Publications
] .
2022. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Frontiers in Molecular Biosciences. 9:826136.
.
2022. Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions. Proteins: Structure, Function, and Bioinformatics. 90:858-868.
.
2021. Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom. Bio-protocol. 11:e4097.
.
2017. Mobility and core-protein binding patterns of disordered C-terminal tails in β-tubulin isotypes.. Biochemistry. 56(12):1746–1756.
.
2016. Hybridizing Rapidly Exploring Random Trees and Basin Hopping Yields an Improved Exploration of Energy Landscapes. J. Comput. Chem.. 37:752.
.
2015. Changes in protein structure at the interface accompanying complex formation.. Iucrj. 2:643–652.
.
2015. Conformational ensembles and sampled landscapes: analysis and comparison. J. Comp. Chem.. 36:1213–31.
.
2015. An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. Plos One. in press:e0116414.
.
2015. Investigating the Structural Variability and Binding Modes of the Glioma Targeting NFL-TBS.40-63 Peptide on Tubulin. Biochemistry. 54:3660–3669.
.
2013. Modeling macromolecular complexes: a journey across scales. Modeling in Computational Biology and Biomedicine: A Multidisciplinary Endeavor.
.
2013. Reassessing buried surface areas in protein-protein complexes.. Protein Sci.. 22:1453–57.
.
2013. Towards Morse theory for point cloud data.. Inria Tech Reports.
.
2011. Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
.
2011. Free energy profiles along consensus normal modes provide insight into HIV-1 protease flap opening. J. Chem. Theor. Comput.. 7:2348–52.
.
2011. Receptor Flexibility in Ligand Docking and Virtual Screening.. In-silico lead discovery.
.
2010. A computational study of a recreated G protein-GEF reaction intermediate competent for nucleotide exchange: fate of the Mg ion. Plos One. 5:e9142.
.
2010. Consensus Modes, a robust description of protein collective motions from multiple-minima normal mode analysis–application to the HIV-1 protease.. Phys. Chem. Chem. Phys.. 12:2850–2859.
.
2010. How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics. Bmc Genomics. 11, S5
.
2010. Side-chain rotamer transitions at protein-protein interfaces. Proteins: Struct., Funct., Bioinf.. 78:3219–25.
.
2009. Disulfide bond substitution by directed evolution in an engineered binding-protein scaffold.. Chembiochem. 10:1349–1359.
.
2009. Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers.. Biochemistry. 48:276–288.
.
2006. Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors. Febs Lett.. 580:5130–5136.
.
2006. Odorant Binding and Conformational Dynamics in the Odorant-binding Protein. J. Biol. Chem.. 281:29929–29937.
.
2004. Integrating three views of Arf1 activation dynamics. J. Mol. Biol.. 337:969–983.