About

My name is David De Sancho and currently I am an Ikerbasque Research Fellow at nanoGUNE. Over the last few years of work as a postdoc in the laboratory of Robert B. Best I have extensively used master equation / Markov state models (usually termed MSMs) to analyze data from molecular dynamics simulations. My work is heavily indebted to massive contributions from other groups. So before you get any further I would suggest reading the following volume

• An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation, edited by Pande, Bowman and Noe.

It surely contains all you need to know about this methodology.

However, there is a gradually increasing number of papers where we have used our own flavour of MSMs, and we have even made some small methodological contributions.

• What is the time scale for alpha-helix nucleation? J. Am. Chem. Soc. 133 (17), 6809-6816 (2011).

• Folding kinetics and unfolded state dynamics of the GB1 hairpin from molecular simulation. J. Chem. Theory Comput. 9 (3) 1743-1753 (2013)

• Engineering Folding Dynamics from Two-State to Downhill: Application to lambda-Repressor J. Phys. Chem. B 117 (43) 13435-13443 (2013).

• Molecular origins of internal friction effects on protein-folding rates Nat. Commun. 5 (2014).

• Dependence of Internal Friction on Folding Mechanism J. Am. Chem. Soc. 137 (9) 3283-3290 (2015)

• Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin J. Chem. Theory Comput. 1549-9618 (2015).

At some point it became evident that it would be a good idea to make my own code open, version controlled, tested and well documented.