Biblio
Found 308 results
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2007. Wordom: A program for efficient analysis of molecular dynamics simulations. Bioinformatics. 23(19):2625-2627.
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2006. Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking. Journal of Medicinal Chemistry. 49(25):7384-7392.
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2006. Computational models for the prediction of polypeptide aggregation propensity. Current Opinion in Chemical Biology. 10(5):437-444.
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2006. In silico discovery of beta-secretase inhibitors. Journal of the American Chemical Society. 128(16):5436-5443.
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2006. Interpreting the aggregation kinetics of amyloid peptides. Journal of Molecular Biology. 360(4):882-892.
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2006. A molecular dynamics approach to the structural characterization of amyloid aggregation. Journal of Molecular Biology. 357(4):1306-1321.
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2006. Network and graph analyses of folding free energy surfaces. Current Opinion in Structural Biology. 16(1):71-78.
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2006. Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane. Biophysical Journal. 91(9):3276-3284.
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2006. Unfolding transition state and intermediates of the tumor suppressor p16INK4a investigated by molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics. 64(1):178-192.
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2005. Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody-hapten complex. Protein Science. 14(10):2499-2514.
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2005. Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations. Journal of Medicinal Chemistry. 48(16):5108-5111.
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2005. Estimation of protein folding probability from equilibrium simulations. Journal of Chemical Physics. 122(18):184901.
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2005. Fragment-based high-throughput docking. Virtual Screening in Drug Discovery. :349-378.
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2005. Functional plasticity in the substrate binding site of beta-secretase. Structure. 13(10):1487-1498.
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2005. Local modularity measure for network clusterizations. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics. 72(5.2):056107.
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2005. Molecular dynamics simulations to study protein folding and unfolding. Protein Folding Handbook. 1:1143-1169.
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2005. Organism complexity anti-correlates with proteomic beta-aggregation propensity. Protein Science. 14(10):2735-2740.
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2005. Phi-value analysis by molecular dynamics simulations of reversible folding. Proceedings of the National Academy of Sciences of the United States of America. 102(3):628-633.
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2005. Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Science. 14(10):2723-2734.
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2005. Spontaneous formation of detergent micelles around the outer membrane protein OmpX. Biophysical Journal. 88(5):3191-3204.
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2004. Automated docking of highly flexible ligands by genetic algorithms: A critical assessment. Journal of Computational Chemistry. 25(3):412-422.
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2004. Efficient evaluation of binding free energy using continuum electrostatics solvation. Journal of Medicinal Chemistry. 47(23):5791-5797.
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2004. The folding and dimerization of HIV-1 protease: Evidence for a stable monomer from simulations. Journal of Molecular Biology. 340(1):67-79.
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2004. Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations. Biophysical Journal. 86(3):1691-1701.
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2004. Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations. Journal of the American Chemical Society. 126(46):15277-15286.