Here you can find some suggested readings on the topics covered during the course.

Fundamental concepts in protein physics

Folding Graciously. Levinthal C, Proc. Mössebaun Spect. Biol. Sys. (1969).
Studies on Protein Folding, Unfolding and Fluctuations by Computer Simulation. Taketomi H, Ueda Y, and Go N. Int J Pep. Prot. Res. (1974).
Funnels, Pathways, and the Energy Landscape of Protein Folding: A Synthesis. Bryngelson JD et al. Proteins (1995).

Sampling & enhanced sampling methods

Essential Dynamics of Proteins. Amadei A, Linssen ABM, Berendsen HJC. Proteins (1993).
Equilibrium Sampling in Biomolecular Simulations. Zuckerman DM. Annu. Rev. Biophys. (2011).
Simplified and improved string method for computing the minimum energy paths in barrier-crossing events. Weinian E, Eiquing R, Vanden-Ejinden E. Jour Chem Phys (2007).
Ratcheted molecular-dynamics simulations […] protein folding. Tiana G and Camilloni C. Jour. Chem. Phys. (2012).

Quantifying uncertainty and sampling quality in biomolecular simulations. Grossfield A and Zuckerman DM. Annu Rep Comp Chem (2009).
A tutorial on Principal Component Analysis. Shlens J. ArXiv (2014).
Principal Component Analysis: A Method for Determining the Essential Dynamics of Proteins. David CC and Jacobs DJ. Methods Mol Biol (2014).
PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins. Tiberti M et al. Chem. Info and Model. (2014).
PyInteraph2 and PyInKnife2 to Analyze Networks in Protein Structural Ensembles. V Sora, M Tiberti, L Beltrame, D Dogan, S Mahdi Robbani, J Rubin, and E Papaleo. (2023)

Molecular mechanisms of activation in CDK2. Bešker N, Amadei A, D’Abramo M. Jour. Biomol. Struc. Dyn. (2013).
Alanine mutation of […] Pantothenate Synthetase […]. Pandey B et al. Nat. Sci. Rep. (2017).
Effects of Membrane and Biological Target on the […] Properties of Recoverin[…]. Borsatto A, et al, IJMS (2019).