Publications
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2010. A putative extracellular salt bridge at the subunit interface contributes to the ion channel function of the ATP-gated P2X2 receptor. J. Biol. Chem.. 285:15805–15815.
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2009. PTools: an opensource molecular docking library.. Bmc Struct. Biol.. 9:27–37.
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2017. Protein-RNA complexation driven by the charge regulation mechanism.. Biochem Biophys Res Commun.
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2013. Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information. Plos Comput. Biol.. 9:e1003369.
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2010. Protein-Protein Docking. Protein-Protein Complexes. Analysis, Modeling and Drug Design. :147–181.
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2020. Protein thermal stability. Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly.
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2015. Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. J. Chem. Theory Comput.. 11:1843–1853.
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2006. `Protein Peeling': an approach for splitting a 3D protein structure into compact fragments. Bioinformatics. 22:129–133.
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2006. Protein Peeling 2: a web server to convert protein structures into series of protein units. Nucleic Acids Res.. 34:W75-W78.
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2007. Protein mechanics: a route from structure to function. Journal of Biosciences. 32:891–898.
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2020. Protein Interaction Energy Landscapes are Shaped by Functional and also Non-functional Partners.. J Mol Biol. 432(4):1183-1198.
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2007. A prokaryotic proton-gated ion channel from the nicotinic acetylcholine receptor family. Nature. 445:116–119.
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2018. Probing the quality control mechanism of the twin-arginine translocase with folding variants of a -designed heme protein.. J Biol Chem. 293(18):6672-6681.
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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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2006. Probing a model of a GPCR/ligand complex in an explicit membrane environment: The human cholecystokinin-1 receptor. Biophys. J.. 90:1232–1240.
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2019. Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca Ions.. J Phys Chem B. 123(12):2645-2653.
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1991. A probabilistic view on steady state enzyme kinetics. J. Theor. Biol.. 148:229–242.
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2008. Pressure-induced core packing and interfacial dehydration in nonionic C12E6 micelle in aqueous solution. Langmuir. 24:6067–71.
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2000. Predicting helical hairpins from sequences by Monte Carlo simulations. J. Comput. Chem.. 21:582–589.
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2015. Predicting and exploring complex nucleic acids architectures through a coarse-grained model. Journal of Biomolecular Structure & Dynamics. 33:30–31.
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2014. A predicted binding site for cholesterol on the GABAA receptor.. Biophys. J.. 106:1938–1949.
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2020. A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization.. J Chem Phys. 153(5):050901.
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1985. On the possible mechanism of multiple enzyme attack in polysaccharide degradation. Mol. Biol.. 19:1400–1408.
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2019. The positioning of Chi sites allows the RecBCD pathway to suppress some genomic rearrangements. Nucleic Acids Res. 47:1836-1846.
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2003. The position of Q B in the photosynthetic reaction center depends on pH: A theoretical analysis of the proton uptake upon Q B reduction. Biophys. J.. 84:2090–2098.