List of publications

Transcription

1 List of publications 42. Kazemi, S., Krueger, D. M., Sirockin, F., Gohlke, H. (2009) Elastic potential grids: Accurate and efficient representation of intermolecular interactions for fullyflexible docking. ChemMedChem, in press. 41. Fulle, S., Gohlke, H. (2009) Constraint counting on RNA structures: Linking flexibility and function. Methods, in press. 40. Fulle, S., Gohlke, H. (2009) Statics of the ribosomal exit tunnel: Implications for co-translational peptide folding, elongation regulation, and antibiotics binding. J. Mol. Biol., 387, Radestock, S., Gohlke, H. (2008) Constraint Network Analysis: Exploiting the link between protein rigidity and thermostability. In: "From Computational Biophysics to Systems Biology (CBSB08)", U.H.E. Hansmann, J. H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (eds.), NIC Series, Jülich, 40, Fulle, S., Gohlke, H. (2008). Determining RNA flexibility by graph theory: Ribosomal exit tunnel as a case study. In: "From Computational Biophysics to Systems Biology (CBSB08)", U.H.E. Hansmann, J. H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (eds.), NIC Series, Jülich, 40, Radestock, S., Gohlke, H. (2008). Exploiting the link between protein rigidity and thermostability for data-driven protein engineering. Eng. Life Science, 8, Kopitz, H., Zivkovic, A., Engels, J. W., Gohlke, H. (2008). Determinants of the unexpected stability of RNA fluorobenzene self pairs. ChemBioChem, 9, Cozzini, P., Kellog, G.E., Spyrakis, F., Abraham, D. J., Constantino, G., Emerson, A., Fanelli, F., Gohlke, H., Kuhn, L.A., Morris, G.M., Orozco, M., Pertinhez, T.A., Rizzi, M:, Sotriffer, C. (2008). Target flexibility: An emerging consideration in drug discovery and design. J. Med. Chem., 51, Koller, A. N., Schwalbe, H., Gohlke, H. (2008). Starting structure dependence of NMR order parameters derived from MD simulations: Implications for judging force field quality. Biophys. J., 95, L4-L6. Fulle, S., Gohlke, H., (2008). Analyzing the flexibility of RNA structures by

2 constraint counting. Biophys. J., 94, Wendel, C., Gohlke, H. (2008). Predicting transmembrane helix pair configurations with knowledge-based distance-dependent pair potentials. Proteins, 70, Breu, B., Silber, K., Gohlke, H. (2007). Consensus AFMoC models incorporate ligand and receptor conformational variability into tailor-made scoring functions. J. Chem. Inf. Model., 47, Pfeffer, P., Gohlke, H. (2007). DrugScore RNA Knowledge-based scoring function to predict RNA-ligand interactions. J. Chem. Inf. Model., 47, Radestock, S., Gohlke, H. (2007). Molekulare Bioinformatik in der Pharmaforschung. GIT Bioforum, 3, Ahmed, A., Kazemi, S., Gohlke, H. (2007). Protein flexibility and mobility in structure-based drug design. Frontiers Drug Des. Discov., 3, Rashid, U. J., Peternov, D., Koglin, A., Chandra, T., Gohlke, H., Piehler, J., Chen, J. C.-H. (2007). Structure of Aquifex aeolicus Argonaute highlights conformational flexibility of the PAZ domain as a potential regulator of RISC function. J. Biol. Chem., 282, Gohlke, H., Thorpe, M. F. (2006). A natural coarse graining for simulating large biomolecular motion. Biophys. J., 91, Gonzalez Ruiz, D., Gohlke, H. (2006). Targeting protein-protein interactions with small molecules: Challenges and perspectives for computational binding epitope detection and ligand finding. Curr. Med. Chem., 13, Ahmed, A., Gohlke, H. (2006). Multiscale modelling of macromolecular conformational changes combining concepts from rigidity and elastic network theory. Proteins, 63, Velec, H., Gohlke, H., Klebe, G. (2005). DrugScore CSD Knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near native ligand poses and better affinity prediction. J. Med. Chem. 48, Radestock, S., Böhm, M., Gohlke, H. (2005). Improving binding mode predictions by docking into protein-specifically adapted potential fields. J. Med. Chem., 48, 2

3 Case, D. A., Cheatham, T., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling C., Wang, B., Woods, R. (2005). The Amber Biomolecular Simulation Programs, J. Comp. Chem., 26, a Ferrara, P., Gohlke, H., Price, D. J., Klebe, G., Brooks III, C. L. (2004). Assessing scoring functions for protein-ligand interactions. J. Med. Chem., 47, Gohlke, H., Kuhn, L. A., Case, D. A. (2004). Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach. Proteins, 56, Gohlke, H., Case, D. A. (2004). Converging free energy estimates: MM- PB(GB)SA studies on the protein-protein complex Ras-Raf. J. Comput. Chem., 25, Evers, A., Gohlke, H., Klebe, G. (2003). Ligand-supported homology modelling of protein binding sites using knowledge-based potentials. J. Mol. Biol., 334, Gohlke, H., Kiel, C., Case, D. A. (2003). Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J. Mol. Biol., 330, Gohlke, H., Schwarz, S., Gündisch, D., Tilotta, M. C., Weber A., Wegge, T., Seitz, G. (2003). 3D-QSAR Analyses-guided Rational Design of Novel Ligands for the (α4) 2 (β2) 3 Nicotinic Acetylcholine Receptor. J. Med. Chem., 46, Gohlke, H., Klebe, G. (2002). DrugScore meets CoMFA: Adaptation of Fields for Molecular Comparison (AFMoC) or How to Tailor Knowledge-Based Pair- Potentials to a Particular Protein. J. Med. Chem., 45, Gohlke H., Klebe, G. (2002). Ansätze zur Beschreibung und Vorhersage der Bindungsaffinität niedermolekularer Liganden an makromolekulare Rezeptoren. Angew. Chem., 114, Gohlke H., Klebe, G. (2002). Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors. Angew. Chem. Int. Ed., 41, Sotriffer, C. A., Gohlke, H., Klebe, G. (2002). Docking into knowledge-based potential fields: A comparative evaluation of DrugScore. J. Med. Chem., 45,

4 Gohlke, H., Gündisch, D., Schwarz, S., Seitz, G., Tilotta, M. C., Wegge, T. (2002). Synthesis and Nicotinic Binding Studies on Enantiopure Diazine Analogs of the Novel (2-Chloro-5-pyridyl)-9-azabicyclo[4.2.1]-non-2-ene UB165. J. Med. Chem., 45, Kamm, W., Stürzebecher, J., Behrens, I., Hauptmann, J., Dullweber, F., Gohlke, H., Klebe, G., Kissel, T. (2001). Transport of peptidomimetic thrombin inhibitors with a 3-amidino-phenylalanine structure: Permeability and efflux mechanism in monolayers of human intestinal cell line (Caco-2). Pharm. Res., 18, Gohlke, H., Klebe, G. (2001). Scoring protein-ligand interactions: developments and applications in virtual screening. Eur. J. Biochem., 268, Suppl. 1, 30. Gohlke H., Klebe, G. (2001). Statistical potentials and scoring functions applied to protein-ligand binding. Curr. Opin. Struct. Biol., 11, (Invited review) Gohlke, H., Dullweber, F., Kamm, W., März, J., Kissel, T., Klebe, G. (2001). Prediction of Human Intestinal Absorption Using a Combined Simulated Annealing/Backpropagation Neural Network Approach. In Rational Approaches to Drug Design 13 th European Symposium on QSAR (Höltje, H.-D., Sippl, W., Ed.), S , Prous Science, Barcelona. Gohlke, H., Hendlich M., Klebe G. (2000). Predicting binding modes, binding affinities and hot spots for protein-ligand complexes using a knowledge-based scoring function. Persp. Drug Design Discov., 20, Klebe, G., Grädler, U., Grüneberg, S., Krämer, O., Gohlke, H. (2000). Understanding Receptor-Ligand Interactions as a Prerequisite for Virtual Screening. In Virtual Screening for Bioactive Molecules (Böhm, H. J., Schneider, G., Ed.), S , Wiley-VCH, Weinheim. Gohlke H., Hendlich M., Klebe G. (2000). Knowledge-based Scoring Function to Predict Protein-Ligand Interactions. J. Mol. Biol., 295, Klebe, G., Böhm, M., Dullweber, F., Grädler, U., Gohlke, H., Hendlich, M. (1999). Structural and Energetic Aspects of Protein-Ligand Binding in Drug Design. In Molecular Modelling and Prediction of Bioactivity (Gundertofte, K., Jorgensen, F., Ed.), S , KLUWER Academic / Plenum Publ., New York. Gohlke, H., Immel, S., Lichtenthaler, F.W. (1999). Conformations and lipophilicity profiles of some cyclic β-(1 3)- and β-(1 6)-linked 4

5 oligogalactofuranosides. Carbohydr. Res., 321, Gohlke, H., Immel, S., Lichtenthaler, F. W., Schmitt, G. E. (1998). β(1 3)- and β(1 6)-Linked Cyclogalactofuranosides: Conformations and Molecular Shapes, In Proceedings of the 9 th International Symposium on Cyclodextrins (J.J. Torres- Labandeira, J. L. Vila Jato, Ed.), S , Kluwer Acad. Publ., Dordrecht. 5