<?xml version="1.0" encoding="utf-8"?>
<export-example>
  <doc>
    <id>4257</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2013-09-27</completedDate>
    <publishedDate>2013-09-27</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Efficient Conformational Analysis by Partition-of-Unity Coupling</title>
    <abstract language="eng">Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.</abstract>
    <parentTitle language="eng">Math Chem</parentTitle>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-42570</identifier>
    <author>Alexander Bujotzek</author>
    <submitter>Konstantin Fackeldey</submitter>
    <author>Ole Schütt</author>
    <author>Adam Nielsen</author>
    <author>Konstantin Fackeldey</author>
    <author>Marcus Weber</author>
    <series>
      <title>ZIB-Report</title>
      <number>13-58</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov State Models</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Meshfree</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Molecular Simulation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Partition of Unity</value>
    </subject>
    <collection role="ccs" number="G.4">MATHEMATICAL SOFTWARE</collection>
    <collection role="ccs" number="">Markov processes (NEW)</collection>
    <collection role="pacs" number="87.10.-e">General theory and mathematical aspects</collection>
    <collection role="msc" number="60Jxx">Markov processes</collection>
    <collection role="msc" number="92-08">Computational methods</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="MIP_FORMATION">MIP_FORMATION</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</collection>
    <collection role="projects" number="Salsa-Klimm">Salsa-Klimm</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/4257/MolPyPUM.pdf</file>
  </doc>
  <doc>
    <id>2255</id>
    <completedYear>2011</completedYear>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>333</pageFirst>
    <pageLast>346</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>65(2)</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Direct Reweighting Strategies in Conformation Dynamics</title>
    <parentTitle language="eng">MATCH Commun. Math. Comp. Chem.</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Martina Klimm</author>
    <author>Alexander Bujotzek</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="Salsa-Klimm">Salsa-Klimm</collection>
  </doc>
  <doc>
    <id>2397</id>
    <completedYear>2011</completedYear>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>770</pageFirst>
    <pageLast>775</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>2</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">DNA-programmed spatial screening of carbohydrate-lectin interactions</title>
    <parentTitle language="eng">Chem. Sci.</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Ch. Scheibe</author>
    <author>Alexander Bujotzek</author>
    <author>Jens Dernedde</author>
    <author>Marcus Weber</author>
    <author>O. Seitz</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>2450</id>
    <completedYear>2011</completedYear>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Computational entropy estimation of linear polyether modified surfaces and correlation with protein resistant properties of such surfaces</title>
    <parentTitle language="eng">J. Mol. Sim.</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Marcus Weber</author>
    <author>Alexander Bujotzek</author>
    <author>Karsten Andrae</author>
    <author>M. Weinhart</author>
    <author>Rainer Haag</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>2646</id>
    <completedYear>2012</completedYear>
    <publishedYear>2012</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>054111</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>5</issue>
    <volume>137</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Quantifying the rebinding effect in multivalent chemical ligand-receptor systems</title>
    <parentTitle language="eng">J. Chem. Phys.</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Marcus Weber</author>
    <author>Alexander Bujotzek</author>
    <author>Rainer Haag</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>2647</id>
    <completedYear/>
    <publishedYear>2012</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>141</pageFirst>
    <pageLast>154</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>89</volume>
    <type>conferenceobject</type>
    <publisherName>Springer</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A meshless discretization method for Markov state models applied to explicit water peptide folding simulations</title>
    <parentTitle language="eng">Meshfree Methods for Partial Differential Equations VI</parentTitle>
    <enrichment key="Series">Lecture Notes in Computational Science and Engineering</enrichment>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Konstantin Fackeldey</author>
    <author>Alexander Bujotzek</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>2627</id>
    <completedYear>2007</completedYear>
    <publishedYear>2007</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>2</issue>
    <volume/>
    <type>other</type>
    <publisherName>DFG-Forschungszentrum Matheon</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Vom Dietrich zum Sicherheitsschlüssel – Mathematiker des Matheon simulieren neuen Wirkstoff für die Diabetes-Behandlung</title>
    <author>R. Kellermann</author>
    <author>Marcus Weber</author>
    <author>Alexander Bujotzek</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>2629</id>
    <completedYear>2009</completedYear>
    <publishedYear>2009</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>811</pageFirst>
    <pageLast>831</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>7(5)</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Efficient Simulation of Ligand-Receptor Binding Processes Using the Conformation Dynamics Approach</title>
    <parentTitle language="eng">Journal of Bioinformatics and Computational Biology</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Alexander Bujotzek</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>1913</id>
    <completedYear>2011</completedYear>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">DNA-controlled bivalent presentation of ligands for the estrogen receptor</title>
    <parentTitle language="eng">Angew. Chem. Int. Ed.</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Frank Abendroth</author>
    <author>Alexander Bujotzek</author>
    <author>Min Shan</author>
    <author>Rainer Haag</author>
    <author>Marcus Weber</author>
    <author>Oliver Seitz</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>1990</id>
    <completedYear>2011</completedYear>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>253</pageFirst>
    <pageLast>262</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>25(3)</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Towards a rational spacer design for bivalent inhibition of estrogen receptor</title>
    <parentTitle language="eng">J. Comput.-Aided Mol. Des.</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Alexander Bujotzek</author>
    <author>Min Shan</author>
    <author>Rainer Haag</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
</export-example>
