Scientific Commons: Jan Meinke

Dimensionality Reduction Techniques for Protein Folding Trajectories (2009)

T. Eitrich, S. Mohanty, X. Xiao, Jan Meinke, ...

Proceedings of the NIC Workshop 2007,

http://www.fz-juelich.de/nic-series/volume36 Mechanism of Fibril Formation of Aβ16−22 Peptides (2009)

M. S. Li, P. H. Nguyen, D. Thirumalai, Jan Meinke, Ipan Mohanty, ...

published in

Determinations of Protein Structure and Protein Folding Pathways (2009)

H. A. Scheraga, A. Liwo, C. Czaplewski, S. Ołdziej, Jan Meinke, ...

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http://www.fz-juelich.de/nic-series/volume36 Knots in Macromolecular Systems: Concepts and Challenges (2009)

P. Virnau, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, Peter Virnau

published in

http://www.fz-juelich.de/nic-series/volume36 Photosensory Proteins as a Tool in Synthetic Biology: Bridging Computational Biophysics and Systems Biology (2009)

J. Hendriks, M. Avila Perez, F. Bruggeman, K. J. Hellingwerf, Jan Meinke, ...

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From Computational Biophysics to Systems Biology, (2009)

Dominik Gront, Sebastian Kmiecik, Andrzej Kolinski, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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http://www.fz-juelich.de/nic-series/volume36 Steered Classical and Quantum Path-Integral Molecular Dynamics Simulations of Strongly Coupled Protons Motions in Porphycene (2009)

Ł. Walewski, P. Bała, B. Lesyng, Jan Meinke, Ipan Mohanty, ...

published in

http://www.fz-juelich.de/nic-series/volume36 Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity (2009)

M. Held, E. Meerbach, St. Hinderlich, W. Reutter, Ch. Schütte, ...

Proceedings of the NIC Workshop 2007,

Outcome of Poisson Boltzmann Calculations Performed to Obtain Solvation Free Energies (2009)

Solvation Free Energies, Parimal Kar, Yanjie Wei, Jan Meinke, Olav Zimmermann, ...

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From Computational Biophysics to Systems Biology (CBSB07), (2009)

B. Fischer, W. Wenzel, Jan Meinke, Ipan Mohanty, ...

Proceedings of the NIC Workshop 2007,

http://www.fz-juelich.de/nic-series/volume36 Aggregation of the Amyloid-β Protein: Monte Carlo Optimization Study (2009)

Optimization Study, S. M. Gopal, K. V. Klenin, W. Wenzel, Jan Meinke, ...

Proceedings of the NIC Workshop 2007,

From Computational Biophysics to Systems Biology, (2009)

Matthias Bolten, Godehard Sutmann, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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http://www.fz-juelich.de/nic-series/volume34 Cross-Check Methods in Protein Simulations (2009)

Christoph Junghans, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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From Computational Biophysics to Systems Biology (CBSB07), (2009)

F. Fredel, J. Meinke, S. Mohanty, O. Zimmermann, ...

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NIC Workshop 2006, From Computational Biophysics to Systems Biology, (2009)

Franciszek Rakowski, Paweł Grochowski, Bogdan Lesyng, Adam Liwo, Harold A. Scheraga, Jan Meinke, ...

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http://www.fz-juelich.de/nic-series/volume36 Simulation of Linker Histone-Chromatin Interactions (2009)

G. V. Pachov, R. R. Gabdoulline, R. C. Wade, Jan Meinke, Ipan Mohanty, ...

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Exploring the Conformational Energy Landscape of Proteins. (2009)

Stanislaw Ołdziej, Adam Liwo, Harold A. Scheraga, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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Geometrical Constraints Favour the Two-Start Helical Structure of Chromatin (2009)

G. La Penna, G. Cinacchi, A. Perico, Jan Meinke, Ipan Mohanty, ...

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Integrating Structural and Kinetic Enzymatic Information in Systems Biology (2009)

Matthias Stein, Razif R. Gabdoulline, Rebecca C. Wade, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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http://www.fz-juelich.de/nic-series/volume36 Chemical Space of Auxins, their Multi-Phenomenology and Multiple Protein Interaction (2009)

N. Ferro, P. Bultinck, Th. Bredow, Th. Reinard, Jan Meinke, ...

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Forcefield Validation with the Rosetta Protein Decoy Set (2009)

A. Verma, W. Wenzel, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

Proceedings of the NIC Workshop 2007,

Proteins by MD Simulations and EPR Spectroscopy. (2009)

Prasad Gajula, Igor V. Borovykh, Christian Beier, Peter Gast, Martina Huber, ...

published in

http://www.fz-juelich.de/nic-series/volume34 Side-Chain Ordering in PolyGlutamic Acid (2009)

Yanjie Wei, Walter Nadler, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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From Computational Biophysics to Systems Biology (CBSB07), (2009)

C. Hyeon, D. Thirumalai, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

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http://www.fz-juelich.de/nic-series/volume36 Coarse-Grained Lattice Model for Molecular Recognition (2009)

H. Behringer, A. Degenhard, F. Schmid, Jan Meinke, Ipan Mohanty, ...

Proceedings of the NIC Workshop 2007,

Simulation of Small Peptide Using Combined Wang-Landau-Transition Matrix Monte Carlo Algorithm (2009)

Monte Carlo Algorithm, Sh. Hayryan, R. Ghulghazaryan, N. Poklar Ulrih, Jan Meinke, ...

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http://www.fz-juelich.de/nic-series/volume36 Multiple Beta-Sheet Molecular Dynamics of Two Abl-SH3 Domain Peptides (2009)

I. Liepina, S. Ventura, C. Czaplewski, A. Liwo, Jan Meinke, ...

published in

http://www.fz-juelich.de/nic-series/volume36 REMD Simulations of Aβ16−22 Peptide Aggregation in Explicit Solvent (2009)

R. R. Burri, D. Paschek, A. Geiger, Jan Meinke, Ipan Mohanty, ...

Proceedings of the NIC Workshop 2007,

Assemblies (2009)

A. Griewel, M. Rarey, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

Proceedings of the NIC Workshop 2007,

Protein Complex Folding (2009)

Ruhong Zhou, Jan Meinke, Olav Zimmermann, Ipan Mohanty, Ruhong Zhou

published in

http://www.fz-juelich.de/nic-series/volume36 The Zinc-Finger Motif of T.thermophilus Ribosomal Protein S14 and the Functionality of E.coli Ribosomes (2009)

G. Papadopoulos, M. A. Xaplanteri, F. Leontiadou, Th. Choli-papadopoulou, D. L. Kalpaxis, ...

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Modified Ensembles (2009)

M. Magiera, T. Neuhaus, Jan Meinke, Ipan Mohanty, ...

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Double Proton Transfer in Porphyrins (2009)

In Porphyrins, M. Hallay-suszek, P. Grochowski, B. Lesyng, Jan Meinke, ...

published in

http://www.fz-juelich.de/nic-series/volume36 Aggregate Size and Shape Distributions in Amyloid-β Peptide Solutions (2009)

L. Nagel-steger, B. Demeler, D. Willbold, Jan Meinke, Ipan Mohanty, ...

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Secondary Structure of Compstatin Analogues: Insights from Molecular Dynamics Simulations in Explicit Water (2009)

Phanourios Tamamis, Georgios Archontis, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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Using Simple Fluid Wetting as a Model for Cell Spreading (2009)

Matthew Reuter, Caroline Taylor, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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Water Percolation Governs Polymorphic Transition and Conductivity of DNA (2009)

I. Brovchenko, A. Krukau, A. Oleinikova, A. Mazur, Jan Meinke, ...

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From Computational Biophysics to Systems Biology, (2009)

Giovanni La Penna, Sara Furlan, Luca Arcesi, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and...

From Computational Biophysics to Systems Biology (CBSB07), (2009)

J. Langowski, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, Jörg Langowski

Proceedings of the NIC Workshop 2007,

Thermodynamics with Reduced Representation of (2009)

Andrzej Kolinski, Mateusz Kurcinski, Dorota Latek, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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http://www.fz-juelich.de/nic-series/volume34 From Microscopic Monte-Carlo Simulations to Macroscopic Solvation Models (2009)

Magdalena Gruziel, Witold R. Rudnicki, Bogdan Lesyngs, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

published in

From Computational Biophysics to Systems Biology, (2009)

T. Neuhaus, O. Zimmermann, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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From Computational Biophysics to Systems Biology (CBSB07), (2009)

Ch. A. Floudas, H. K. Fung, M. S. Taylor, Jan Meinke, Ipan Mohanty, ...

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Receptor Specific Forcefield: Improving Classical Forcefields with Quantum Mechanical Calculations (2009)

B. Fischer, H. Merlitz, K. Fukuzawa, W. Wenzel, ...

published in

From Computational Biophysics to Systems Biology (CBSB07), (2009)

B. Borm, S. Born, R. Merkel, B. Hoffmann, ...

Proceedings of the NIC Workshop 2007,

Simulations (2009)

Monte Carlo Simulations, S. Mohanty, Jan Meinke, Ipan Mohanty, ...

published in

From Computational Biophysics to Systems Biology, (2009)

Solvation Free Energies, Piotr Kmieć, Jaroslaw Kalinowski, Bogdan Lesyng, Jan Meinke, Olav Zimmermann, ...

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Multiscale Simulation of Protein Cluster Dynamics – the Encounter Complex (2009)

J. Schluttig, D. Alamanova, V. Helms, U. Schwarz, Jan Meinke, ...

published in

http://www.fz-juelich.de/nic-series/volume36 Molecular Dynamics in Excited States: Landau-Zener Model of Nitric Oxide Geminate Recombination to Nitrile (2009)

K. Kubiak, W. Nowak, Jan Meinke, Ipan Mohanty, ...

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The Two Aspects of the Protein Folding Problem (2009)

Harold A. Scheraga, Adam Liwo, Stanislaw Ołdziej, Cezary Czaplewski, Mey Khalili, Jorge A. Vila, ...

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A Very General Solvation Model for BioMolecular Simulation (2009)

Siegfried Höfinger, Jan Meinke, Olav Zimmermann, Ipan Mohanty, Siegfried Höfinger

Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and...

Tool for Studying the Kinetics and Thermodynamics of Protein Folding (2009)

A. Liwo, C. Czaplewski, S. Ołdziej, M. Chinchio, A. V. Rojas, M. Khalili, ...

published in

http://www.fz-juelich.de/nic-series/volume36 Side-Chain Ordering in Homopolymers (2009)

Y. Wei, W. Nadler, Jan Meinke, Ipan Mohanty, ...

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An Improved Evolutionary Strategy for Protein Structure Prediction (2009)

Srinivasa Murthy Gopal, Kyu Hwan Lee, Wolfgang Wenzel, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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Folding of Two Helical Peptide with Free Energy Methods and Molecular Dynamics (2009)

A. Quintilla, W. Wenzel, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

Proceedings of the NIC Workshop 2007,

Derivation of Solvation Free Energies of Strongly Hydrophobic Molecules (2009)

Reema Mahajan, Dieter Kranzlmüller, Jens Volkert, Siegfried Höfinger, Jan Meinke, Olav Zimmermann, ...

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NIC Workshop 2006, From Computational Biophysics to Systems Biology, (2009)

Francesca Fanelli, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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Growth Factor- Fibroblast Growth Factor Receptor Complex (2009)

L. Degrève, G. H. Brancaleoni, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

Proceedings of the NIC Workshop 2007,

http://www.fz-juelich.de/nic-series/volume34 Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction for Amino-Acid Side Chains in Water. Tests with Simple Spherical Systems (2009)

Mariusz Makowski, Adam Liwo, Katarzyna Maksimiak, Joanna Makowska, Lech Chmurzyński, Harold A, ...

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NIC Workshop 2006, From Computational Biophysics to Systems Biology, (2009)

Faruck Morcos, Mike Boxem, Niels Klitgord, Marc Vidal, Jesús A. Izaguirre, Jan Meinke, ...

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Polypeptide as a Phase Transition: A Cluster Analysis (2009)

G. Singh, I. Brovchenko, A. Oleinikova, R. Winter, Jan Meinke, ...

Proceedings of the NIC Workshop 2007,

http://www.fz-juelich.de/nic-series/volume36 A Network-Based Approach to Biomolecular Dynamics (2009)

F. Noé, J. C. Smith, Ch. Schütte, Jan Meinke, Ipan Mohanty, ...

published in

From Computational Biophysics to Systems Biology (CBSB07), (2009)

B. A. Berg, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, Bernd A. Berg

published in

http://www.fz-juelich.de/nic-series/volume36 Global Persistence Exponent of the Helix-Coil Transition (2009)

E. Arashiro, Jan Meinke, Ipan Mohanty, ...

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Hairpins by MD Simulations: Structure-Function Correlation of HIV-1 Genome Regulatory Elements (2009)

K. Kulinska, T. Kulinski, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

published in

Folding and Structure Prediction of Proteins Containing (2009)

Containing Disulfide Bridges, I. Kondov, A. Verma, W. Wenzel, Jan Meinke, ...

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Structure Prediction (2009)

M. Mönnigmann, C. A. Floudas, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

published in

http://www.fz-juelich.de/nic-series/volume34 Sub-type Specific Sites for SMAD Receptor Binding Identified by Sequence Comparison Using “Sequence Harmony” (2009)

Sequence Harmony, K. Anton Feenstra, Walter Pirovano, Jaap Heringa, Jan Meinke, Olav Zimmermann, ...

published in

http://www.fz-juelich.de/nic-series/volume36 Comparing Semi-Empirical versus Classic Charge Assignments in BioMolecules and their Effect on Electrostatic Potentials (2009)

P. Kar, M. Seel, S. Höfinger, Jan Meinke, ...

published in

http://www.fz-juelich.de/nic-series/volume34 Determination of Short-Range Potentials for Physics-Based Protein-Structure Prediction (2009)

Urszula Kozłowska, Katarzyna Wachucik, Adam Liwo, Harold A. Scheraga, Jan Meinke, Olav Zimmermann, ...

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Protein Aggregation and Unfolding Studied Using an All-Atom Model with a Simplified Energy Function (2009)

Anders Irbäck, Simon Mitternacht, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

published in

From Computational Biophysics to Systems Biology (CBSB07), (2009)

P. An, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, Priya An

Proceedings of the NIC Workshop 2007,

Propensity Scale for Predicting Exposed Transmembrane Beta Barrel Residues from Protein Sequence (2009)

S. Hayat, Y. Park, V. Helms, Jan Meinke, Ipan Mohanty, ...

Proceedings of the NIC Workshop 2007,

Microscope (2009)

W. Nowak, S. Wasilewski, L. Peplowski, Jan Meinke, Ipan Mohanty, ...

published in

http://www.fz-juelich.de/nic-series/volume36 Interaction of Biological Matter with Nanomaterials: A First-Principles Approach (2009)

S. Gowtham, R. H. Scheicher, R. Ahuja, Jan Meinke, Ipan Mohanty, ...

published in

N-Terminal Region of PrP (2009)

S. Furlan, F. Guerrieri, G. La Penna, S. Morante, G. C. Rossi, Jan Meinke, ...

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http://www.fz-juelich.de/nic-series/volume34 Optimization of the United-Residue UNRES Force Field for Langevin Dynamics Simulations (2009)

Adam Liwo, Mey Khalili, Cezary Czaplewski, Sebastian Kalinowski, Stanisław Ołdziej, Harold A. Scheraga, ...

published in

http://www.fz-juelich.de/nic-series/volume36 The Slip-Length Effects in Molecular Dynamics of Bead-Like Models of Proteins (2009)

P. Szymczak, M. Cieplak, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

published in

Channel Transport and Molecular Motors without Brownian Ratchets (2009)

W. Nadler, W. R. Bauer, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

published in

http://www.fz-juelich.de/nic-series/volume36 Verification of Protein-Protein Interactions by Use of Docking Techniques (2009)

F. Fink, R. Merkl, W. Gronwald, Jan Meinke, Ipan Mohanty, ...

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Molecular Transport Through Channels and Pores (2009)

Walter Nadler, Wolfgang R. Bauer, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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Processes: X-ray Spectroscopy and Numerical Simulations (2009)

V. Minicozzi, S. Morante, G. C. Rossi, F. Stellato, K. Jansen, ...

published in

NIC Workshop 2006, From Computational Biophysics to Systems Biology, (2009)

A. Verma, S. Murthy, K. H. Lee, E. Starikov, Wolfgang Wenzel, Jan Meinke, ...

published in

Adsorption Phenomena at Organic-Inorganic Interfaces (2009)

Michael Bachmann, Wolfhard Janke, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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Reduction to the Simplest – The Complexity of Minimalistic Heteropolymer Models (2009)

Published In, Michael Bachmann, Wolfhard Janke, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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Phase Separation in Peptide Aggregation Processes – Multicanonical Study of a Mesoscopic Model (2009)

Ch. Junghans, M. Bachmann, W. Janke, Jan Meinke, Ipan Mohanty, ...

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Study of Protein Structural Descriptors: Towards Similarity and Classification (2008)

P. Jain, J. D. Hirst, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

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Parallelization of ECEPP/3 in SMMP (2008)

J. H. Meinke, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

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Prediction of Parallel and Antiparallel Beta Sheets Based on Sequence Profiles Using Support Vector Machines (2008)

Longhui Wang, Olav Zimmermann, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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A Load Balanced Force-Domain Decomposition Algorithm for Parallel Molecular Dynamics Simulations (2008)

Published In, G. Sutmann, F. Janoschek, Jan Meinke, Ipan Mohanty, ...

c ○ 2007 by John von Neumann Institute for Computing Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not...

PSO@Autodock: A Novel Bio-Algorithm-Based Fast Flexible Docking Tool for Virtual Screening (2008)

V. Namasivayam, R. Günther, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

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From Simulation to Therapy: A Systems Biology Approach to Oncogene Detection (2008)

Avijit Ghosh, Dhruv Pant, Aparna Kumar, Rui Zou, Jan Meinke, Olav Zimmermann, ...

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DNA Packaging and Electrostatic Interactions (2008)

N. Korolev, L. Nordenskiöld, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

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Modeling of Water Explicitly in the Replica-Exchange Simulation Method for Protein Folding (2008)

Published In, Mu Yuguang, Yang Ye, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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The E-Cell Project and Challenges in Computational Systems Biology (2008)

K. Takahashi, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, Koichi Takahashi

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Causality and Correlation Analyses of Molecular Dynamics Simulation Data (2008)

A. Gorecki, J. Trylska, B. Lesyng, Jan Meinke, Ipan Mohanty, ...

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Analysis and Optimization of the Flex-Screen Docking Approach Using DUD Benchmarking Database (2008)

D. Kokh, B. Fischer, W. Wenzel, Jan Meinke, Ipan Mohanty, ...

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Mixed QM/MM Calculations in Biological Systems (2008)

G. M. Seabra, J. Torras, R. C. Walker, A. Roitberg, Jan Meinke, ...

published in

Boundary Element Method (BEM) with Parametric Surfaces (2008)

S. Grudinin, A. Baumgaertner, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

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A Parameterized Procedure for Consensus Sequences- Validation of the Method (2008)

Sławomir Walkowiak, Bogdan Lesyng, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

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Cluster Distance Geometry and Protein Folding (2008)

Jan Meinke, Olav Zimmermann, Ipan Mohanty

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Evolutionary Analysis in Pathogenesis-Related Proteins (2008)

Nicole M. Scherer, Claudia E. Thompson, Loreta B. Freitas, Ro L. Bonatto, Francisco M. Salzano, Jan Meinke, ...

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Algorithmic Refinements to an Enhanced Poisson-Boltzmann Approach Used in BioMolecular Simulation (2008)

P. Kar, M. Seel, S. Höfinger, Jan Meinke, ...

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The Locally Enhanced Sampling Study of Large Ligands (2008)

L. Peplowski, K. Kubiak, W. Nowak, Jan Meinke, Ipan Mohanty, ...

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Parallel Cost-Sensitive Support Vector (2008)

Tatjana Eitrich, Bruno Lang, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

Software for Classification published in

Die Gaststudenten und ihre Betreuer waren: (2008)

Interner Bericht, Matthias Bolten (hrsg, Jülich Supercomputing Centre, Interner Bericht, Matthias Bolten (hrsg, ...

Entsprechend dem fächerübergreifenden Charakter des Wissenschaftlichen Rechnens waren Studenten der Natur- und Ingenieurwissenschaften, der Mathematik und Informatik angesprochen. Die Bewerber

From Computational Biophysics to Systems Biology (CBSB07). Proceedings (2007)

Hansmann, Ulrich H.E., Meinke, Jan, Mohanty, Sandipan, Zimmermann, Olav

Dihedral Angle Patterns in Coil Regions of Protein Structures (2007)

O. Zimmermann, Jan Meinke, Ipan Mohanty, Olav Zimmermann (editors, ...

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NIC Workshop: From Computational Biophysics to Systems Biology 2006 (2006)

Hansmann, Ulrich H.E., Meinke, Jan, Mohanty, Sandipan, Zimmermann, Olav

From computational biophysics to systems biology NIC workshop 2006 (2006)

Meinke, Jan (Hrsg.)

A Fast Wavelet Based Evaluation of Coulomb Potentials in Molecular Systems (2006)

Godehard Sutmann, Silke Wädow, Jan Meinke, Olav Zimmermann, Ipan Mohanty, ...

published in