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Irene’s work has been featured on The Times!
Irene’s work has been featured on The Times!
We are very happy that Irene's work on simulating self-assembly of an antimicrobial nanocapsule has been featured on The Times. Read the story on the...
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Symposium on Networks and Machine Learning @ The Crick
Symposium on Networks and Machine Learning @ The Crick
The Systems and Network Medicine Forum is hosting a Symposium on Network Analysis and Machine Learning Applications in Biology, on Monday 3rd February, 09:00am-13:00pm in...
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New paper on eLife
New paper on eLife
Our lab has just published a new paper on eLife, investigating the allosteric effects of multiple ligands on the PKM2 enzyme - superb experimental and...
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HTCC4 Structural Biology Workshop
HTCC4 Structural Biology Workshop
Franca will be organising a section on Biomolecular simulations at the upcoming Hot Topics in Contemporary Crystallography (HTCC4) workshop at Dubrovnik, Croatia in the coming...
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Rasha’s project featured on MND materials
Rasha’s project featured on MND materials
Our post-doc Rasha's work on analysing protein-protein interaction networks in the context of the gene C9orf72 affected in Amyotrophic lateral sclerosis (ALS) is featured on promotional materials...
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Franca appointed Head of Randall Centre
Congratulations to Franca appointed to be the new Head of the Randall Centre of Cell and Molecular Biophysics [link to announcement], under the new School...
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About

Research at the Fraternali group aims to identify molecular determinants in the functioning or mis-functioning of protein structures and protein-protein interactions.  The wider objective is to understand, at a molecular level, the nature of the interactions occurring in the cell. We use bioinformatics methods to analyse available data on protein structures and protein interactions, and molecular simulations and/or computational biology methods to characterize and determine their stability.

Read more about our research at the Research tab.

 

People

 

Current members:

Franca Fraternali

Group Leader

Franca Fraternali, Group Leader / Head and Professor of Bioinformatics and Computational Biology, Randall Centre, King’s College London

Tel (direct): +44 (0) 207 848 6843
Fax: +44 (0) 207 8486 435
Email: franca [dot] fraternali@kcl.ac.uk

Biography

  • Head, Randall Centre of Cell and Molecular Biophysics, King’s College London
  • Professor of Bioinformatics and Computational Biology, Randall Centre, King’s College London
  • Staff Scientist, National Institute for Medical Research of London
  • Research Associate, EMBL Heidelberg
  • Post Doctoral Research Fellow, University of Strasbourg
  • EMBO Fellowship, ETHZ, Zurich
  • PhD in Physical Chemistry, University of Naples

Research Interests : Structural Bioinformatics of Proteins and Nucleic acids; Protein Structure Prediction; Molecular Dynamics of folded and misfolded proteins; Systems Biology; Statistical Analysis of Protein Interaction Networks.

 

The research of the group aims at identifying the molecular determinants in the functioning or misfunctioning of protein structures and protein-protein interactions. The wider objective is to understand, at a molecular level, the nature of the interactions occurring in the cell.

I am particularly interested in the study of the physical nature of the interactions between protein-protein, protein-solvent, protein-lipid and protein-nucleic acid. We develop methods in Bioinformatics and Computational Biology to analyse the available data on such interactions and molecular simulations and to characterize and determine their stability. Once these key molecular signatures have been identified, one can propose ‘rescue’ mutants to restore the protein function, one can design proteins with enhanced binding; one can design inhibitors to disrupt the binding.

Joseph Ng

Post-doc

Joseph (Chi-Fung) Ng, Post-doctoral Research Associate
Email: chi_fung_joseph [dot] ng@kcl.ac.uk

Joseph was born and raised in Hong Kong, and graduated with first class honours the degree of Bachelor of Biomedical Sciences at the University of Hong Kong (HKU). He did his PhD in the Fraternali lab, supported by the Croucher Foundation from Hong Kong, on mutators (proteins which generate mutations) and cancers, specifically focusing on the mechanism of the APOBEC3 family of proteins. He is broadly interested in cataloguing signatures of biological sequences, structures and networks, and use these to formularise the “molecular grammar”. His work at the lab centres around annotation of mutational impact, mapping pathway and functional information on biological networks, and analysis of transcriptomics and proteomics data. He is currently a post-doc, working on the MACSMAF (Mapping antibody class switch mechanisms and function) project supported by a BBSRC sLoLa grant.

Outside science, Joseph is also interested in ethical and policy questions surrounding medicine. He is particularly fascinated by directed-to-consumer genomic testing.

Link to Joseph’s page on Croucher was at the top of this window. Read also his featured article on Croucher.

Representative Publications

Ng JCF, Quist J, Grigoriadis A, Malim MH & Fraternali F. (2019) “Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases.” Nucleic Acids Res. 47(3):1178-1194. doi: 10.1093/nar/gky1316.

Cheng CWH, Chung MWH & *Ng JCF. (2016) “Structural dynamics of Alzheimer’s amyloid-? aggregation: computational and experimental approaches.” Journal of Young Investigators. doi: 10.22186/jyi.31.6.44-50.  (Equal contribution from all authors)

Chung MWH & *Ng JCF. (2016) “Personal utility is inherent to direct-to-consumer genomic testing.” Journal of Medical Ethics, 42:649-652. doi:10.1136/medethics-2015-103057. (Equal contribution from all authors)

Irene Marzuoli

Post-doc

Irene Marzuoli, PhD Student / CANES Student
Email: irene [dot] marzuoli@kcl.ac.uk

Irene pursued a Master in Theoretical Physics at the University of Padova, focussing on statistical mechanics and its applications to soft matter systems. She then joined the EPSRC funded CANES master programme at King’s College of London, to gain a more interdisciplinary approach to research, developing an interest for biological problems.

Irene now works on Molecular Dynamics simulations of self-assembling antimicrobial peptides, applying her physical and mathematical expertise in the field of biophysics (CANES project P44, co-supervised by Dr. Chris Lorenz). She focuses on the interaction between protein, tackling their assembly process with multiscale simulations techniques, and on the interaction with lipids, contributing to their parameterisation in the GROMOS force field context.

Have a look at a coarse grain simulation of an antimicrobial capsule on a model bacterial membrane and an atomistic simulation of the capsule in solution. Combining the MD results with a bioinformatics approach, the project aims at investigating new sequences and designing new functional antimicrobial molecules. In this aim, Irene is partnered by the National Physics Laboratories, which biotechnology section provides experimental support, and co-funds the project.

Marius Kausas

PhD Student

Marius Kausas, King’s/Crick PhD Student
Email: marius [dot] kausas@kcl.ac.uk

Marius completed his MSc in Biochemistry with Industrial Placement in Computational Chemistry (First Class) at University of Aberdeen in 2016. Following, he began his PhD in a collaboration between Prof Franca Fraternali (King’s College London) and Dr Katrin Rittinger (The Francis Crick Institute). His research interests are focused on investigating multidomain protein dynamics using combination of experimental and computational methods. The aim of the PhD project is to characterize intrinsic dynamic phenomena of the Ring-Between-Ring (RBR) E3 ligase ubiquitin transfer mechanism using enhanced sampling molecular dynamics and solution-based biophysical characterization.

Timir Weston

Timir Weston

PhD Student

Timir Weston, NIHR BRC PhD Student

Email: timir [dot] weston [at] kcl [dot] ac [dot] uk

Timir studied for a BA in Biological Sciences at Somerville College, University of Oxford. From there, he graduated from Imperial College London with an MSc in Applied Biosciences and Biotechnology before attending King’s College London as part of the NIHR BRC Doctoral Training Programme, being awarded an MRes in Biomedical and Translational Science, and joining Prof Franca Fraternali’s lab as a PhD Student. His current work involves the study of the giant sarcomeric protein obscurin and elucidation of its relationship to cardiomyopathies using computational and dynamical methods, and trying to develop predictive tools that can be used to identify and characterise novel variants, with the aim of expanding this work to other giant proteins such as titin.

Affiliated members:

Enrico Spiga

Affiliated member

Enrico Spiga, Research Associate / Post Doc
Google Scholar: https://scholar.google.co.uk/citations?user=RWNukWoAAAAJ&hl=en

Email: enrico [dot] spiga@crick.ac.uk

Biography

  • 2014 – now Research Associate / PostDoc in the lab of Dr. William R. Taylor (The Francis Crick Institute)
  • 2008 – 2013 PhD studies in Bioengineering and Biotechnology, Swiss Federal Institute of Technology in Lausanne (EPFL), Lausanne, Switzerland; Research developed under the supervision of Prof. Matteo Dal Peraro
  • 2004 – 2008 MSc in Physics (Major in Theoretical Condensed Matter), University of Cagliari, Italy; Thesis written under the supervision of Prof Matteo Ceccarelli
  • 2000 – 2004 BSc in General Physics, University of Cagliari, Italy; Thesis written under the supervision of Prof Matteo Ceccarelli and Prof Paolo Ruggerone

Research interests

  • Development and application of coarse-grained models for molecular dynamics simulations of biomolecules
  • Rationalising the binding of homeodomain transcription factors to DNA by using molecular modelling tools
  • Probing the elastic properties of Structural Maintenance Complexes by using atomistic molecular dynamics simulations
  • Development of non-standard analysis of molecular dynamics simulations

Other Interest

  • Swimming
  • Smiling

 

Francesca Collu

Affiliated member

Francesca Collu
Researchgate: https://www.researchgate.net/profile/Francesca_Collu/publications
Email: Francesca [dot] collu@gmail.com

Biography

  • 2017 – now Imaging Clinical Operation Coordinator at Bioclinica
  • 2013 – 2016 Research Associate / PostDoc in Computational Chemistry in the lab of Prof. Franca Fraternali
  • 2012 – 2013 Research Associate / PostDoc in Computational Chemistry in the lab of Prof. Michele Cascella
  • 2008 – 2012 PhD studies in Chemistry, University of Bern, Switzerland; Research developed under the supervision of Prof. Michele Cascella
  • 2004 – 2008 MSc in Physics (Major in Theoretical Condensed Matter), University of Cagliari, Italy; Thesis written under the supervision of Prof Paolo Ruggerone
  • 2000 – 2004 BSc in General Physics, University of Cagliari, Italy; Thesis written under the supervision of Prof Matteo Ceccarelli and Prof Paolo Ruggerone

Research interests

Alumni:
  • Flavia Autore
  • Rasha Boulos
  • Sun Sook Chung
  • Carlos Cruz
  • Anna Laddach
  • Grace Lu
  • Jamie Macpherson
  • Christian Margreitter

Software and Web-tools

 

Biomembrane simulations

Lipid parameters for Molecular Dynamics simulations of biomembrane have been updated to the most recent version of the GROMOS 54a8 force field to improve solvation properties in the head region. The resulting parameters and topology files can be found here.
UNIPPIN

UNIPPIN is an integrated protein-protein interaction network the group has been collecting and curating for our analyses on protein-protein interactions. Find out more here.
BRepertoire

BRepertoire a suite of user-friendly web-based software tools for large-scale statistical analyses of antibody repertoire data. It works on data preprocessed by IMGT, and performs statistical and comparative analyses on-the-fly with versatile plotting options.
Cite: Margreitter C, Lu HC, Townsend C, Stewart A, Dunn-Walters DK, Fraternali FBRepertoire: a user-friendly web server for analysing antibody repertoire data, Nucleic Acids Research, gky276, https://doi.org/10.1093/nar/gky276
TITINdb

TITINdb is a web application which integrates titin structure, sequence, isoform, variant and disease information. Disease-associated nonsynonymous SNPs (nsSNPs) from the literature and population nsSNPs from the 1000 genomes project and ExAC database to be visualised on structure. Additionally the impact of these nsSNPs has been predicted computationally using both structure and sequence based methods.
Cite: Laddach A, Gautel M, Fraternali FTITINdb – a Computational Tool to Assess Titin’s Role as a Disease Gene.Bioinformatics 2017 btx424. doi: 10.1093/bioinformatics/btx424 [PMID: 29077808]
PinSnps

PinSnps is an interactive tool for the analysis of common variants, disease-related single-nucleotide polymorphisms (SNPs), Post-Translational Modifications (PTMs) and related functional sites mapped onto human protein interaction networks. One can search for and retrieve information about SNPs data and interacting proteins of the query.
Cite:
Lu, HC, Herrera Braga, J, Fraternali, F – PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks. Bioinformatics 32(16):2534-6, 2016. [PMID: 27153707]
POPSCOMP
POPSCOMP is a method to analyse interactions between individual complex components of proteins and/or nucleic acids by calculating the solvent accessible surface area (SASA) buried upon complex formation. It is based on POPS*, which calculates SASAs of individual proteins and nucleic acid molecules at atomic (default) and residue (coarse-grained) level.
The underlying heuristic algorithm of POPS* uses a geometric approximation to the shielding of atomic surface areas by nearest neighbour atoms.

Cite:Kleinjung, J, Fraternali, FPOPSCOMP: An automated interaction analysis of biomolecular complexes. Nuc. Acids Res. 33:W342-W346, 2005 [PMID:15980485]Cavallo, L, Kleinjung, J, Fraternali, FPOPS: a fast algorithm for Solvent Accessible Surface Areas at atomic and residue level. Nuc. Acids Res. 31:3364-3366, 2003 [PMID:12824328]