Publications
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2014. Motions and mechanics: investigating conformational transitions in multi-domain proteins with coarse-grain simulations. Mol. Simul.. 40:229–236.
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2015. Docking Peptides on Proteins: How to Open a Lock, in the Dark, with a Flexible Key. Structure. 23:1373–1374.
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2019. Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins.. J R Soc Interface. 16(156):20190075.
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2016. Bridging Enzymatic Structure Function via Mechanics: A Coarse-Grain Approach. Methods in Enzymology. :227–248.
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2003. Fluid phase transitions at chemically heterogeneous, nonplanar solid substrates: Surface versus confinement effects. J. Chem. Phys.. 118:1453–1465.
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2008. Identification of Protein Interaction Partners and Protein-Protein Interaction Sites. J. Mol. Biol.. 382:1276–1289.
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2003. Nanoscopic liquid bridges exposed to a torsional strain. Physical Review E. 68:066103.
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2006. Investigating the local flexibility of functional residues in hemoproteins. Biophys. J.. 90:2706–2717.
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2012. α7-Nicotinic acetylcholine receptors: an old actor for new different roles. Curr. Drug Targets. 13:574–578.
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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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2018. The major β-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation .. Elife. 7
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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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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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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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2015. Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion. Structure. 23:584–597.
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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.