2738 |
| ispartof | Journal of biomolecular NMR, 2008-05, Vol.41 (1), p.29-41 |
| issn | 0925-2738 1573-5001 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_70743968 |
| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Algorithms Amino Acid Sequence BACUS Biochemistry Biological and Medical Physics Biophysics Fragment Monte Carlo Monte Carlo Method NOE identification Nuclear Magnetic Resonance, Biomolecular Physics Physics and Astronomy Proteins - chemistry Resonance assignment Spectroscopy/Spectrometry Studies |
| title | Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-04T15%3A59%3A24IST&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=Sequence%20specific%20resonance%20assignment%20via%20Multicanonical%20Monte%20Carlo%20search%20using%20an%20ABACUS%20approach&rft.jtitle=Journal%20of%20biomolecular%20NMR&rft.au=Lemak,%20Alexander&rft.date=2008-05-01&rft.volume=41&rft.issue=1&rft.spage=29&rft.epage=41&rft.pages=29-41&rft.issn=0925-2738&rft.eissn=1573-5001&rft_id=info:doi/10.1007/s10858-008-9238-2&rft_dat=%3Cproquest_cross%3E70743968%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=881378295&rft_id=info:pmid/18458824&rfr_iscdi=true |