Please scroll down for a list of software developed by our Supervisors.
Chain-length dependent growth dynamics of n-alkanes on silica investigated by energy-dispersive x-ray reflectivity in situ and in real-time. Weber, C., et al. 2012. 2012, Journal of Chemical Physics. 10.1063/1.4719530.
FERM domain interaction with myosin negatively regulates FAK in cardiomyocyte hypertrophy. Santos, Aline M., et al. 2012. 2012, Nature Chemical Biology. 10.1038/nchembio.717.
Rapid and accurate prediction and scoring of water molecules in protein binding sites. Ross, Gregory A., Morris, Garrett M. and Biggin, Philip C. 2012. 2012, PLoS ONE. 10.1371/journal.pone.0032036.
Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating. Bavro, Vassiliy N., et al. 2012. 2012, Nature Structural and Molecular Biology. 10.1038/nsmb.2208.
Stochastic detection of Pim protein kinases reveals electrostatically enhanced association of a peptide substrate. Harrington, L., et al. 2013. 47, 2013, Proceedings of the National Academy of Sciences, Vol. 110, pp. E4417-E4426. 10.1073/pnas.1312739110.
Feature selection using genetic algorithms for fetal heart rate analysis. Xu, Liang, et al. 2014. 2014, Physiological Measurement. 10.1088/0967-3334/35/7/1357.
Feshbach resonances, molecular bound states, and prospects of ultracold-molecule formation in mixtures of ultracold K and Cs. Patel, Hannah J., et al. 2014. 2014, Physical Review A - Atomic, Molecular, and Optical Physics. arXiv:1409.1099v1.
Helix kinks are equally prevalent in soluble and membrane proteins. Wilman, Henry R., Shi, Jiye and Deane, Charlotte M. 2014. 2014, Proteins: Structure, Function and Bioinformatics. 10.1002/prot.24550.
Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study. Knapp, Bernhard, Dunbar, James and Deane, Charlotte M. 2014. 2014, PLoS Computational Biology. 10.1371/journal.pcbi.1003748.
Mathematical modelling of turning delays in swarm robotics. Taylor-King, Jake P., et al. 2014. 2014, IMA Journal of Applied Mathematics (Institute of Mathematics and Its Applications). 1401.7612.
Resolving Structural Variability in Network Models and the Brain. Klimm, Florian, et al. 2014. 2014, PLoS Computational Biology. 1306.2893.
SAbDab: The structural antibody database. Dunbar, James, et al. 2014. 2014, Nucleic Acids Research. 10.1093/nar/gkt1043.
A Structure-activity relationships and colorimetric properties of specific probes for the putative cancer biomarker human arylamine N-acetyltransferase 1. Egleton, James E., et al. 2014. 2014, Bioorganic and Medicinal Chemistry. 10.1016/j.bmc.2014.03.015.
The roles of Jumonji-type oxygenases in human disease. Johansson, Catrine, et al. 2014. 2014, Epigenomics. 10.2217/epi.13.79.
Keys to the kingdom. Wong, Sybil C.K., et al. 2015. Nature Biotechnology. 2015. 10.1038/nbt.3159.
Protein-protein interaction networks identify targets which rescue the MPP+ cellular model of Parkinson's disease. Keane, Harriet, et al. 2015. 2015, Scientific Reports. 10.1038/srep17004.
Topological data analysis of contagion maps for examining spreading processes on networks. Taylor, Dane, et al. 2015. 2015, Nature Communications. 1408.1168.
A Multi-Crystal Method for Extracting Obscured Signal from Crystallographic Electron Density. Pearce, Nicholas, et al. 2016. 2016, bioRxiv. http://biorxiv.org/content/early/2016/09/05/073411.full.pdf.
A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Cox, Oakley B., et al. 2016. 2016, Chem. Sci. 10.1039/C5SC03115J.
Accurate calculation of the absolute free energy of binding for drug molecules. Aldeghi, Matteo, et al. 2016. 2016, Chem. Sci. 10.1039/C5SC02678D.
Analysis of JmjC Demethylase-Catalyzed Demethylation Using Geometrically-Constrained Lysine Analogues. Langley, Gareth W., et al. 2016. 2016, ACS Chemical Biology. 10.1021/acschembio.5b00738.
Arginine demethylation is catalysed by a subset of JmjC histone lysine demethylases. Walport, Louise J., et al. 2016. 2016, Nature Communications. 10.1038/ncomms11974.
Examining the Conservation of Kinks in Alpha Helices. Law, Eleanor C., et al. 2016. 2016, PLoS ONE. 10.1371/journal.pone.0157553.
Isoxazole-Derived Amino Acids are Bromodomain-Binding Acetyl-Lysine Mimics: Incorporation into Histone H4 Peptides and Histone H3. Sekirnik (née Measures), Angelina R., et al. 2016. 2016, Angewandte Chemie - International Edition. 10.1002/anie.201602908.
Modeling longitudinal preclinical tumor size data to identify transient dynamics in tumor response to Antiangiogenic Drugs. Hutchinson, L. G., et al. 2016. 2016, CPT: Pharmacometrics and Systems Pharmacology. 10.1002/psp4.12142.
SAbPred: a structure-based antibody prediction server. Dunbar, James, et al. 2016. 2016, Nucleic acids research. 10.1093/nar/gkw361.
Simultaneous in vivo assessment of cardiac and hepatic metabolism in the diabetic rat using hyperpolarized MRS. Le Page, Lydia M., et al. 2016. 2016, NMR in Biomedicine. 10.1002/nbm.3656.
Structural analysis of human KDM5B guides histone demethylase inhibitor development. Johansson, Catrine, et al. 2016. 2016, Nature Chemical Biology. 10.1038/nchembio.2087.
A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Pearce, Nicholas M., et al. 2017. 2017, Nature Communications. 10.1038/ncomms15123.
Adenosine Monophosphate Binding Stabilizes the KTN Domain of the Shewanella denitrificans Kef Potassium Efflux System. Pliotas, Christos, et al. 2017. 2017, Biochemistry. 10.1021/acs.biochem.7b00300.
Association between a common immunoglobulin heavy chain allele and rheumatic heart disease risk in Oceania. Parks, Tom, et al. 2017. 2017, Nature Communications. 10.1038/ncomms14946.
Derisking the Cu-Mediated <sup>18</sup> F-Fluorination of Heterocyclic Positron Emission Tomography Radioligands. Taylor, Nicholas J., et al. 2017. 2017, Journal of the American Chemical Society. 10.1021/jacs.7b03131.
Discovery of a Selective Allosteric Inhibitor Targeting Macrodomain 2 of Polyadenosine-Diphosphate-Ribose Polymerase 14. Schuller, Marion, et al. 2017. 2017, ACS Chemical Biology. 10.1021/acschembio.7b00445.
Gentle, fast and effective crystal soaking by acoustic dispensing. Collins, Patrick M., et al. 2017. 2017, Acta Crystallographica Section D: Structural Biology. 10.1107/S205979831700331X.
Integrating models to quantify environment mediated drug resistance. Picco, Noemi, et al. 2017. 2017, Cancer Research. 10.1158/0008-5472.CAN-17-0835.
KDM3A coordinates actin dynamics with intraflagellar transport to regulate cilia stability. Yeyati, Patricia L., et al. 2017. 2017, Journal of Cell Biology. 10.1083/jcb.201607032.
Metabotypes of breast cancer cell lines revealed by non-targeted metabolomics. Dubuis, Sébastien, et al. 2017. 2017, Metabolic Engineering, Vol. 43, pp. 173-186. 10. 10.1016/j.ymben.2016.12.009.
Microvessel Chaste: An Open Library for Spatial Modeling of Vascularized Tissues. Grogan, James A., et al. 2017. 2017, Biophysical Journal. 10.1016/j.bpj.2017.03.036.
Ocular Pharmacokinetics of Therapeutic Antibodies Given by Intravitreal Injection: Estimation of Retinal Permeabilities Using a 3-Compartment Semi-Mechanistic Model. Hutton-Smith, Laurence A., et al. 2017. 2017, Molecular Pharmaceutics. 10.1021/acs.molpharmaceut.7b00164
Persistent homology of time-dependent functional networks constructed from coupled time series. Stolz, Bernadette J., Harrington, Heather A. and Porter, Mason A. 2017. 2017, Chaos. 1605.00562.
Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes. Duncan, Anna L., et al. 2017. 2017, Scientific Reports. 10.1038/s41598-017-16865-6
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction. de Oliveira, Saulo H P, et al. 2017. 2017, Bioinformatics. 10.1093/bioinformatics/btx722.
Sphinx: Merging knowledge-based and ab initio approaches to improve protein loop prediction. Marks, Claire, et al. 2017. 2017, Bioinformatics. 10.1093/bioinformatics/btw823.
Split dosing of artemisinins does not improve antimalarial therapeutic efficacy. White, N. J., Watson, J. and Ashley, E. A. 2017. 2017, Scientific Reports. 10.1038/s41598-017-12483-4.
Tailoring mathematical models to stem-cell derived cardiomyocyte lines can improve predictions of drug-induced changes to their electrophysiology. Lei, Chon Lok, et al. 2017. 2017, Frontiers in Physiology. 10.3389/fphys.2017.00986.
The RCSB protein data bank: Integrative view of protein, gene and 3D structural information. Rose, Peter W., et al. 2017. 2017, Nucleic Acids Research. 10.1093/nar/gkw1000.
GPCRs: What can we learn from molecular dynamics simulations? Velgy, Naushad, Hedger, George and Biggin, Philip C. 2018. Methods in Molecular Biology. 2018. 10.1007/978-1-4939-7465-8_6
Selectively Targeting the Kinome-Conserved Lysine of PI3Kδ as a General Approach to Covalent Kinase Inhibition. Dalton, Samuel E., et al. 2018. 2018, Journal of the American Chemical Society. 10.1021/jacs.7b08979.