Publications
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2021. Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces.. Proteins.
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2008. Searching for Homology by Filaments of RecA-like Proteins. Genome Dynamics & Stability. Recombination and Meiosis. Models, Means and Evolution:65–89.
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2003. Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination. Q. Rev. Biophys.. 36:429–53.
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1993. Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2. Biopolymers. 33:335–50.
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2009. Deforming DNA: from physics to biology. Chemphyschem. 10:1399–404.
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2022. Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. J. Phys. Chem. B. 126(22):4022-4034.
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2006. HDAC1 acetylation is linked to progressive modulation of steroid receptor-induced gene transcription.. Mol. Cell. 22:669–679.
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2013. The effect of protein composition on hydration dynamics. Phys. Chem. Chem. Phys.. 15:3570–3576.
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2017. Configurational Disorder of Water Hydrogen Bond Network at the Protein Dynamical Transition. J. Phys. Chem. B. 121:6792−6798.
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2015. Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains.. J. Phys. Chem. B. 119:8939–49.
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2015. Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion. Structure. 23:584–597.
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2009. Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis. J. Phys. Chem. B. 113:16660–16668.
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1990. A hierarchical `nesting' approach to describe the stability of alpha helices with side-chain interactions. Biopolymers. 30:335–347.
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1995. Estimating friction coefficients of mixed globular/chain molecules, such as protein/DNA complexes. Biophys. J.. 69:840–848.
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1989. Allosteric formulation of thermal transitions in macromolecules, including effects of ligand binding and oligomerization. Biopolymers. 28:1705–1729.
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1998. A soft, mean–field potential derived from crystal contacts for predicting protein–protein interactions. J. Mol. Biol.. 283:1037–1047.
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1988. Quantitative analysis of linkage in macromolecules when one ligand is present in limited total quantity. Biochemistry. 27:6829–6835.
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1995. Significance of bound water to local chain conformations in protein crystals. Proc. Natl. Acad. Sci. U.s.a.. 92:7600–7604.
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1988. Linkage of organic phosphates to oxygen binding in human hemoglobin at high concentrations. Biochemistry. 27:6835–6843.
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2004. Integrating three views of Arf1 activation dynamics. J. Mol. Biol.. 337:969–983.
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1987. Nesting: hierarchies of allosteric interactions. Proc. Natl. Acad. Sci. U.s.a.. 84:1891–1895.
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2020. Structural transitions in the RNA 7SK 5' hairpin and their effect on HEXIM binding. Nucleic Acids Res. 48:373-389.
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2018. The major β-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation .. Elife. 7
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2016. Hybridizing Rapidly Exploring Random Trees and Basin Hopping Yields an Improved Exploration of Energy Landscapes. J. Comput. Chem.. 37:752.
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2012. α7-Nicotinic acetylcholine receptors: an old actor for new different roles. Curr. Drug Targets. 13:574–578.