Members

Francesco Luigi Gervasio

Group Leader, PhD


Prof. Francesco Luigi Gervasio is the Professor of Chemistry, Professor of Structural and Molecular Biology, Chair of Biomolecular Modelling and the Graduate Tutor, University College London. His multidisciplinary research spans computational chemistry, computational biophysics, structural biology, bioinformatics and drug discovery and focusses on the development of computational methods to study conformational changes and molecular recognition in biomolecules. While he was at ETH Zurich (2002-2009), he crucially contributed to the development of 3 widely used methods for overcoming the timescale problem of classical and first-principles molecular dynamics simulations and compute free energy surfaces: metadynamics, parallel-tempering metadynamics and the path-like collective variables method. These “enhanced-sampling” algorithms can efficiently sample complex events in biomolecules computing the associated free energy surfaces. He contributed to establishing and developing the widely used PLUMED plug-in for free energy calculations (www.plumed.org).

As the leader of the Computational Biophysics group at the Spanish National Cancer Research Centre (2009-2013) and more recently as a professor at UCL, he continued the development of computational methods, including a combined path sampling/metadynamics method (TS-PPTIS) to compute binding and folding kinetics. He also combined the simulations with experiments (NMR) to better understand the mode of action of cancer-causing mutations and allosteric drugs. A highlight, published in 2 back-to-back paper in Cancer Cell, was the prediction of a previously unknown cryptic binding pocket on an extracellular domain of fibroblast growth factor receptor (FGFR) by enhanced-sampling molecular simulations. Other highlights were the development of the first computational approach combining evolutionary principles with a physics-based coarse-grained model to predict protein structure and dynamics and the discovery of a novel and unexpected molecular activity for glutamine synthetase (published in Nature).

 

Current Positions

  • Since 02/2013 Professor (full professor), Chemistry Department, University College London (UCL), UK
  • Since 02/2013 Professor (full professor), Research Department of Molecular and Structural Biology, UCL, UK
  • Since 2016 Graduate Tutor, Chemistry Department, UCL, UK
  • Since 2017 Chief Editor, Frontiers in Biomolecular Modeling and Simulations

Previous Positions

  • 2/2009-6/2013 Group leader, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
  • 2/2006-2/2009 Assistant Professor (Ober-assistant), Chemistry and Appl. Biosciences, ETH Zurich, CH
  • 2/2004-2/2006 Post-doctoral Research Assistant, Chemistry and Applied Biosciences, ETH Zurich, CH
  • 2/2002-2/2004 Junior Scientist, Swiss National Supercomputing Center (CSCS), Manno, Switzerland

Institutional Responsibilities

  • 2016-present Member of the Extended Management Workgroup – Chemistry Department UCL, UK
  • 2016-present UCL representative of the JC Maxwell CECAM Node
  • 2016-present Consultant for UCB pharma and EVOTEC, UK
  • 2011-2013 Member of the Scientific Committee – CNIO, Spain
  • 2010-2012 Visiting Associate Professor – University of Cagliari, Italy
  • 2000-2001 Visiting Scientist – International School for Advanced Studies, Trieste, Italy

Other Appointments and Management of Research Networks

  • Member of the Management Committee (UCL representative), JC Maxwell CECAM node
  • Member of the Management Committee, Collaborative Computational Project for Biomolecular Simulation (CCPBioSim), UK

Education

  • 20/12/2001 PhD in Chemistry, Università degli studi di Firenze, Italy
  • 18/03/1997 Master in Chemistry, Università degli studi di Firenze, Italy

Antonija Kuzmanic

Postdoc


Antonija splits her time between trying to understand what makes kinases active and cryptic pockets hidden using molecular dynamics simulations and enhanced sampling. She got her master’s degree in molecular biology at the University of Zagreb in a wet lab. She thought better of it and then switched to computational biophysics for her PhD at the University of Vienna with Prof. Bojan Zagrovic during which she explored the effects of dynamics on crystallographic observables. For her first postdoc, she joined Prof. Modesto Orozco’s group at IRB Barcelona where she studied DNA crystals and started her kinase saga. She joined UCL in November 2017 for what she hopes is her last postdoc.

 

Contact information
a.kuzmanic@ucl.ac.uk
LinkedIn
Researchgate

 

Carolina Estarellas

Postdoc


Carol’s current projects involve i) the comprehension of action mechanism of Aurora Kinase-A, mainly focus on the study of inhibition process by means of enhanced sampling techniques, and ii) the application of machine learning potentials to small biological systems by means of hybrid methods QM/MM. Her research lines have been centred in i) the study of non-covalent interactions in supramolecular systems, ii) the study of reaction mechanisms, both via quantum mechanics methods, and iii) the study of the conformational behaviour of protein-ligand complexes for rational drug design by means of molecular dynamics simulations.

 

Contact information
c.estarellas@ucl.ac.uk

Silvia Gutierrez

Postdoc


Silvia studies druggable allosteric sites in central nervous systems within the EU H2020 Human Brain Project CDP6 combining atomistic-simulations and state of the art enhanced sampling techniques. She got her master’s degree in Theoretical and Computational Physics at the University La Laguna. She then jumped from small water clusters and fullerenes to Biomolecular systems for her PhD in Physics as part of Maria Skłodowska Curie Initial Training Network: Translocation at Cagliari University with Prof. Matteo Ceccarelli. Within the translocation consortia, she studied small molecule’s permeability through the outer membrane of Gram-negative bacteria and developed permeability prediction tools. She joined UCL in fall 2018 for her first postdoc.

 

Contact information
silviaa.gutierrez@gmail.com
LinkedIn
Researchgate
sacosta-gutierrez.weebly.com

Giulio Mattedi

PhD student


Giulio joined the group as a PhD student in January 2017 and his research involves deciphering ligand binding selectivity in G protein-coupled receptors (GPCRs) using molecular dynamics and metadynamics. He is developing a new implementation of transition state-partial path transition interface sampling (TS-PPTIS) for predicting kinetic rate constants in systems of pharmaceutical interest, most notably ligand binding kinetics. His interests also include studying the activation of GPCRs and their interaction with G-proteins. As part of his MSci in Pharmaceutical Chemistry and Technology at the University of Padova, he carried out his final project research at King’s College London.

 

Contact information
giulio.mattedi.16@ucl.ac.uk
LinkedIn

Havva Yalinca

PhD student


Havva is a final year PhD student in the London Interdisciplinary Doctoral (LIDo) programme. After her undergraduate degree in Biochemistry at UCL with a focus on protein NMR spectroscopy and a brief biotech escapade in Cambridge at Iontas Ltd, she settled back in London for a PhD combining experimental structural biology with molecular dynamics simulations of intrinsically disordered peptides. She is mainly working on the link between post-translational modifications of the N-terminal tail of huntingtin and its secondary structure. When she is not busy debugging her python scripts, she enjoys learning Greek and baking all things sourdough.

 

Contact information
havva.yalinca.10@ucl.ac.uk
LinkedIn

Ladislav Hovan

PhD student


Ladislav is a theoretical chemist by training, who now likes to apply his coding skills to biophysical problems. He joined the lab in 2015 after finishing his degree in natural sciences at the University of Cambridge. His main research project involves looking at the effects of a point mutation in the PQBP1 protein, which causes the Golabi-Ito-Hall syndrome. He has spent two years in Singapore at the Mechanobiology Institute on an ARAP programme, where he also learned some wet lab skills including how to use magnetic tweezers to manipulate single proteins. Other research topics include improvements to the path collective variables and a study of interactions between talin and integrin. Most recently, he has been trying to learn Chinese and hopes to finish his PhD soon.

 

Contact information
ladislav.hovan.15@ucl.ac.uk

Rhys Evans

PhD student


Rhys is a physicist by trade but has decided to apply his skills to the study of the self-assembly of small peptides. Early in his life, Rhys was diagnosed with a strong preference for interdisciplinary science, something which even many years of structured education were unable to cure. He graduated from a Masters degree in Natural Sciences from UCL in 2017, during which he specialised in Particle Physics and Physical Chemistry. Now, Rhys works closely with other members of the UCL Chemistry Department to improve and refine a drug-delivery system using self-assembled polypeptide vesicles, mimicking the properties and action of viruses. As the youngest PhD of the group, Rhys still has many years of study ahead of him, which may just give him chance to learn all the acronyms he will need to know in his new life as a biophysicist.

 

Contact information
rhys.evans.13@ucl.ac.uk

Yiannis Galdadas

PhD student


After a traineeship on MD simulations and computer-aided drug design at the BRFAA in Athens and on biochemical analysis techniques at a general hospital, Yiannis joined the lab hoping that he will manage to shed some light on the molecular mechanisms underlying clinically-identified activating mutations on EGFR and the resulting effect of these mutations on the sensitivity of the receptor against FDA approved tyrosine kinase inhibitors.

 

Contact information
ioannis.galdadas.16@ucl.ac.uk
LinkedIn