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Einträge mit Organisationseinheit "10 Fachbereich Biologie > Computational Biology and Simulation"

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Anzahl der Einträge auf dieser Ebene: 63.

B

Buß, O. ; Jager, S. ; Dold, S.-M. ; Zimmermann, S. ; Hamacher, K. ; Schmitz, K. ; Rudat, J. :
Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of β-Keto Esters.
In: PloS one, 11 (1) e0146104. ISSN 1932-6203
[Artikel], (2016)

Bensinger, Dennis ; Neumann, Theresa ; Scholz, Christoph ; Voss, Constantin ; Knorr, Sabine ; Kuckelkorn, Ulrike ; Hamacher, K. ; Kloetzel, Peter-Michael ; Schmidt, Boris :
Elastase-like Activity Is Dominant to Chymotrypsin-like Activity in 20S Proteasome's β5 Catalytic Subunit.
In: ACS chemical biology, 11 (7) pp. 1800-1804. ISSN 1554-8937
[Artikel], (2016)

Bose, Ranjan ; Thiel, Gerhard ; Hamacher, K. :
Clustering of Giant Virus-DNA Based on Variations in Local Entropy.
In: Viruses, 6 (6) pp. 2259-67. ISSN 1999-4915
[Artikel], (2014)

Bose, Ranjan ; Hamacher, K. :
Alternate entropy measure for assessing volatility in financial markets.
In: Physical review. E, Statistical, nonlinear, and soft matter physics, 86 (5 Pt 2) 056112. ISSN 1550-2376
[Artikel], (2012)

Bremm, S. ; Schreck, T. ; Boba, P. ; Held, S. ; Hamacher, K. :
Computing and Visually Analyzing Mutual Information in Molecular Co-Evolution.
[Online-Edition: http://www.biomedcentral.com/1471-2105/11/330]
In: BMC Bioinformatics, 11 p. 330.
[Artikel], (2010)

Boba, P. ; Weil, P. ; Hoffgaard, F. ; Hamacher, K.
Fred, A. ; Filipe, J. ; Gamboa, H. (eds.) :

Co-Evolution in HIV Enzymes.
[Online-Edition: http://bioserver.bio.tu-darmstadt.de/HIV/paper_co-evolution_...]
In: Proc. of BIOINFORMATICS 2010 (11% acceptance ratio). , pp. 39-47. ISBN 978-989-674-019-1
[Buchkapitel], (2010)

C

Carbon-Mangels, Miriam :
Intra-host HIV-1 evolution and the co-receptor switch.
[Online-Edition: http://tuprints.ulb.tu-darmstadt.de/3770]
TU Darmstadt
[Dissertation], (2013)

G

Groß, Christine ; Hamacher, K. ; Schmitz, Katja ; Jager, Sven :
Cleavage Product Accumulation Decreases the Activity of Cutinase during PET Hydrolysis.
In: Journal of chemical information and modeling, 57 (2) pp. 243-255. ISSN 1549-960X
[Artikel], (2017)

Greiner, Timo ; Bolduan, Sebastian ; Hertel, Brigitte ; Groß, Christine ; Hamacher, K. ; Schubert, Ulrich ; Moroni, Anna ; Thiel, Gerhard :
Ion Channel Activity of Vpu Proteins Is Conserved throughout Evolution of HIV-1 and SIV.
In: Viruses, 8 (12) p. 325. ISSN 1999-4915
[Artikel], (2016)

Gehrmann, Eva ; Gläßer, Christine ; Jin, Yaochu ; Sendhoff, Bernhard ; Drossel, Barbara ; Hamacher, K. :
Robustness of glycolysis in yeast to internal and external noise.
[Online-Edition: http://dx.doi.org/10.1103/PhysRevE.84.021913]
In: Physical Review E, 84 021913, 1-11. ISSN 1539-3755
[Artikel], (2011)

Gebhardt, M. ; Hoffgaard, F. ; Hamacher, K. ; Kast, S. M. ; Moroni, A. ; Thiel, Gerhard :
Membrane Anchoring and Interaction between Transmembrane Domains are Crucial for K+ Channel Function.
In: The Journal of biological chemistry, 286 (13) pp. 11299-306. ISSN 1083-351X
[Artikel], (2011)

Gros, C. ; Hamacher, K. ; Wenzel, W. :
Breakdown of the Luttinger sum rule at the Mott-Hubbard transition in the one-dimensional t1-t2 Hubbard model.
[Online-Edition: http://dx.doi.org/10.1209/epl/i2004-10379-x]
In: Europhys. Lett., 69 (4) p. 616. ISSN 0295-5075
[Artikel], (2005)

Gros, C. ; Valenti, R. ; Alvarez, J. V. ; Hamacher, K. ; Wenzel, W. :
Test of the frustrated spin-cluster model to describe the low-temperature physics of NaV2O5.
[Online-Edition: http://www.kay-hamacher.de/PDF/PRB_NaV2O5.pdf]
In: Phys. Rev. B. (Rapid Comm.), 62 (22) R14617-R14620.
[Artikel], (2000)

H

Hess, Martin ; Keul, Frank ; Goesele, Michael ; Hamacher, K. :
Addressing inaccuracies in BLOSUM computation improves homology search performance.
[Online-Edition: https://bmcbioinformatics.biomedcentral.com/articles/10.1186...]
In: BMC Bioinformatics, 17 (1) p. 189. ISSN 1471-2105
[Artikel], (2016)

Hoffgaard, Franziska ; Kast, S. M. ; Moroni, Anna ; Thiel, Gerhard ; Hamacher, K. :
Tectonics of a K(+) channel: The importance of the N-terminus for channel gating.
In: Biochimica et biophysica acta, 1848 (12) pp. 3197-3204. ISSN 0006-3002
[Artikel], (2015)

Hess, Martin ; Bremm, Sebastian ; Weissgraeber, Stephanie ; Hamacher, K. ; Goesele, Michael ; Wiemeyer, Josef ; von Landesberger, Tatiana :
Visual exploration of parameter influence on phylogenetic trees.
In: IEEE computer graphics and applications, 34 (2) pp. 48-56. ISSN 1558-1756
[Artikel], (2014)

Hamacher, K. ; Greiner, Timo ; Ogata, Hiroyuki ; Van Etten, James L. ; Gebhardt, Manuela ; Villarreal, Luis P. ; Cosentino, Cristian ; Moroni, Anna ; Thiel, Gerhard :
Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis.
[Online-Edition: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjourna...]
In: PloS one, 7 (6) e38826. ISSN 1932-6203
[Artikel], (2012)

Hamacher, K. :
Dynamical regimes due to technological change in a microeconomical model of production.
In: Chaos (Woodbury, N.Y.), 22 (3) 033149. ISSN 1089-7682
[Artikel], (2012)

Hamacher, K. :
Resilience to leaking - dynamic systems modeling of information security.
In: PloS one, 7 (12) e49804. ISSN 1932-6203
[Artikel], (2012)

Hamacher, K. :
Efficient quantification of the importance of contacts for the dynamical stability of proteins.
In: Journal of computational chemistry, 32 (5) pp. 810-5. ISSN 1096-987X
[Artikel], (2011)

Hamacher, K. :
Free energy of contact formation in proteins: Efficient computation in the elastic network approximation.
In: Physical review. E, Statistical, nonlinear, and soft matter physics, 84 (1-2) 016703. ISSN 1550-2376
[Artikel], (2011)

Hamacher, K.
Fred, A. ; Filipe, J. ; Gamboa, H. (eds.) :

Protein Domain Phylogenies - Information Theory and Evolutionary Dynamics.
[Online-Edition: http://www.kay-hamacher.de/PDF/BIOINFORMATICS2010_Phylogeny....]
In: Proc. of BIOINFORMATICS 2010 (11% acceptance ratio). , pp. 114-122. ISBN 978-989-674-019-1
[Buchkapitel], (2010)

Hamacher, K. :
Temperature dependence of fluctuations in HIV1-protease.
[Online-Edition: http://www.springerlink.com/content/d500277715206011/?p=574e...]
In: Eur. Biophys. J., 39 (7) pp. 1051-1056. ISSN 1432-1017
[Artikel], (2010)

Hoffgaard, F. ; Weil, P. ; Hamacher, K. :
BioPhysConnectoR : Connecting sequence information and biophysical models.
[Online-Edition: http://www.biomedcentral.com/1471-2105/11/199/abstract]
In: BMC Bioinformatics, 11 p. 199.
[Artikel], (2010)

Hamacher, K. :
Efficient perturbation analysis of elastic network models – Application to acetylcholinesterase of T. californica.
[Online-Edition: http://dx.doi.org/10.1016/j.jcp.2010.06.015]
In: Journal of Computational Physics, 229 (19) pp. 7309-7316.
[Artikel], (2010)

Hamacher, K. :
Relating sequence evolution of HIV1-Protease to its underlying molecular mechanics.
[Online-Edition: http://dx.doi.org/10.1016/j.gene.2008.06.007]
In: Gene (422) pp. 30-36.
[Artikel], (2008)

Hamacher, K. :
Coarse-grained molecular models for high-throughput and multi-scale functional investigations.
[Online-Edition: http://www.journal.chemistrycentral.com/content/2/S1/S14]
In: Chem. Cent. J. (2) p. 14.
[Artikel], (2008)

Hamacher, K.
Hansmann, U. H. E. (ed.) :

Coarse-grained molecular models for high-throughput and multi-scale functional investigations.
[Online-Edition: http://www.fz-juelich.de/nic-series/volume40/hamacher.pdf]
In: Proceedings of CBSB08 (From computational biophysics to systems biology). NIC Series (40). , pp. 97-100. ISBN 978-3-9810843-6-8
[Buchkapitel], (2008)

Hamacher, K. :
Information Theoretical Measures to Analyze Trajectories in Rational Molecular Design.
[Online-Edition: http://www3.interscience.wiley.com/cgi-bin/abstract/11425060...]
In: J. Comp. Chem., 28 (16) pp. 2576-2580.
[Artikel], (2007)

Hamacher, K. :
Adaptive Extremal Optimization by Detrended Fluctuation Analysis.
[Online-Edition: http://dx.doi.org/10.1016/j.jcp.2007.09.013]
In: J. Comp. Phys., 227 (2) pp. 1500-1509. ISSN 00219991
[Artikel], (2007)

Hamacher, K. :
Energy landscape paving as a perfect optimization approach under detrended fluctuation analysis.
[Online-Edition: http://dx.doi.org/10.1016/j.physa.2006.11.071]
In: Physica A, 378 (2) pp. 307-314. ISSN 03784371
[Artikel], (2007)

Hamacher, K. :
Adaptation in stochastic tunneling global optimization of complex potential energy landscapes.
[Online-Edition: http://dx.doi.org/10.1209/epl/i2006-10058-0]
In: Europhys. Lett., 74 (6) p. 944. ISSN 0295-5075
[Artikel], (2006)

Hamacher, K. ; Trylska, J. ; Mc Cammon, J. A. :
Dependency map of proteins in the small ribosomal subunit.
[Online-Edition: http://dx.doi.org/10.1371/journal.pcbi.0020010]
In: PLoS Comp. Biol., 2 (2) e10.
[Artikel], (2006)

Hamacher, K. ; Hübsch, A. ; McCammon, J. A. :
A minimal model for stabilization of biomolecules by hydrocarbon cross-linking.
[Online-Edition: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=n...]
In: J. Chem. Phys. (124) p. 164907.
[Artikel], (2006)

Hamacher, K. ; McCammon, J. A. :
Computing the amino acid specifity of fluctuations in biomolecular systems : application to HIV1-protease.
[Online-Edition: http://pubs.acs.org/cgi-bin/abstract.cgi/jctcce/2006/2/i03/a...]
In: J. Chem. Theo. Comp. (2) p. 873.
[Artikel], (2006)

Hamacher, K. :
Accelerating changes in our epoch and the role of time-horizons.
In: The future of life and the future of our civilization. Springer , pp. 205-215.
[Buchkapitel], (2006)

Hamacher, K. :
Accelerated technological change and the role of time horizons.
In: The Future of Life, Frankfurt / Main.
[Konferenz- oder Workshop-Beitrag], (2005)

Hamacher, K. :
On stochastic global optimization of one-dimensional functions.
[Online-Edition: http://dx.doi.org/10.1016/j.physa.2005.02.028]
In: Physica A, 354 p. 547. ISSN 03784371
[Artikel], (2005)

Hamacher, K. ; Stolze, J. ; Wenzel, W. :
Disorder induced quantum phase transition in random-exchange spin-1/2 chains.
[Online-Edition: http://prola.aps.org/abstract/PRL/v89/i12/e127202]
In: Phys. Rev. Lett., 89 p. 127202.
[Artikel], (2002)

Hamacher, K. ; Gros, C. ; Wenzel, W. :
Interaction-induced collapse of a section of the Fermi sea in the zig-zag Hubbard ladder.
[Online-Edition: http://www.kay-hamacher.de/PDF/PRL_Hubbard.pdf]
In: Phys. Rev. Lett., 88 (21) p. 217203.
[Artikel], (2002)

Hamacher, K. ; Wenzel, W. :
The scaling behavior of stochastic minimization algorithms in a perfect funnel landscape.
[Online-Edition: http://prola.aps.org/abstract/PRE/v59/i1/p938_1]
In: Phys. Rev. E, 59 (1) pp. 938-941.
[Artikel], (1999)

Hamacher, K. ; Wenzel, W. :
Scaling behavior of minimization algorithms in a simple model of protein folding.
[Online-Edition: http://www.kay-hamacher.de/PDF/HLRZ_Juelich_97_Prot_Scaling....]
In: Proceedings of the HLRZ-Workshop "Monte Carlo Approach to Bioplymers and Protein Folding". World Scientific, Singapore
[Buchkapitel], (1998)

J

Jager, Sven ; Schiller, Benjamin ; Babel, Philipp ; Blumenroth, Malte ; Strufe, Thorsten ; Hamacher, K. :
StreAM-Tg: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs.
In: Algorithms for molecular biology : AMB, 12 p. 15. ISSN 1748-7188
[Artikel], (2017)

Jager, Sven ; Schiller, Benjamin ; Babel, Philipp ; Blumenroth, Malte ; Strufe, Thorsten ; Hamacher, Kay :
StreAM-Tg : algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs.
[Online-Edition: http://tuprints.ulb.tu-darmstadt.de/6794]
In: Algorithms for Molecular Biology, 12 (1) ISSN 1748-7188
[Artikel], (2017)

K

Keul, Frank ; Hess, Martin ; Goesele, Michael ; Hamacher, K. :
PFASUM: a substitution matrix from Pfam structural alignments.
[Online-Edition: https://bmcbioinformatics.biomedcentral.com/articles/10.1186...]
In: BMC Bioinformatics, 18 (1) p. 293. ISSN 1471-2105
[Artikel], (2017)

Knorr, Sabine :
In Silico Strategies to Modulate DNA Damage Response.
[Online-Edition: http://tuprints.ulb.tu-darmstadt.de/4213]
Technische Universität , Darmstadt
[Dissertation], (2014)

L

Lauss, Georg ; Schroeder, Christina ; Dabrock, Peter ; Eder, Johann ; Hamacher, K. ; Kuhn, Klaus A. ; Gottweis, Herbert :
Towards Biobank Privacy Regimes in Responsible Innovation Societies: ESBB Conference in Granada 2012.
In: Biopreservation and Biobanking, 11 (5) pp. 319-323. ISSN 1947-5535
[Artikel], (2013)

P

Pape, Susanne ; Hoffgaard, Franziska ; Dür, Mirjam ; Hamacher, K. :
Distance dependency and minimum amino acid alphabets for decoy scoring potentials.
In: Journal of computational chemistry, 34 (1) pp. 10-20. ISSN 1096-987X
[Artikel], (2013)

Pape, S. ; Hoffgaard, F. ; Hamacher, K. :
Distance-dependent classification of amino acids by information theory.
[Online-Edition: http://dx.doi.org/10.1002/prot.22744]
In: Proteins: Structure, Function, and Bioinformatics, 78 (10) pp. 2322-2328.
[Artikel], (2010)

R

Reker, D. ; Katzenbeisser, S. ; Hamacher, K. :
Computation of mutual information from Hidden Markov Models.
In: Computational biology and chemistry, 34 (5-6) pp. 328-33. ISSN 1476-928X
[Artikel], (2010)

S

Scholz, Christoph ; Knorr, Sabine ; Hamacher, K. ; Schmidt, Boris :
DOCKTITE-A Highly Versatile Step-by-Step Workflow for Covalent Docking and Virtual Screening in the Molecular Operating Environment.
In: Journal of chemical information and modeling, 55 (2) pp. 398-406. ISSN 1549-960X
[Artikel], (2015)

Seehafer, Carsten :
Identifikation von RNA-Motiven durch Datenbankanalysen.
[Online-Edition: http://tuprints.ulb.tu-darmstadt.de/3386]
TU Darmstadt
[Dissertation], (2013)

Strunk, Timo ; Hamacher, K. ; Hoffgaard, Franziska ; Engelhardt, Harald ; Zillig, Martina Daniela ; Faist, Karin ; Wenzel, Wolfgang ; Pfeifer, Felicitas :
Structural Model of the Gas Vesicle Protein GvpA and Analysis of GvpA Mutants in vivo.
In: Molecular microbiology, 81 (1) pp. 56-68. ISSN 1365-2958
[Artikel], (2011)

Sirker, J. ; Klümper, A. ; Hamacher, K. :
Ground-state properties of two-dimensional dimerized Heisenberg models.
[Online-Edition: http://dx.doi.org/10.1103/PhysRevB.65.134409]
In: Phys. Rev. B, 65 (13) p. 134409. ISSN 0163-1829
[Artikel], (2002)

Stampfuß, P. ; Hamacher, K. ; Wenzel, W. :
A massively parallel configuration-selecting multi-reference configuration interaction implementation.
[Online-Edition: http://www.kay-hamacher.de/PDF/Massively_parallel.pdf]
In: J. Mol. Struc. (THEOCHEM), 506 pp. 99-106.
[Artikel], (2000)

V

Voss, Constantin ; Scholz, Christoph ; Knorr, Sabine ; Beck, Philipp ; Stein, Martin L. ; Zall, Andrea ; Kuckelkorn, Ulrike ; Kloetzel, Peter-Michael ; Groll, Michael ; Hamacher, K. ; Schmidt, Boris :
α-Keto Phenylamides as P1'-Extended Proteasome Inhibitors.
In: ChemMedChem, 9 (11) pp. 2557-2564. ISSN 1860-7187
[Artikel], (2014)

W

Weißgraeber, Stephanie ; Saponaro, Andrea ; Thiel, Gerhard ; Hamacher, K. :
A reduced mechanical model for cAMP-modulated gating in HCN channels.
In: Scientific reports, 7 p. 40168. ISSN 2045-2322
[Artikel], (2017)

Weißgraeber, Stephanie :
Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels—Structure and Evolution.
[Online-Edition: http://tuprints.ulb.tu-darmstadt.de/4212]
Technische Universität , Darmstadt
[Dissertation], (2014)

Wulfmeyer, Timo ; Polzer, Christian ; Hiepler, Gregor ; Hamacher, K. ; Shoeman, Robert ; Dunigan, David D. ; Van Etten, James L. ; Lolicato, Marco ; Moroni, Anna ; Thiel, Gerhard ; Meckel, Tobias :
Structural Organization of DNA in Chlorella Viruses.
[Online-Edition: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjourna...]
In: PLoS ONE, 7 (2) e30133.
[Artikel], (2012)

Weißgraeber, Stephanie ; Hoffgaard, Franziska ; Hamacher, K. :
Structure-based, biophysical annotation of molecular coevolution of acetylcholinesterase.
In: Proteins, 79 (11) pp. 3144-3154. ISSN 1097-0134
[Artikel], (2011)

Weil, P. ; Hoffgaard, F. ; Hamacher, K. :
Estimating sufficient statistics in co-evolutionary analysis by mutual information.
[Online-Edition: http://dx.doi.org/10.1016/j.compbiolchem.2009.10.003]
In: Computational Biology and Chemistry, 33 (6) pp. 440-444. ISSN 1476-928X
[Artikel], (2009)

Wenzel, W. ; Hamacher, K. :
A stochastic tunneling approach for global minimization.
[Online-Edition: http://prola.aps.org/abstract/PRL/v82/i15/p3003_1]
In: Phys. Rev. Lett., 82 (15) pp. 3003-3007.
[Artikel], (1999)

Wenzel, W. ; Hamacher, K.
Reguera, D. ; Vilar, J. M. G. ; Rubi, J. M. (eds.) :

Scaling Laws for Protein Folding.
In: Statistical Mechanics of Biocomplexity. Springer Lecture Notes in Physics. Springer, New York , pp. 62-71.
[Buchkapitel], (1999)

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