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Ran Friedman

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All Publications

2011: Ran Friedman; Amedeo Caflisch
Surfactant effects on amyloid aggregation kinetics.
Journal of molecular biology 2011;414(2):303-12.
2010: Ran Friedman; Amedeo Caflisch
On the orientation of the catalytic dyad in aspartic proteases.
Proteins 2010;78(6):1575-82.
2009: Ran Friedman; Amedeo Caflisch
Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring.
ChemMedChem 2009;4(8):1317-26.
2009: Ran Friedman; Riccardo Pellarin; Amedeo Caflisch
Amyloid aggregation on lipid bilayers and its impact on membrane permeability.
Journal of molecular biology 2009;387(2):407-15.
2008: Svetlana Dashevskaya; Ronen Benjamine Kopito; Ran Friedman; Michael Elbaum; Bernard L Epel
Diffusion of anionic and neutral GFP derivatives through plasmodesmata in epidermal cells of Nicotiana benthamiana.
Protoplasma 2008;234(1-4):13-23.
2008: Ran Friedman; Amedeo Caflisch
Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis.
Proteins 2008;73(4):814-27.
2007: Assaf Ganoth; Esther Nachliel; Ran Friedman; Menachem Gutman
Myosin V movement: lessons from molecular dynamics studies of IQ peptides in the lever arm.
Biochemistry 2007;46(50):14524-36.
2007: Ran Friedman; Amedeo Caflisch
The protonation state of the catalytic aspartates in plasmepsin II.
FEBS letters 2007;581(21):4120-4.
2007: Ran Friedman; Stefan Fischer; Esther Nachliel; Steve Scheiner; Menachem Gutman
Minimum energy pathways for proton transfer between adjacent sites exposed to water.
The journal of physical chemistry. B 2007;111(21):6059-70.
2007: Yossi Tsfadia; Ran Friedman; Jonathan Kadmon; Anna Selzer; Esther Nachliel; Menachem Gutman
Molecular dynamics simulations of palmitate entry into the hydrophobic pocket of the fatty acid binding protein.
FEBS letters 2007;581(6):1243-7.
2006: Assaf Ganoth; Ran Friedman; Esther Nachliel; Menachem Gutman
A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides.
Biophysical journal 2006;91(7):2436-50.
2006: Menachem Gutman; Esther Nachliel; Ran Friedman
The mechanism of proton transfer between adjacent sites on the molecular surface.
Biochimica et biophysica acta 2006;1757(8):931-41.
2006: Assaf Ganoth; Esther Nachliel; Ran Friedman; Menachem Gutman
Molecular dynamics study of a calmodulin-like protein with an IQ peptide: spontaneous refolding of the protein around the peptide.
Proteins 2006;64(1):133-46.
2006: Menachem Gutman; Esther Nachliel; Ran Friedman
The dynamics of proton transfer between adjacent sites.
Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology 2006;5(6):531-7.
2006: Elad Project; Ran Friedman; Esther Nachliel; Menachem Gutman
A molecular dynamics study of the effect of Ca2+ removal on calmodulin structure.
Biophysical journal 2006;90(11):3842-50.
2006: Ran Friedman; Esther Nachliel; Menachem Gutman
Fatty acid binding proteins: same structure but different binding mechanisms? Molecular dynamics simulations of intestinal fatty acid binding protein.
Biophysical journal 2006;90(5):1535-45.
2005: Ran Friedman; Esther Nachliel; Menachem Gutman
Application of classical molecular dynamics for evaluation of proton transfer mechanism on a protein.
Biochimica et biophysica acta 2005;1710(2-3):67-77.
2005: Ran Friedman; Esther Nachliel; Menachem Gutman
Protein surface dynamics: interaction with water and small solutes.
Journal of biological physics 2005;31(3-4):433-52.
2005: Ran Friedman; Esther Nachliel; Menachem Gutman
Molecular dynamics of a protein surface: ion-residues interactions.
Biophysical journal 2005;89(2):768-81.
2005: Aviv Mezer; Ran Friedman; Orly Noivirt; Esther Nachliel; Menachem Gutman
The mechanism of proton transfer between adjacent sites exposed to water.
The journal of physical chemistry. B 2005;109(22):11379-88.
2005: Ran Friedman; Esther Nachliel; Menachem Gutman
Molecular dynamics simulations of the adipocyte lipid binding protein reveal a novel entry site for the ligand.
Biochemistry 2005;44(11):4275-83.
2003: Ran Friedman; Esther Nachliel; Menachem Gutman
The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin.
Biophysical journal 2003;85(2):886-96.