Joannis Apostolakis

Robert Körner, Joannis Apostolakis. Determination of Reaction Mappings and Reaction Center Information: The Imaginary Transition State Energy approach. J. Chem. Inf. Model., vol 48, no. 6, pp. 1181–1189, 2008.

Joannis Apostolakis, Oliver Sacher, Robert Körner, Johann Gasteiger. Automatic Determination of Reaction Mappings and Reaction Center Information. 2. Validation on a Biochemical Reaction Database. J. Chem. Inf. Model., vol 48, no. 6, pp. 1190–1198, 2008.

Jörn Marialke, Simon Tietze, Joannis Apostolakis. Similarity based docking. J. Chem. Inf. Model., vol 48, no. 1, pp. 186–196, 2008.

Andreas Steffen, Joannis Apostolakis. On the ease of predicting the thermodynamic properties of beta-cyclodextrin inclusion complexes. Chem Cent J. , vol 1, no. 29, 2007.

Stefan Zahler, Simon Tietze, Frank Totzke, Michael Kubbutat, Laurent Meijer, Angelika M. Vollmar, Joannis Apostolakis. Inverse in silico screening of 5/6/67 substituted Halogenoindirubins reveals PDK1 as target. Chem. Biol., vol 14, no. 11, pp. 1207-1214, 2007.

Andreas Steffen, Maximilian Karasz, Carolin Thiele, Thomas Lengauer, Andreas Kämper, Gerhard Wenz, Joannis Apostolakis. Combined Similarity and QSPR Virtual Screening for Guest Molecules of β-Cyclodextrin. New Journal of Chemistry, vol 31, pp. 1941 - 1949, 2007.

Markus Böhl, Simon Tietze, Andrea Sokoll, Sineej Madathil, Frank Pfennig, Joannis Apostolakis, Karim Fahmy, Herwig O. Gutzeit. Flavonoids Affect Actin Functions in Cytoplasm and Nucleus. Biophysical Journal, vol 93, no. 8, pp. 2767-2780, 2007.

Andreas Steffen, Carolin Thiele, Simon Tietze, Christian Strassnig, Andreas Kämper, Thomas Lengauer, Gerhard Wenz, Joannis Apostolakis. Improved Cyclodextrin-Based Receptors for Camptothecin by Inverse Virtual Screening. Chemistry 2007, vol 13, no. 24, pp. 6801-6809, 2007.

Simon Tietze, Joannis Apostolakis. GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein−Ligand Complexes. Journal of Chemical Information and Modelling, vol 47, no. 4, pp. 1657–1672, 2007.

Simon Tietze, Jörn Marialke, Robert Körner, Joannis Apostolakis. Graph-Based Molecular Alignment (GMA). Journal of Chemical Information and Modelling, vol 47, no. 2, pp. 591-601, 2007.

Joannis Apostolakis, Jörn Marialke, Robert Körner, Simon Tietze. Predicting activated conformations of substrates in enzyme binding sites. 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), 2007.

Andreas Kämper, Joannis Apostolakis, Matthias Rarey, Christel M. Marian, Thomas Lengauer. Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies. Journal of Chemical Information and Modelling, vol 46, no. 2, pp. 903–911, 2006.

Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis. A simple approach for protein name identification: prospects and limits. BMC Bioinformatics, vol 6, no. (Suppl.1), pp. S15, May 2005.

Joannis Apostolakis, Robert Körner, Jörn Marialke. Embedded subgraph isomorphism and its applications in cheminformatics and metabolomics. 1st German Conference in Chemoinformatics, 2005.

Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis. Exact versus approximate string matching for protein name identification. BioCreative Challenge Evaluation Workshop, 2004.

Christoph Best, Ralf Zimmer, Joannis Apostolakis. Probabilistic methods for predicting protein functions in protein-protein interaction networks. Robert Giegerich, Jens Stoye (eds.): German Conference on Bioinformatics, GCB 2004, Bielefeld, Germany, October 4-6, 2004, Lecture Notes in Informatics, vol P-53, pp. 159-168, Gesellschaft für Informatik, 2004.

Niklas von Öhsen, Joannis Apostolakis, Ralf Zimmer. Dopro: Automatic Protein Domain Structure Prediction using a Stochastic Model for Analyzing Homology Search Results. CAFASP 2004, pp. extended abstract, 2004.

D. Hofmann, Joannis Apostolakis. Crystal structure prediction with data mining. J. Mol. Struct., vol 647, no. 1, pp. 17-39, 2003.

Philippe Ferrara, Joannis Apostolakis, Amedeo Caflisch. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics, vol 46, no. 1, pp. 24-33, 2002.

Joannis Apostolakis, D. Güttler, Florian Sohler, Ralf Zimmer. Biological context and the analysis of gene expression data. H.-P. Lenhof (ed.): ECCB 2002, vol Poster, 2002.

Joannis Apostolakis, D. Güttler, Florian Sohler, Ralf Zimmer. Prediction of gene functions from biological interactions. M. Vingron (ed.): RECOMB 2002, vol Poster, 2002.

D. Hofmann, Joannis Apostolakis, Thomas Lengauer. Derivation of a scoring function for crystal structure prediction. Acta Crystallogr A., vol 57, no. Pt4, pp. 442-50, 2001.

Joannis Apostolakis, D. Hofmann, Thomas Lengauer. Using simple learning machines to derive a new potential for molecular modelling, in Rational Approaches to Drug Design. Proc. of 13th Eur. Symp. on QSAR, Prous Science, pp. 125-134, 2001.

Philippe Ferrara, Joannis Apostolakis, Amedeo Caflisch. Computer simulations of protein folding by targeted molecular dynamics. Proteins: Struct. Funct. Genet, vol 39, no. 3, pp. 252-260, 2000.

Philippe Ferrara, Joannis Apostolakis, Amedeo Caflisch. Thermodynamics and Kinetics of Folding of Two Model Peptides Investigated by Molecular Dynamics Simulations. J. Phys. Chem. B, vol 104, no. 20, pp. 5000–5010, 2000.

Philippe Ferrara, Joannis Apostolakis, Amedeo Caflisch. Targeted Molecular Dynamics Simulations of Protein Unfolding. J. Phys. Chem. B 104, pp. 4511–4518, 2000.

Nicolas Majeux, Marco Scarsi, Joannis Apostolakis, Claus Ehrhardt, Amedeo Caflisch. Exhaustive docking of molecular fragments with electrostatic solvation. Proteins: Struct. Funct. Genet., vol 37, no. 1, pp. 88-105, 1999.

Joannis Apostolakis, Amedeo Caflisch. Computational ligand design. Comb. Chem. & H.T.S, vol 2, pp. 91-104, 1999.

Joannis Apostolakis, Philippe Ferrara, Amedeo Caflisch. Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water. J. Chem. Phys., vol 110, no. 4, pp. 2099-2108, 1999.

Joannis Apostolakis, Andreas Plückthun, Amedeo Caflisch. Docking Small ligands in flexible binding sites. Journal of Computational Chemistry, vol 19, no. 1, pp. 21 - 37, 1998.

Marco Scarsi, Joannis Apostolakis, Amedeo Caflisch. Comparison of a GB Solvation Model with Explicit Solvent Simulations: Potentials of Mean Force and Conformational Preferences of Alanine Dipeptide and 1,2-Dichloroethane. J. Phys. Chem. B, vol 102, no. 18, pp. 3637–3641, 1998.

R. Gupta, J. DeLapp, G. Batrouni, G.C. Fox, C.F. Baillie, Joannis Apostolakis. Phase transition in the 2D XY model. Physical Review Letters, vol 61, no. 17, pp. 1996-1999, 1998.

Marco Scarsi, Joannis Apostolakis, Amedeo Caflisch. Continuum electrostatic energies of macromolecules in aqueous solutions. J. Phys. Chem. A, vol 101, no. 43, pp. 8098–8106, 1997.

I. Muegge, Joannis Apostolakis, U. Ermler, G. Fritzsch, W. Lubitz, E.W. Knapp. Shift of the special pair redox potential: Electrostatic energy computations of mutants of the reaction center from Rhodobacter sphaeroides. Biochemistry, vol 35, no. 25, pp. 8359–8370, 1996.

Joannis Apostolakis, I. Muegge, U. Ermler, G. Fritzsch, E.W. Knapp. Free energy computations on the shift of the special pair redox potential. J. Am. Chem. Soc., vol 118, no. 15, pp. 3743–3752, 1996.