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Publications of the SimLab Biology

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2014

  • S. Holl, O. Zimmermann, M. Palmblad, Y. Mohammed, M. Hofmann-Apitius
    A New Optimization Phase for Scientific Workflow Management Systems
    Future generation computer systems, Vol. -, pp. -, 2014, akzeptiert vom Herausgeber
  • URL       DOI       BibTeX       

 

2013

  • S. Mohanty, J.H. Meinke, O. Zimmermann
    Folding of Top7 in unbiased all‐atom Monte Carlo simulations
    Proteins: Structure, Function, and Bioinformatics, Vol. 81, pp. 1446-1456, 2013
  • URL       DOI       BibTeX       
  • S. Mohanty, X. Cong, N. Casiraghi, G. Rosetti, G. Giachin, G. Legname, P. Carloni
    Role of prion disease-linked mutations in the intrinsically disordered N-terminal domain of the prion protein
    Journal of Chemical Theory and Computation, Vol. 9 (11), pp. 5158–5167, 2013
  • URL       DOI       BibTeX       
  • A. Adinetz, J. Kraus, J.H. Meinke, D. Pleiter
    GPUMAFIA: Efficient Subspace Clustering with MAFIA on GPUs
    Euro-Par 2013 Parallel ProcessingF./ ed.: F. Wolf, B. Mohr, D. an Mey, Lecture Notes in Computer Science Vol. 8097, pp. 838-849, 2013
  • URL       DOI       BibTeX       

 

2012

  • S. Ægir Jónsson, I. Staneva, S. Mohanty, A. Irbäck
    Monte Carlo Studies of Protein Aggregation
    Proceedings of the 25th Workshop on Computer Simulation Studies in Condensed Matter Physics, Physics Procedia Vol. 34, Elsevier, pp. 49–54, 2012
  • BibTeX       
  • A. Irbäck, S. Mohanty
    All-atom Monte Carlo simulations of protein folding and aggregation
    Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes- from Bioinformatics to Molecular Quantum MechanicsA./ ed.: A. Liwo, Springer, 2012
  • BibTeX       
  • P. Carloni, U.H.E. Hansmann, T. Lippert, J.H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann
    From Computational Biophysics to Systems Biology (CBSB11) Celebrating Harold Scheragas 90th Birthday
    Schriften des Forschungszentrums Jülich : IAS Series Vol. 8, Forschungszentrum Jülich, Zentralbibliothek, Jülich, 2012, Record converted from JUWEL: 18.07.2013
  • URL       BibTeX       
  • O. Zimmermann, E. von Lieres
    Mehrskalige Simulation räumlicher Inhomogenitäten in biochemischen Netzwerken
    , 16. Heiligenstädter Kolloquium Technische Systeme für die Lebenswissenschaften, Heiligenstadt(Germany), September 2012
  • URL       BibTeX       
  • S. Ægir Jónsson, A. Irbäck, S. Mohanty
    Distinct phases of free α-synuclein — a Monte Carlo study
    PROTEINS: Structure, Function, and Bioinformatics, Vol. 80 (9), pp. 2169–2177, August 2012
  • URL       DOI       BibTeX       
  • P. Gibbon, L. Arnold, D. Brömmel, V. Chihaia, S. Griessbach, R. Halver, L. Hoffmann, A. Karmakar, J.H. Meinke, S. Mohanty, T. Müller, A. Schiller, G. Sutmann, O. Zimmermann
    High-Level Support Initiative of the JSC Simulation Laboratories 2011
    Jül-4351, Forschungszentrum Jülich, May, 2012
  • BibTeX       
  • S. Holl, O. Zimmermann, B. Demuth, B. Schuller, M. Hofmann-Apitius
    Secure Multi-Level Parallel Execution of Scientific Workflows on HPC Grid Resources by Combining Taverna and UNICORE Services
    UNICORE Summit 2012, Proceedings, 30 - 31 May 2012 | Dresden, Germany, Jülich, UNICORE Summit 2012, Dresden(Germany), Schriften des Forschungszentrums Jülich, IAS Series Vol. 15, ISBN 978-3-89336-829-7, Forschungszentrum Jülich, pp. 27-34, May 2012
  • URL       BibTeX       

 

2011

  • A. Irbäck, S. Mohanty
    Multiscale Approaches to Protein Modeling
    chapter Chapter 5: Effective all-atom potentials for proteinsA./ ed.: A. Kolinski. Springer, edition 1st Edition, 2011
  • BibTeX       
  • A. Irbäck, S. Mohanty, S. Ægir Jónsson
    Accelerating atomic-level protein simulations by flat-histogram techniques
    Journal of Chemical Physics, Vol. 135 (12), pp. 125102, September 2011
  • URL       DOI       BibTeX       
  • S. Holl, O. Zimmermann, M. Hofmann-Apitius
    A UNICORE Plugin for HPC-enabled Scientific Workflows in Taverna 2.2
    Proceedings of the 2011 IEEE Seventh World Congress on Services (SERVICES 2011), ISBN 978-0-7695-4461-8, pp. 220-223, July 2011
  • DOI       BibTeX       

 

2010

  • J.H. Meinke, S. Mohanty, O. Zimmermann
    Protein Folding and Structure Prediction at the Simulation Laboratory Biology
    NIC Symposium 2010G./ ed.: G. Münster, D. Wolf, M. Kremer, Jülich, Forschungszentrum Jülich, IAS Series Vol. 3, ISBN 978-3-89336-606-4, pp. 87-94, 2010
  • BibTeX       
  • J.H. Meinke
    Protein Folding with Python on Supercomputers
    Proceedings of the 9th Python in Science ConferenceS./ ed.: S. van der Walt, J. Millman, Austin, TX USA, pp. 11–15, 2010
  • URL       BibTeX       

 

2009

  • J.H. Meinke, U.H.E. Hansmann
    Free-energy-driven folding and thermodynamics of the 67-residue protein GS-alpha3W - A large-scale Monte Carlo study
    Journal of Computational Chemistry, Vol. 30, pp. 1642 -1648, 2009
  • DOI       BibTeX       
  • J.H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann, U.H.E. Hansmann
    Computer Simulation of Proteins - Thermodynamics and Structure Predictions
    European Physical Journal D, Vol. 51, pp. 33 -40, 2009
  • DOI       BibTeX       
  • A. Irbäck, S. Mitternacht, S. Mohanty
    An effective all-­atom potential for proteins
    PMC Biophysics, Vol. 2, pp. 2, 2009
  • URL       BibTeX       

 

2008

  • O. Zimmermann, U.H.E. Hansmann
    Understanding protein folding: Small proteins in silico
    BBA - Proteins and Proteomics, Vol. 1784, pp. 252 -258, 2008
  • BibTeX       
  • O. Zimmermann, U.H.E. Hansmann
    LOCUSTRA: Accurate Prediction of Local Protein Structure Using a Two-Layer Support Vector Machine Approach
    Journal of Chemical Information and Modeling, Vol. 48, pp. 1903 -1908, 2008
  • BibTeX       
  • W. Nadler, J.H. Meinke, U.H.E. Hansmann
    Folding Proteins by First-Passage-Times Optimized Replica Exchange
    Physical Review E, Vol. 78, pp. 061905, 2008
  • BibTeX       
  • J.H. Meinke, S. Mohanty, W. Nadler, T. Neuhaus, O. Zimmermann, U.H.E. Hansmann
    Protein Simulations on Massively Parallel Computers
    NIC Symposium 2008, Jülich, Forschungszentrum Jülich, NIC Series Vol. 39, ISBN 978-3-9810843-5-1, John von Neumann Institute for Computing, 2008
  • BibTeX       
  • D.W. Li, S. Mohanty, A. Irbäck, S. Huo
    Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment
    PLoS Biology, 2008
  • BibTeX       
  • U.H.E. Hansmann (Ed.), J.H. Meinke (Ed.), S. Mohanty (Ed.), W. Nadler (Ed.), O. Zimmermann (Ed.)
    From Computational Biophysics to Systems Biology (CBSB08)
    NIC Series Vol. 40, John von Neumann Institute for Computing, Forschungszentrum Jülich, July , 2008, 19-21 May 2008, Jülich, Germany - Journal of Chemical Information and Modeling
  • BibTeX       

 

2007

  • O. Zimmermann, L. Wang, U.H.E. Hansmann
    BETTY: Prediction of beta-strand type from sequence
    In Silico Biology, Vol. 7, pp. 0037-7, 2007
  • BibTeX       

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