Publications
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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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2007. Probing the flexibility of the bacterial reaction center: The wild-type protein is more rigid than two site-specific mutants. Biochemistry. 46:14960–14968.
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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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2010. Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress. Biophys. J.. 99:3412–3419.
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2015. Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus? J. R. Soc. Interface. 12
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2021. When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes. Biomolecules. 11:1529.
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2002. Fluids confined by nanopatterned substrates of low symmetry. Mol. Phys.. 100:2971–2982.
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2004. Torsion-induced phase transitions in fluids confined between chemically decorated substrates. J. Chem. Phys.. 121:9077–9086.
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2009. Modeling the Mechanical Response of Proteins to Anisotropic Deformation. Chemphyschem. 10:115–118.
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2007. Locating the active sites of enzymes using mechanical properties. Proteins: Struct., Funct., Bioinf.. 67:350–359.
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2018. Mechanical variations in proteins with large-scale motions highlight the formation of structural locks. Journal of Structural Biology.
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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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2010. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res.. 38:6313–6323.
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2009. PTools: an opensource molecular docking library.. Bmc Struct. Biol.. 9:27–37.
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2010. Protein-Protein Docking. Protein-Protein Complexes. Analysis, Modeling and Drug Design. :147–181.
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2018. A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol.. Journal of Chemical Theory and Computation. 14:6560–6573.
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2004. In silico assembly of Alzheimer's A beta(16-22) peptide into beta-sheets. J. Am. Chem. Soc.. 126:11509–11516.
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2003. Impact of the tail and mutations G131V and M129V on prion protein flexibility. Proteins-structure Function and Genetics. 51:258–265.