Photo of Prof Dan Rigden

Prof Dan Rigden BA, PhD

Professor of Protein Bioinformatics Biochemistry

    Research

    AMPLE: Molecular Replacement using unconventional protein models

    Ensembles search models of different sizes (magenta) solve protein crystal structures (cartoon)
    Ensembles search models of different sizes (magenta) solve protein crystal structures (cartoon)

    Our program AMPLE clusters and truncates sets of protein models to efficiently solve crystal structures by Molecular Replacement. Initially, it was designed to process cheaply obtained ab initio models from ROSETTA. More recently we have found it to work exceptionally well with NMR ensemble inputs, and for solving the structures of coiled-coil proteins. Having secured 5-year funding from BBSRC as part of the CCP4 grant renewal, we are currently exploring several new lines of research including application to membrane proteins.

    Protein structure modelling

    A model of a DUF2086 protein
    A model of a DUF2086 protein

    I have a broad interest in prediction of protein structures and complexes, whether by conventional homology modelling, ab initio methods or the recently arrived contract-driven algorithms. This feeds directly into AMPLE (above), often helps predict function (below) but has many other applications including interpreting the consequences of single nucleotide polymorphisms.

    Protein function prediction

    Convergently evolved calcium-binding motifs
    Convergently evolved calcium-binding motifs

    I am interested in using diverse bioinformatics methods to shed light on function of unannotated sequences - 'hypothetical proteins', Domains of Unknown Function' and the like. This often starts by detecting distant evolutionary relationships with sensitive database searches, but often requires input from, for example, gene context, domain architectures, and structural bioinformatics.

    Research Grants

    Studentship Agreement between University of Liverpool and Diamond Light Source Ltd

    DIAMOND LIGHT SOURCE LTD (UK)

    October 2018 - September 2022

    Facilitating access to advanced Molecular Replacement pipelines via CCP4i2, CCP4 online and CCP4cloud

    SCIENCE AND TECHNOLOGY FACILITIES COUNCIL (STFC)

    July 2017 - June 2019

    Identification of novel double-stranded RNA elements in developing antibiotic resistance in the agricultural environment

    NATURAL ENVIRONMENT RESEARCH COUNCIL (NERC)

    April 2016 - March 2018

    Identification and evaluation of algal sulphatransferases for enzymatic polysaccharide modifications

    BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL (BBSRC)

    July 2017 - December 2017

    Wellcome Trust Vacationship Miss Kiani A Jeacock

    WELLCOME TRUST (UK)

    June 2015 - August 2015

    A Simkin Studentship

    SOCIETE CIVILE SYNCHROTRON SOLEIL (FRANCE)

    October 2015 - September 2019

    Molecular function in post-genome biology (MOLFUN).

    EUROPEAN COMMISSION

    October 2006 - September 2010

    The genotypic and phenotypic impacts of Shiga toxin encoding bacteriophage interactions with their host cells: consequences for food borne zoonoses

    BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL (BBSRC)

    August 2011 - November 2014

    Dealkylation of plant sterols during utilization in invertebrates

    LEVERHULME TRUST (UK)

    May 2007 - May 2009

    Tools for motif recognition in fungi

    BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL (BBSRC)

    April 2009 - July 2010

    CCP4 Grant Renewal 2014-2019: Question-driven crystallographic data collection and advanced structure solution

    BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL (BBSRC)

    June 2015 - June 2019

    Ab initio modelling for X-ray crystal structure solution

    BIOTECHNOLOGY & BIOLOGICAL SCIENCE RESEARCH COUNCIL (BBSRC)

    August 2010 - July 2012

    The structure-function relationship of anti-microbial peptides approached by ab initio protein modelling.

    BRITISH SOCIETY FOR ANTIMICROBIAL CHEMOTHERAPY (UK)

    June 2014 - August 2014

    Development of lead compounds for trypanocidal drugs based on inhibitors targeted against parasite glycolysis (TRYGLYCHEMO).

    EUROPEAN COMMISSION

    November 2003 - October 2004

    Exploring covariance-based models for protein crystal structure solution with AMPLE.

    SCIENCE AND TECHNOLOGY FACILITIES COUNCIL (STFC)

    October 2014 - September 2018

    The titin myofilament as emerging factor in cardiomyopathy

    BRITISH HEART FOUNDATION (UK)

    September 2013 - September 2016

    Research Collaborations

    Prof. Michael Clague

    Internal

    Dr Michael Ginger

    External: The University of Lancaster

    Dr Martyn Winn

    External: STFC

    Research collaboration

    Prof Paul Michels

    External: Université catholique de Louvain

    Dr Heather Allison

    Internal

    Dr Michael Galperin

    External: National Center for Biotechnology Information

    Dr Mark Caddick

    Internal

    Prof Dave Fernig

    Internal