Selected Publications
- D. Prada-Gracia, R. Shevchuk, P. Hamm, F. Rao: Towards a microscopic description of the free-energy landscape of water. J Chem Phys, 2012; 137 (14): 144504. http://dx.doi.org/10.1063/1.4755746
- R. Shevchuk, D. Prada-Gracia, F. Rao: Water Structure-Forming Capabilities are Temperature Shifted for Different Models. J Phys Chem B, 2012; 116 (25):7538-7543. http://dx.doi.org/10.1021/jp303583f
- R. Shevchuk, F. Rao: Note: Microsecond long atomistic simulation of supercooled water. J Chem Phys, 2012; 137 (3): 036101. http://dx.doi.org/10.1063/1.4737867
- S. Mostarda, D. Gfeller, F. Rao: Beyond the Binding Site: The Role of the beta2 – beta3 Loop and Extra-Domain Structures in PDZ Domains. Plos Comput Biol, 2012; 8 (3) : e1002429-e1002429. http://dx.doi.org/10.1371/journal.pcbi.1002429
- F. Rao: Protein Inherent Structures by Different Minimization Strategies J Comput Chem, 2011; 32 (6): 1113-1116
- M. Seeber, F. Rao, F. Fanelli: Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces J Comput Chem, 2011; 32 (6): 1183-1194
- S. Garrett-Roe, F. Perakis, F. Rao, P. Hamm: Three-Dimensional Infrared Spectroscopy of Isotope-Substituted Liquid Water Reveals Heterogeneous Dynamics J Phys Chem B, 2011; 115 (21): 6976-6984
- F. Rao, Local Transition Gradients Indicating the Global Attributes of Protein Energy Landscapes, J. Phys. Chem. Lett. (2010), 1, 1580-1583
- F. Rao and M. Karplus, Protein dynamics investigated by inherent structure analysis, Proc. Natl. Acad. Sci. USA (2010) 107, 9152-9157
- D. Gfeller, D. Morton de Lachapelle, P. De Los Rios, G. Caldarelli, and F. Rao, Uncovering the topology of configuration space networks, Phys. Rev. E (2007) 76, 026113
- D. Gfeller, P. De Los Rios, A. Caflisch, and F. Rao, Complex network analysis of free-energy landscapes, Proc. Natl. Acad. Sci. USA (2007) 104, 1817-1822
- M. Seeber , M. Cecchini , F. Rao , G. Settanni and A. Caflisch, Wordom: a program for efficient analysis of molecular dynamics simulations, Bionform. (2007) 23, 2625
- F. Rao and A. Caflisch, The protein folding network, J. Mol. Biol. (2004) 342, 299-306
- F. Rao and A. Caflisch, Replica exchange molecular dynamics simulations of reversible folding, J. Chem. Phys. (2003) 119, 4035-42
FRIAS Project
Proteins are fascinating complex systems. The traditional structure-function paradigm, “to know function study structure” which goes back to Watson and Crick, have guided our interpretation of protein function for decades. But our mechanistic understanding of how those processes are regulated is still unclear. It is only rather recently that the possible role of dynamics in signaling, allostery and catalytic activity, per se, has been recognized. The goal of our research is to understand and elucidate the role of dynamics in the context of protein function. To this aim we use the tools of molecular dynamics simulations and complex network analysis to obtain high resolution mappings of the underlying free-energy landscape. The latter, driving the biologically relevant conformational transition, provide a quantitative insight on both the thermodynamics and kinetics of the process.