TYC@UCL Lunchtime Get-Together: When all your system needs is a push..

Antonija Kuzmanic, UCL

Friday 23rd March 2018
Time: 1-2pm
Venue: Nyholm Room, Christopher Ingold Building, UCL Chemistry
Contact: Karen Stoneham
Tel: 0207 6797306

Despite the progress in computer architectures, specialised hardware for molecular dynamics (MD) simulations, and the parallelization of MD codes, the typical timescales that atomistic MD simulations can access are mostly shorter than those of interest.  This has stimulated the development of many enhanced sampling methods which can broadly be categorised by according to their dependence on collective variables (CVs).  I will review some of the approaches using the successful application in explaining complex biophysical phenomena, such as mechanisms of protein (de)activation 1, 2, 3 and cryptic binding pocket formation 4.

1Sutto L, Gervasio FL (2013).  Effects of oncogenic mutations on the conformational free-energy landscap of EGFR kinase.  PNAS 110, 10616-21.

2Kuzmanic A, Sutto L, Saladino G, Nebreda A, Gervasio FL, Orozco M (2017).  Changes in the free-energy landscape of p38a MAP kinase through its canical activation and binding events as studied by enhanced molecular dynamics simulations. eLife 6, e22175

3Cavalli A, Spitaleri A, Saladino G, Gervasio FL (2015).  Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms.  Acc Chem Res 48 (2), 277-85

4Oleinikovas V, Saladino G, Cossins BP, Gervasio FL (2016).  Understanding crytic pocket formation in protein targets enhanced sampling simulations.  J Am Chem Soc 138 (43), 14257-63

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    Antonija Kuzmanic

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