Search

link to homepage

Institute for Advanced Simulation (IAS)

Navigation and service


Publications of the SimLab Biology

2019, 2018, 2017, 2016, 2015, 2014, 2013, 2012, 2011, 2010, 2009, 2008, 2007

2019

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Structural Determinants of the Prion Protein N-Terminus and Its Adducts with Copper Ions
International journal of molecular sciences 20(1), 18 () [10.3390/ijms20010018] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a book
Peptide Folding in Cellular Environments: A Monte Carlo and Markov Modeling Approach
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes / Liwo, Adam (Editor) ; Cham : Springer International Publishing, 2019, Chapter 13 ; ISBN: 978-3-319-95842-2=978-3-319-95843-9 Cham : Springer International Publishing, Springer Series on Bio- and Neurosystems 8, 453 - 466 () [10.1007/978-3-319-95843-9_13] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Stability and Local Unfolding of SOD1 in the Presence of Protein Crowders
The journal of physical chemistry <Washington, DC> / B B, Condensed matter, materials, surfaces, interfaces & biophysical 123(9), 1920-1930 () [10.1021/acs.jpcb.8b10774] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
High-throughput screening discovers antifibrotic properties of haloperidol by hindering myofibroblast activation
JCI insight 4(8), e123987 () [10.1172/jci.insight.123987] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
RhoA regulates translation of the Nogo-A decoy SPARC in white matter-invading glioblastomas
Acta neuropathologica 138(2), 275 - 293 () [10.1007/s00401-019-02021-z] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Investigating targets for neuropharmacological intervention by molecular dynamics simulations
Biochemical Society transactions 47(3), 909 - 918 () [10.1042/BST20190048] BibTeX | EndNote: XML, Text | RIS

2018

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Markov modeling of peptide folding in the presence of protein crowders
The journal of chemical physics 148(5), 055101 () [10.1063/1.5017031] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Structural Prediction of the Dimeric Form of the Mammalian Translocator Membrane Protein TSPO: A Key Target for Brain Diagnostics
International journal of molecular sciences 19(9), 2588 - () [10.3390/ijms19092588] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study
Molecules 23(10), 2616 - () [10.3390/molecules23102616] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Vibrational Energy in Proteins Correlates with Topology
The journal of physical chemistry letters 9(22), 6393 - 6398 () [10.1021/acs.jpclett.8b02380] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Nucleolar-nucleoplasmic shuttling of TARG1 and its control by DNA damage-induced poly-ADP-ribosylation and by nucleolar transcription
Scientific reports 8(1), 6748 () [10.1038/s41598-018-25137-w] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Reducing Mutant Huntingtin Protein Expression in Living Cells by a Newly Identified RNA CAG Binder
ACS chemical neuroscience 9(6), 1399 - 1408 () [10.1021/acschemneuro.8b00027] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a book
Assessment of Intracellular Auto-Modification Levels of ARTD10 Using Mono-ADP-Ribose-Specific Macrodomains 2 and 3 of Murine Artd8
ADP-ribosylation and NAD+ Utilizing Enzymes / Chang, Paul (Editor) ; New York, NY : Springer New York, 2018, Chapter 4 ; ISSN: 1064-3745=1940-6029 ; ISBN: 978-1-4939-8587-6=978-1-4939-8588-3 ; doi:10.1007/978-1-4939-8588-3 New York, NY : Springer New York, Methods in Molecular Biology 1813, 41 - 63 () [10.1007/978-1-4939-8588-3_4] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
The Conorfamide RPRFa Stabilizes the Open Conformation of Acid-Sensing Ion Channel 3 via the Nonproton Ligand–Sensing Domain
Molecular pharmacology 94(4), 1114 - 1124 () [10.1124/mol.118.112375]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Effect of in vivo post-translational modifications of the HMGB1 protein upon binding to platinated DNA: a molecular simulation study
Nucleic acids symposium series 46(22), 11687 - 11697 () [10.1093/nar/gky1082] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

2017

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Unifying view of mechanical and functional hotspots across class A GPCRs
PLoS Computational Biology 13(2), e1005381 - () [10.1371/journal.pcbi.1005381] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Structural prediction of the interaction of the tumor suppressor p27$^{KIP1}$ with cyclin A/CDK2 identifies a novel catalytically relevant determinant
BMC bioinformatics 18(1), 15 () [10.1186/s12859-016-1411-0] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Proton Dynamics in Protein Mass Spectrometry
The journal of physical chemistry letters 8(6), 1105 - 1112 () [10.1021/acs.jpclett.7b00127]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Sulfoximines as ATR inhibitors: Analogs of VE-821
Bioorganic & medicinal chemistry letters 27(12), 2659 - 2662 () [10.1016/j.bmcl.2017.04.026]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Copper(II) and the pathological H50Q α-synuclein mutant: Environment meets genetics
Communicative & integrative biology 10(1), e1270484 - () [10.1080/19420889.2016.1270484] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
The conserved macrodomains of the non-structural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases
Scientific reports 7, 41746 - () [10.1038/srep41746] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
The PRACE 2017 Winterschool
Innovatives Supercomputing in Deutschland 15(1), 45 () OpenAccess  Download fulltext Files  Download fulltextFulltext Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Protein folding/unfolding in the presence of interacting macromolecular crowders
European physical journal special topics 226(4), 627 - 638 () [10.1140/epjst/e2016-60316-9] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
A covalent PIN1 inhibitor selectively targets cancer cells by a dual mechanism of action
Nature Communications 8, 15772 - () [10.1038/ncomms15772] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a book
Backbone Dihedral Angle Prediction
Prediction of Protein Secondary Structure / Zhou, Yaoqi (Editor) ; New York, NY : Springer New York, 2017, Chapter 7 ; ISSN: 1064-3745=1940-6029 ; ISBN: 978-1-4939-6404-8=978-1-4939-6406-2 ; doi:10.1007/978-1-4939-6406-2 New York, NY : Springer New York, Methods in Molecular Biology 1484, 65 - 82 () [10.1007/978-1-4939-6406-2_7] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a book
Structural Modeling of Human Prion Protein's Point Mutations
Prion Protein / Rossetti, Giulia ; : Elsevier, 2017, ; ISSN: 18771173 ; ISBN: 9780128112267 ; doi:10.1016/bs.pmbts.2017.07.001 Amsterdam [u.a.] : Elsevier, Progress in Molecular Biology and Translational Science 150, 105 - 122 () [10.1016/bs.pmbts.2017.07.001] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Molecular Dynamics Simulations of the [2Fe-2S] Cluster-Binding Domain of NEET Proteins Reveal Key Molecular Determinants That Induce Their Cluster Transfer/Release
The journal of physical chemistry <Washington, DC> / B 121(47), 10648–10656 () [10.1021/acs.jpcb.7b10584] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a book
Chapter 12. Molecular Modelling and Simulations Applied to Challenging Drug Discovery Targets
Computational Tools for Chemical Biology / Martín-Santamaría, Sonsoles (Editor) ; Cambridge : Royal Society of Chemistry, 2017, ; ISBN: ; doi:10.1039/9781788010139 Cambridge : Royal Society of Chemistry 317 - 348 () [10.1039/9781788010139-00317]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Diminazene Is a Slow Pore Blocker of Acid-Sensing Ion Channel 1a (ASIC1a)
Molecular pharmacology 92(6), 665 - 675 () [10.1124/mol.117.110064]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

2016

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Conformational effects in protein electrospray-ionization mass spectrometry
Mass spectrometry reviews 35(1), 111 - 122 () [10.1002/mas.21465] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Discrete-continuous reaction-diffusion model with mobile point-like sources and sinks
The European physical journal / E 39(1), 11 () [10.1140/epje/i2016-16011-0]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings
Structural Predictions of Intrinsically Disordered Proteins with Computational Methods
NIC Symposium 2016
NIC Symposium 2016, JülichJülich, Germany, 11 Feb 2016 - 12 Feb 20162016-02-112016-02-12
Jülich : Forschungszentrum Jülich GmbH, Zentralbibliothek, NIC Series 48, 89-96 () OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Peptide folding in the presence of interacting protein crowders
The journal of chemical physics 144(17), 175105 - () [10.1063/1.4948462] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
CECAM Tutorial - Atomistic Monte Carlo Simulation
Innovatives Supercomputing in Deutschland 14(1), 95 () OpenAccess  Download fulltext Files  Download fulltextFulltext Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Carnosine and Homocarnosine Degradation Mechanisms by the Human Carnosinase Enzyme CN1: Insights from Multiscale Simulations
Biochemistry 55(19), 2772 - 2784 () [10.1021/acs.biochem.5b01263]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Conformational ensemble of human α-synuclein physiological form predicted by molecular simulations
Physical chemistry, chemical physics 18(8), 5702 - 5706 () [10.1039/C5CP04549E]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
Mehrskalenmodellierung von Reaktions-Diffusions Prozessen in lebenden Systemen
18. Heiligenstädter Kolloquium, HeiligenstadtHeiligenstadt, Germany, 19 Sep 2016 - 21 Sep 20162016-09-192016-09-21 Beckmann, D.; Kaufhold, S. 57 - 68 () BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Environmental and genetic factors support the dissociation between α-synuclein aggregation and toxicity
Proceedings of the National Academy of Sciences of the United States of America 113(42), E6506 - E6515 () [10.1073/pnas.1606791113]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
The Mont-Blanc Prototype: An Alternative Approach for HPC Systems
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis
SC '16, Salt Lake City, UtahSalt Lake City, Utah, USA, 13 Nov 2016 - 18 Nov 20162016-11-132016-11-18
Piscataway, NJ, USA : IEEE Press 444-455 () [10.1109/SC.2016.37]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Simulation Laboratories - Supercomputer-Support und Forschung für Communities
Systembiologie.de 10(April 2016), 56-59 ()   Download fulltextFulltext BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization
Scientific reports 6, 35454 - () [10.1038/srep35454] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

2015

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Comprehensive large-scale assessment of intrinsic protein disorder
Bioinformatics 31(2), 201-208 () [10.1093/bioinformatics/btu625]  Download fulltext Files  Download fulltextFulltext BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Structural predictions of neurobiologically relevant G-protein coupled receptors and intrinsically disordered proteins
Archives of biochemistry and biophysics 582, 91–100 () [10.1016/j.abb.2015.03.011]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling
Journal of the American Society for Mass Spectrometry 26(3), 472 - 481 () [10.1007/s13361-014-1048-z]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
The effect of composition on Diffusion of macromolecules in a crowded environment
Physical biology 12(4), 046003 - () [10.1088/1478-3975/12/4/046003]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Copper Binding to the N-Terminally Acetylated, Naturally Occurring Form of Alpha-Synuclein Induces Local Helical Folding
Journal of the American Chemical Society 137(20), 6444 - 6447 () [10.1021/jacs.5b01911]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Binding of the Antagonist Caffeine to the Human Adenosine Receptor hA2AR in Nearly Physiological Conditions
PLoS one 10(5), e0126833 () [10.1371/journal.pone.0126833] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Equilibrium simulation of trp-cage in the presence of protein crowders
The journal of chemical physics 143(17), 175102 () [10.1063/1.4934997] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
The Mont-Blanc Project: First Phase successfully finished
Innovatives Supercomputing in Deutschland 13(2), 54-57 () OpenAccess  Download fulltext Files  Download fulltextFulltext Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Molecular View of Ligands Specificity for CAG Repeats in Anti-Huntington Therapy
Journal of chemical theory and computation 11(10), 4911 - 4922 () [10.1021/acs.jctc.5b00208]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
The structural impact of DNA mismatches
Nucleic acids symposium series 43(8), 4309 - 4321 () [10.1093/nar/gkv254] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Insight into the Mechanism of Intramolecular Inhibition of the Catalytic Activity of Sirtuin 2 (SIRT2)
PLoS one 10(9), e0139095 - () [10.1371/journal.pone.0139095] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Rare FLT3 deletion mutants may provide additional treatment options to patients with AML: an approach to individualized medicine
Leukemia 29(12), 2434 - 2438 () [10.1038/leu.2015.131]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Computational metallomics of the anticancer drug cisplatin
Journal of inorganic biochemistry 153, 231 - 238 () [10.1016/j.jinorgbio.2015.10.001]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Scientific Workflow Optimization for Improved Peptide and Protein Identification
BMC bioinformatics 16, 284 () [10.1186/s12859-015-0714-x] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

2014

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
A New Optimization Phase for Scientific Workflow Management Systems
Future generation computer systems 36, 352-362 () [10.1016/j.future.2013.09.005]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Developing predictive rules for coordination geometry from visible circular dichroism of Copper(II) and Nickel(II) ions in histidine and amide main-chain complexes
The FEBS journal 281(17), 3945 - 3954 () [10.1111/febs.12934]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
CECAM Tutorial: Atomistic Monte Carlo Simulations of Bio-Molecular Systems
Innovatives Supercomputing in Deutschland 12(2), 90 () OpenAccess  Download fulltext Files  Download fulltextFulltext Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Molecular Dynamics Simulations Identify Time Scale of Conformational Changes Responsible for Conformational Selection in Molecular Recognition of HIV-1 Transactivation Responsive RNA
Journal of the American Chemical Society 136(44), 15631 - 15637 () [10.1021/ja507812v]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer
PLoS Computational Biology 10(9), e1003838 () [10.1371/journal.pcbi.1003838] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Molecular Recognition of Platinated DNA from Chromosomal HMGB1
Journal of chemical theory and computation 10(8), 3578 - 3584 () [10.1021/ct500402e]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a book
Chemosensorial G-proteins-Coupled Receptors: A Perspective from Computational Methods
Protein Conformational Dynamics Cham : Springer International Publishing, Advances in Experimental Medicine and Biology 805, 441 - 457 () [10.1007/978-3-319-02970-2_18] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
HIV-1 Integrase Binding to its Cellular Partners: A Perspective from Computational Biology
Current pharmaceutical design 20(21), 3412 - 3421 () [10.2174/13816128113199990631] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings
Computer–aided design of ligands targeting RNA polyCAG expansion tracts in Huntington’s disease
International Prion Congress, Prion 2014, TriestTriest, Italy, 27 May 2014 - 30 May 20142014-05-272014-05-30 Austin, Tex. : Landes Bioscience 117 pp. () BibTeX | EndNote: XML, Text | RIS

2013

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Dominant-negative effects in prion diseases: insights from molecular dynamics simulations on mouse prion protein chimeras
Journal of biomolecular structure & dynamics: JBSD 31(8), 829-840 () [10.1080/07391102.2012.712477] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Folding of Top7 in unbiased all-atom Monte Carlo simulations
Proteins 81(8), 1446 - 1456 () [10.1002/prot.24295]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
GPUMAFIA: Efficient Subspace Clustering with MAFIA on GPUs
Euro-Par 2013 Parallel Processing
Euro-Par 2013, AachenAachen, Germany, 26 Aug 2013 - 30 Aug 20132013-08-262013-08-30
New York : Springer New York, Lecture Notes in Computer Science 8097, 838-849 () [10.1007/978-3-642-40047-6_83]  Download fulltext Files  Download fulltextFulltext BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Role of prion disease-linked mutations in the intrinsically disordered N-terminal domain of the prion protein
Journal of chemical theory and computation 9(11), 5158-5167 () [10.1021/ct400534k]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
A Molecular Dynamics Simulation-Based Interpretation of Nuclear Magnetic Resonance Multidimensional Heteronuclear Spectra of α-Synuclein·Dopamine Adducts
Biochemistry 52(38), 6672 - 6683 () [10.1021/bi400367r]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Ligand Binding on Intrinsic Disordered Proteins: Focus on Human Alpha-Synuclein
Biophysical journal 104(2), 379a () [10.1016/j.bpj.2012.11.2111]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Computational Studies on the Prion Protein
Current topics in medicinal chemistry 13(19), 2419 - 2431 () [10.2174/15680266113136660170] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings
On specifying and sharing scientific workflow optimization results using research objects
Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science - WORKS '13 - ACM Press New York, New York, USA, 2013. - ISBN 9781450325028 - doi:10.1145/2534248.2534251
8th Workshop on Workflows in Support of Large-Scale Science, WORKS 2013, DenverDenver, Colorado, 17 Nov 2013 - 17 Nov 20132013-11-172013-11-17
ACM Press New York, New York, USA 28-37 () [10.1145/2534248.2534251] BibTeX | EndNote: XML, Text | RIS

2012

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Event-based simulation of interference with alternatingly blocked particle sources
AIP conference proceedings 1424, 246 - 250 () [10.1063/1.3688976] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Distinct phases of free a-synuclein - A Monte Carlo study
Proteins 80(9), 2169 - 2177 () [10.1002/prot.24107] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Book
From Computational Biophysics to Systems Biology (CBSB11) Celebrating Harold Scheragas 90th Birthday
Jülich : Forschungszentrum Jülich, Zentralbibliothek, Schriften des Forschungszentrums Jülich : IAS Series 8, () OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Local Fluctuations and Conformational Transitions in Proteins
Journal of chemical theory and computation 8(11), 4775 - 4785 () [10.1021/ct300610y] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
HIV-1 Tat Binding to PCAF Bromodomain: Structural Determinants from Computational Methods
Biology 1(2), 277 - 296 () [10.3390/biology1020277] special issue: "Structural and Molecular Biology of HIV" OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings
Mehrskalige Simulation räumlicher Inhomogenitäten in biochemischen Netzwerken
16. Heiligenstädter Kolloquium Technische Systeme für die Lebenswissenschaften, HeiligenstadtHeiligenstadt, Germany, 24 Sep 2012 - 26 Sep 20122012-09-242012-09-26 2 p. () BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
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
UNICORE Summit 2012, DresdenDresden, Germany, 30 May 2012 - 31 May 20122012-05-302012-05-31
Jülich : Forschungszentrum Jülich, Schriften des Forschungszentrums Jülich, IAS Series 15, 8 p. () BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Journal Article
Monte Carlo Studies of Protein Aggregation
25th Workshop on Computer Simulation Studies in Condensed Matter Physics, AthensAthens, USA, 20 Feb 2012 - 24 Feb 20122012-02-202012-02-24 Physics procedia 34, 49 - 54 () [10.1016/j.phpro.2012.05.008] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings
A new optimization phase for scientific workflow management systems
2012 IEEE 8th International Conference on E-Science : [Proceedings] - IEEE, 2012.
2012 IEEE 8th International Conference on E-Science (e-Science), ChicagoChicago, IL, 8 Oct 2012 - 12 Oct 20122012-10-082012-10-12
IEEE 1 - 8 () [10.1109/eScience.2012.6404479] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Corrigendum to “Common Structural Traits across Pathogenic Mutants of the Human Prion Protein and Their Implications for Familial Prion Diseases” [J. Mol. Biol. 411 (2011) 700–712]
Journal of molecular biology 422(1), 157 - () [10.1016/j.jmb.2012.06.007]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Structural Determinants of Cisplatin and Transplatin Binding to the Met-Rich Motif of Ctr1: A Computational Spectroscopy Approach
Journal of chemical theory and computation 8(8), 2912 - 2920 () [10.1021/ct300167m]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

2011

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
Effective All-Atom Potentials for Proteins
Multiscale Approaches to Protein Modeling, Structure Prediction, Dynamics, Thermodynamics and Macromolecular Assemblies, ed./ A. Kolinski, Springer Verlag, 2011. - 978-1-4419-6888-3. - S. 111 - 126 BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
A UNICORE plugin for HPC-enabled scientific workflows in Taverna 2.2
Proceedings of 7th IEEE 2011 World Congress on Services (SERVICES 2011), Washington, DC USA, July 04-July 09, IEEE, CS Digital Library, 2011, 978-0-7695-4461-8, S. 220 - 223 BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Accelerating atomic-level protein simulations by flat-histogram techniques
The journal of chemical physics 135, 125102 () [10.1063/1.3643328] Allianz-OA  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

2010

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
Protein Folding an Structure Prediction at the Simulation Laboratory Biology
NIC Symposium 2010, / ed.: G. Münster, D. Wolf, M. Kremer, Jülich, Forschungszentrum Jülich, IAS Series Vol. 3. - 978-3-89336-606-4. - S. 87 - 94 BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
Protein Folding with Python on Supercomputers
Proceedings of the 9th Python in Science Conference (SciPy 2010), edited by Stéfan van der Walt, Jarrod Millman, 978-1-4583-4619-3, S. 11 - 15 BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Journal Article
Protein folding, aggregation and unfolding in Monte Carlo simulations11
12th Workshop on Computer Simulation Studies in Condensed Matter Physics, CSP-2007, Athens, GAAthens, GA, USA, 19 Feb 2007 - 23 Feb 20072007-02-192007-02-23 Physics procedia 7, 68 - 71 () [10.1016/j.phpro.2010.09.046] BibTeX | EndNote: XML, Text | RIS

2009

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Computer Simulation of Proteins - Thermodynamics and Structure Predictions
The European physical journal / D 51, 33 - 40 () [10.1140/epjd/e2008-00086-2] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Free-energy-driven folding and thermodynamics of the 67-residue protein GS-alpha3W - A large-scale Monte Carlo study
Journal of computational chemistry 30, 1642 - 1648 () [10.1002/jcc.21321] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
An effective all-­atom potential for proteins
PMC Biophysics 2, 2 () [10.1186/1757-5036-2-2] pmc   Download fulltextFulltext Download fulltextFulltext by Pubmed Central BibTeX | EndNote: XML, Text | RIS

2008

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Simulation of Top7-CFr: a transient helix extension guides folding
Proceedings of the National Academy of Sciences of the United States of America 105, 8004 - 8007 () [10.1073/pnas.0708411105] pmc   Download fulltextFulltext by Pubmed Central BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
LOCUSTRA: Accurate Prediction of Local Protein Structure Using a Two-Layer Support Vector Machine Approach
Journal of Chemical Information and Modeling 48, 1903 - 1908 () [10.1021/ci800178a] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Folding Proteins by First-Passage-Times Optimized Replica Exchange
Physical review / E 78, 061905 () [10.1103/PhysRevE.78.061905] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Understanding protein folding: Small proteins in silico
Biochimica et biophysica acta / Proteins and proteomics 1784, 252 - 258 () [10.1016/j.bbapap.2007.10.010] pmc   Download fulltextFulltext by Pubmed Central BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
SMMP v. 3.0 - Simulating proteins and protein interactions in Python and Fortran
Computer physics communications 178, 459 () [10.1016/j.cpc.2007.11.004] BibTeX | EndNote: XML, Text | RIS

2007

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Aggregation of Beta-Amyloid Fragments
The journal of chemical physics 126, 014706 () [10.1063/1.2423013] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Ring polymer simulations with global radius of curvature
Physical review / E 75, 051803 () [10.1103/PhysRevE.75.051803] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
Folding and Aggregation of Proteins in Monte Carlo Simulations
From Computational Biophyscs to Systems Biology (CBSB07). - Jülich, 2007. - (NIC Series ; 36). - S. 227 - 229 BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
Dihedral Angle Patterns in Coil Regions of Protein Structures
From Computational Biophysics to Systems Biology (CBSB07). - Jülich, 2007. - (NIC Series ; 36). - S. 301 - 303 BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Folding of a Miniprotein with mixed Fold
The journal of chemical physics 127, 035102 () [10.1063/1.2753835] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
BETTY: Prediction of beta-strand type from sequence
In silico biology 7, 0037 () BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Improving an all-atom force field
Physical review / E 76, 012901 () [10.1103/PhysRevE.76.012901] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Protein Simulations combining an All-Atom Force Field with a Go-Term
Journal of physics / Condensed matter 19, 285215 () [10.1088/0953-8984/19/28/285215] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS


Servicemeu

Homepage