Metastable conformations via successive Perron-Cluster Cluster Analysis of dihedrals
Abstract: "Decomposition of the high dimensional conformational space of biomolecules into metastable subsets is used for data reduction of long molecular trajectories in order to facilitate chemical analysis and to improve convergence of simulations within these subsets. The metastability is i...
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Berlin
Konrad-Zuse-Zentrum für Informationstechnik
2002
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| Schriftenreihe: | ZIB-Report
2002,40 |
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| 040 | |a DE-604 |b ger |e rakwb | ||
| 041 | 0 | |a eng | |
| 049 | |a DE-703 |a DE-188 | ||
| 100 | 1 | |a Cordes, Frank |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Metastable conformations via successive Perron-Cluster Cluster Analysis of dihedrals |c F. Cordes ; M. Weber ; J. Schmidt-Ehrenberg |
| 264 | 1 | |a Berlin |b Konrad-Zuse-Zentrum für Informationstechnik |c 2002 | |
| 300 | |a 13 S. |b Ill., 1 graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a ZIB-Report |v 2002,40 | |
| 520 | 3 | |a Abstract: "Decomposition of the high dimensional conformational space of biomolecules into metastable subsets is used for data reduction of long molecular trajectories in order to facilitate chemical analysis and to improve convergence of simulations within these subsets. The metastability is identified by the Perron-Cluster Cluster Analysis of a Markov process that describes the thermodynamic distribution. A necessary prerequisite of this analysis is the discretization of the conformational space. A combinatorial approach via discretization of each degree of freedom will end in the so called 'curse of dimension'. In the following paper we analyze Hybrid Monte Carlo simulations of small, drug-like biomolecules and focus on the dihedral degrees of freedom as indicators of conformational changes. To avoid the 'curse of dimension', the projection of the underlying Markov operator on each dihedral is analyzed according to its metastability. In each decomposition step of a recursive procedure, those significant dihedrals, which indicate high metastability, are used for further decomposition. The procedure is introduced as part of a hierarchical protocol of simulations at different temperatures. The convergence of simulations within metastable subsets is used as an 'a posteriori' criterion for a successful identification of metastability. All results are presented with the visualization program AmiraMol." | |
| 650 | 4 | |a Cluster analysis | |
| 650 | 4 | |a Markov processes | |
| 700 | 1 | |a Weber, Marcus |d 1972- |e Verfasser |0 (DE-588)132289881 |4 aut | |
| 700 | 1 | |a Schmidt-Ehrenberg, Johannes |e Verfasser |4 aut | |
| 830 | 0 | |a ZIB-Report |v 2002,40 |w (DE-604)BV013191727 |9 2002,40 | |
| 943 | 1 | |a oai:aleph.bib-bvb.de:BVB01-016238560 | |
Datensatz im Suchindex
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| any_adam_object | |
| author | Cordes, Frank Weber, Marcus 1972- Schmidt-Ehrenberg, Johannes |
| author_GND | (DE-588)132289881 |
| author_facet | Cordes, Frank Weber, Marcus 1972- Schmidt-Ehrenberg, Johannes |
| author_role | aut aut aut |
| author_sort | Cordes, Frank |
| author_variant | f c fc m w mw j s e jse |
| building | Verbundindex |
| bvnumber | BV023034763 |
| classification_rvk | SS 4779 |
| ctrlnum | (OCoLC)52753572 (DE-599)BVBBV023034763 |
| discipline | Informatik |
| format | Book |
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| id | DE-604.BV023034763 |
| illustrated | Illustrated |
| indexdate | 2025-01-27T13:51:20Z |
| institution | BVB |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016238560 |
| oclc_num | 52753572 |
| open_access_boolean | |
| owner | DE-703 DE-188 |
| owner_facet | DE-703 DE-188 |
| physical | 13 S. Ill., 1 graph. Darst. |
| publishDate | 2002 |
| publishDateSearch | 2002 |
| publishDateSort | 2002 |
| publisher | Konrad-Zuse-Zentrum für Informationstechnik |
| record_format | marc |
| series | ZIB-Report |
| series2 | ZIB-Report |
| spelling | Cordes, Frank Verfasser aut Metastable conformations via successive Perron-Cluster Cluster Analysis of dihedrals F. Cordes ; M. Weber ; J. Schmidt-Ehrenberg Berlin Konrad-Zuse-Zentrum für Informationstechnik 2002 13 S. Ill., 1 graph. Darst. txt rdacontent n rdamedia nc rdacarrier ZIB-Report 2002,40 Abstract: "Decomposition of the high dimensional conformational space of biomolecules into metastable subsets is used for data reduction of long molecular trajectories in order to facilitate chemical analysis and to improve convergence of simulations within these subsets. The metastability is identified by the Perron-Cluster Cluster Analysis of a Markov process that describes the thermodynamic distribution. A necessary prerequisite of this analysis is the discretization of the conformational space. A combinatorial approach via discretization of each degree of freedom will end in the so called 'curse of dimension'. In the following paper we analyze Hybrid Monte Carlo simulations of small, drug-like biomolecules and focus on the dihedral degrees of freedom as indicators of conformational changes. To avoid the 'curse of dimension', the projection of the underlying Markov operator on each dihedral is analyzed according to its metastability. In each decomposition step of a recursive procedure, those significant dihedrals, which indicate high metastability, are used for further decomposition. The procedure is introduced as part of a hierarchical protocol of simulations at different temperatures. The convergence of simulations within metastable subsets is used as an 'a posteriori' criterion for a successful identification of metastability. All results are presented with the visualization program AmiraMol." Cluster analysis Markov processes Weber, Marcus 1972- Verfasser (DE-588)132289881 aut Schmidt-Ehrenberg, Johannes Verfasser aut ZIB-Report 2002,40 (DE-604)BV013191727 2002,40 |
| spellingShingle | Cordes, Frank Weber, Marcus 1972- Schmidt-Ehrenberg, Johannes Metastable conformations via successive Perron-Cluster Cluster Analysis of dihedrals ZIB-Report Cluster analysis Markov processes |
| title | Metastable conformations via successive Perron-Cluster Cluster Analysis of dihedrals |
| title_auth | Metastable conformations via successive Perron-Cluster Cluster Analysis of dihedrals |
| title_exact_search | Metastable conformations via successive Perron-Cluster Cluster Analysis of dihedrals |
| title_full | Metastable conformations via successive Perron-Cluster Cluster Analysis of dihedrals F. Cordes ; M. Weber ; J. Schmidt-Ehrenberg |
| title_fullStr | Metastable conformations via successive Perron-Cluster Cluster Analysis of dihedrals F. Cordes ; M. Weber ; J. Schmidt-Ehrenberg |
| title_full_unstemmed | Metastable conformations via successive Perron-Cluster Cluster Analysis of dihedrals F. Cordes ; M. Weber ; J. Schmidt-Ehrenberg |
| title_short | Metastable conformations via successive Perron-Cluster Cluster Analysis of dihedrals |
| title_sort | metastable conformations via successive perron cluster cluster analysis of dihedrals |
| topic | Cluster analysis Markov processes |
| topic_facet | Cluster analysis Markov processes |
| volume_link | (DE-604)BV013191727 |
| work_keys_str_mv | AT cordesfrank metastableconformationsviasuccessiveperronclusterclusteranalysisofdihedrals AT webermarcus metastableconformationsviasuccessiveperronclusterclusteranalysisofdihedrals AT schmidtehrenbergjohannes metastableconformationsviasuccessiveperronclusterclusteranalysisofdihedrals |