MCM Gruppe
Molecular and Cellular Modeling

Publikationen

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

  • Stein M, Gabdoulline R, Beßon B, Wade R (2006). Beilstein Proceedings of the 2nd Conference on ’Experimental Standard Conditions of Enzyme Characterizations (ESCEC)’ em Ruedesheim (2007) em, In The Estimation of Kinetic Parameters in Systems Biology by Comparing Molecular Interaction Fields of Enzymes, pp. 237–253, 19-23 March 746
  • Stein M, Gabdoulline RR, Wade RC (2006). Integrating Structural and Kinetic Enzymatic Information in Systems Biology, In NIC Workshop 2006 ’From Computational Biophysics to Systems Biology’, 6–9 June, John von Neumann Institute for Computing, Juelich, vol. 34 of NIC Series, pp. 129–132 689
  • K. S, T. W, R.C. W (2006). Molecular Docking, In Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, pp. pp1149–1153, Ed. Ganten,D. and Ruckpaul, K., Springer 690
  • Gabdoulline RR, Ulbrich S, Richter S, Wade RC (2006). ProSAT2-Protein Structure Annotation Server, Nucleic Acids Research 34(Web Server):W79-W83 691
  • Hallingbäck HR, Gabdoulline RR, Wade RC (2006). Comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking, Biochemistry 45(9):2940-2950 692
  • Spaar A, Dammer C, Gabdoulline RR, Wade RC, Helms V (2006). Diffusional encounter of barnase and barstar, Biophysical Journal 90(6):1913-1924 693
  • Wang T, Wade RC (2006). Force Field Effects on a beta-sheet Protein Domain Structure in Thermal Unfolding Simulations, J. Chem. Theory Comput. 2(1):140-148 694
  • Jalkanen KJ, Jürgensen VW, Claussen A, Rahim A, Jensen GM, Wade RC, Nardi F, Jung C, Degtyarenko IM, Nieminen RM, Herrmann F, Knapp-Mohammady M, Niehaus TA, Frimand K, Suhai S (2006). Use of Vibrational Spectroscopy to Study Protein and DNA Structure, Hydration, and Binding of Biomolecules: A Combined Theoretical and Experimental Approach, Int. J. Quantum Chem. 106(5):1160-1198 695
  • Cruciani G, Carosati E, Wade R, Baroni M (2006). Characterization of Protein- Binding Sites and Ligands Using Molecular Interaction Fields, In Comprehensive Medicinal Chemistry II, vol. 4, pp. 237–253, Ed. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford 747
  • Motiejunas D, Wade R (2006). Structural, Energetic and Dynamic Aspects of Ligand-Receptor Interactions, In Comprehensive Medicinal Chemistry II, vol. 4, pp. pp.193–213, Ed. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford 748
  • Stein M, Gabdoulline R, Wade R (2006). From Computational Biophysics to Systems Biology 2006, In Integrating Structural and Kinetic Enzymatic Information in Systems Biology, vol. 34 of NIC Series, pp. 129–132, Hansmann, Ulrich H.E.; Meinke, Jan; Mohanty, Sandipan; Zimmermann, Olav (Eds.) 749
  • Wang T, Wade R (2006). Force Field Effects on a b-sheet Protein Domain Structure in Thermal Unfolding Simulations, J Chem Theory and Comput 2:140–148 750

2005

2004

2003

2002

2001

2000

1999

1998

1997

1996

1995

1994

1993

1992

1991

1990

1989

1988

2019

  • Hanke A (2019). Computational characterisation of protein homo- and heterodimer formation, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg, 2019, Ariane Nunes-Alves and Rebecca C. Wade(HITS Tutor) 1010
  • Ullmann P (2019). Molecular dynamics simulation studies of gp41 cytoplasmic tail lateral embedding in phospholipid bilayer, Biosciences, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg, 2019, S. Kashif Sadiq and Rebecca C. Wade(HITS Tutor) 1011
  • Yuan J (2019). Druggability Assessment in TRAPP Procedure using Machine Learning Approaches, Master of Scientific Computing, Fakultät für Mathematik und Informatik, Ruprecht-Karls University, Heidelberg, 2019, Rebecca C. Wade and Daria Kokh(HITS Tutor) 1012
  • Ganotra GK (2019). Computational studies of drug-binding kinetics, Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University, Heidelberg, 2019, Rebecca C. Wade(HITS Tutor) 1013

2018

  • Friedrich P (2018). A novel method to treat gated protein-ligand binding via on-the-fly conformational updates within rigid body BD simulations, Faculty of Physics, Ruprecht-Karls University Heidelberg, 2018, Rebecca C. Wade, S. Kashif Sadiq and Neil Bruce(HITS Tutor) 880
  • Öztuerk MA (2018). A computational approach to decipher chromatosome structure determinants, Combined Faculties of the Natural Sciences and for Mathematics, Ruprecht-Karls University Heidelberg, Rebecca C. Wade (HITS Tutor) 882
  • Dohrke J (2018). Modelling of Neurotrophin Receptors, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg, 2018, Rebecca C. Wade and Goutam Mukherjee(HITS Tutor) 1032

2017

  • Reinhardt M (2017). Development of Hydrodynamic Coarse-Grain Models for Brownian Dynamics Simulations of Crowded Protein Systems, Faculty of Physics, Ruprecht-Karls University Heidelberg, 2017, Rebecca C. Wade and Neil Bruce(HITS Tutor) 877
  • Mustafa G (2017). Modeling and Simulation of Membrane Proteins to Understand their Structure, Dynamics and Function, Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University Heidelberg, 2017, Rebecca C. Wade(HITS Tutor) 878
  • Stank A (2017). Computational Studies on the Relation Between Macromolecular Dynamics and Protein Binding and Function., Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University Heidelberg, 2017, Rebecca C. Wade(HITS Tutor) 879
  • Buerkel C (2017). Towards development of Random Acceleration Molecular Dynamics simulation analysis software for predicting drug residence time, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg, 2017, Rebecca C. Wade, S. Kashif Sadiq and Daria B. Kokh(HITS Tutor) 1031

2016

  • Ozboyaci M (2016). Modeling and Simulation of Protein-Surface Interactions, Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University Heidelberg, 2016, Peter Bastian(Tutor), Rebecca C. Wade(HITS Tutor) 876
  • Stubbusch A (2016). Case Study of Human Growth Hormone Interactions by Brownian Dynamics Simulation, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg, 2016, Rebecca C. Wade and Neil J. Bruce(HITS Tutor) 1030

2015

  • Berinski M (2015). Macromolecular Interactions: in silico prediction of the structures of complexes between proteins, Faculty of Informatics and Mathematics, Johann Wolfgang Goethe Universität, Frankfurt am Main 883
  • Ganotra GK (2015). Methods to Compute and Investigate Drug Binding Kinetics, Life Science Informatics, University of Bonn, Rebecca C. Wade (HITS Tutor) 884
  • Yu X (2015). Multiscale Simulations of Cytochrome P450 Systems, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg 885
  • Horn M (2015). Clustering and Scoring the Druggability of Transient Protein Pockets, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg, 2015, Rebecca C. Wade and Antonia Stank(HITS Tutor) 1028
  • Waldhauer M (2015). Brownian Dynamics Simulations of Chymotrypsin Inhibitor 2 in Concentrated Protein Solutions, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg, 2015, Rebecca C. Wade and Neil J. Bruce(HITS Tutor) 1029

2014

  • Tong R (2014). Comparative analysis of Adenylyl Cyclase binding sites, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg, 2014, Rebecca C. Wade and Neil J. Bruce(HITS Tutor) 1027

2013

  • Banerjee P (2013). An Algorithmic Approach to Peptidomimetics, Masters Programme in Life Science Informatics, Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn 852

2012

  • Monninger T (2012). Dynamische hybride Cloud für wissenschaftliche Anwendungen, Fakultaet fuer Mathematik und Informatik, Ruprecht-Karls University, Heidelberg 853

2011

  • Subramaniam SR (2011). Sequence, Structure and Stability of Collagen and its Interaction with Collagenase., University of Madras, Chennai. 854
  • Garg D (2011). Computational and NMR Studies of Thymidylate Synthase and its Regulation, Faculty of Chemistry, Technical University of Munich 855
  • Veith N (2011). Structural Comparison of Pyruvate Kinases., Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 856
  • Nerini E (2011). System Approach to the Identification of Folate-related Enzyme Inhibitors with Anti-infectious Action, Doctoral School of Science and Technologies for Health Products, University of Modena and Reggio Emilia 857

2010

  • Feldman-Salit A (2010). Computation and Modeling of Molecular Recognition: The Cysteine Synthase Complex, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg 858

2009

  • Pachov GV (2009). Linker Histone-Nucleosome Interactions: A Modelling and Simulation Study, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University,Heidelberg 859
  • Berynskyy M (2009). Automatisierte Analyse von Brownian Dynamics Simulationen, Bioinformatics, Giessen-Friedberg University of Applied Sciences 860

2007

  • Motiejunas D (2007). Modeling of macromolecular interactions, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University, Heidelberg 861

2006

  • Zahran M (2006). Analyse a haut debit des proprietes electrostatiques des proteines de la famille des ubiquitines (High-throughput analysis of the electrostatic properties of proteins of the ubiquitin family), Bioinformatics, University Paris VII 862

2005

  • Besson B (2005). Development of a software to aid the search of protein structural information to estimate kinetic parameters in systems biology applications, Bioinformatics and Modeling, National Institute of Applied Science (INSA) Lyon 863
  • Johann TI (2005). Perturbation Methods in Molecular Dynamics Simulations with Implicit Solvent Models, Diplom Thesis 1014

2004

  • Motiejunas D (2004). Protein-protein docking assisted by sequence conservation and experimental data, Molecular Biology, Ruperto-Carola University,Heidelberg 864
  • R.Hallingbaeck H (2004). Peroxidases: A computational study of ligand binding and enzyme kinetics, Molecular Biotechnology, Uppsala University School of Engineering, Uppsala 865

2003

  • Doudieu OMN (2003). Using Sequence Information in Protein Docking Procedures, Bioinformatics, University of Applied Sciences, Berlin 866
  • Battey JN (2003). High-throughput Structural and Electrostatic Modelling of Ubiquitin Conjugating Enzymes, Bioinformatics, Exeter University, Exeter 867
  • Pulagam LVP (2003). Structure-based design of inhibitors of enzymes of the ubiquitin mediated protein degradation pathway, Bioinformatics, Cologne University Bioinformatics Center, University of Cologne 868
  • Neumann GF (2003). Entwicklung einer erweiterten Anwendung der Hauptkomponentenanalyse fuer das Protein-Protein Dockingproblem, Diplom Thesis 1015

2001

  • Ferrari S (2001). Inhibition studies of enzymes involved in drug resistance phenomena. Library-design and Structure-based approaches towards species-specific inhibitors of Thymidylate Synthase, University of Modena and Reggio Emilia, Modena 869
  • Gonzalez A (2001). Glycolytic Pathway Reaction Animations, Diplom Thesis 1016

1999

  • Nardi F (1999). Molecular Dynamics and NMR Spectroscopic Studies of Local Interactions of Small Peptides in Aqueous Solution Involving Aromatic Residues, Universite Joseph Fourier, Grenoble 870
  • Rienzo FD (1999). Computational studies of blue copper proteins, University of Modena and Reggio Emilia, Modena 871
  • Koboyashi M (1999). Chloride ion exchange routes in Haloalkane Dehalogenase from Xanthobacter autrophicus detected by Thermal Motion Pathway analysis, GRID and Essential Dynamics, University of York 872
  • Gauges R (1999). Molekulardynamische Simulation zur Aufklaerung des Substratzuganges in Cytochrom P450eryF, Diplom Thesis 1017

1998

  • Bitomsky W (1998). Binding of Glycosaminoglycans to Heparin-Binding Proteins, University of Vienna 873

1996

  • Ortiz AR (1996). Rational design of Human Synovial Fluid Phospholipase A2 inhibitors and analysis of their three-dimensional structure-activity relationships, University of Alcala de Henares, Madrid 874
  • Helms V (1996). Hydratation des aktiven Zentrums von Cytochrom P450cam – Untersuchung mit Molekueldynamik-Simulationen, Ludwig-Maximilians University, Munich 875
  • Reimer N (1996). Dynamische Einstellung des Parallelitaetsgrades mit reflexiven Programmen, Diplom Thesis 1018

1995

  • Degenhardt M (1995). De-Novo Design von Liganden zur Blockierung der Substratzugaenlichkeit von Cytochrom P450cam, Diplom Thesis 1019

1988

  • Wade R (1988). Ligand-Macromolecule Interactions, University of Oxford 850

2013

  • Costi MP, Luciani R, Nerini E, D. G, Ferrari S, Venturelli A, Lazzari S, Wade RC, Henrich S, Motiejunas D (2013). Uso di inhibitori della Pteridina Reduttasi per la prevenzione e/o il trattamento di infezioni parassitarie, Italian Patent Nr. 1403584, Date of Patent: 31.10.2013, Filed : 25.11.2010 1034

2009

  • Costi MP, Marverti G, Cardinale D, Venturelli A, Ferrari S, Ponterini G, Henrich S, Salo-Ahen O, Wade RC (2009). Peptides binding to the dimer interface of thymidylate synthase for the treatment of cancer, United States Patent No.: US 8,916,679 B2, Date of Patent: 23.12.2014. Filed: 17.08.2012, 01.12.2009 1033

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