Selected Publications

Small-angle X-ray and neutron scattering (SAXS and SANS) techniques characterize proteins in solution and complement high-resolution structural studies. SCT provides a set of tools for comparing atomistic models of proteins and carbohydrates with experimental data.
Journal of Applied Crystallography, 2015

A detailed analysis of two of the most popular approximate methods for calculating binding free energies from molecular simulations, (MMPBSA and MMGBSA), applied to the 9 FDA-approved HIV-1 protease inhibitors. Our results show that the values obtained from replica simulations of the same protease-drug complex, differing only in initially assigned atom velocities, can vary by as much as 10 kcal/mol, which is greater than the difference between the best and worst binding inhibitors.
Journal of Chemical Theory and Computation, 2014

Recent Publications

More Publications

Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In …

As the application of computational methods in drug discovery pipelines becomes more widespread it is increasingly important to …

The efficacy of drug treatments depends on how tightly small molecules bind to their target proteins. The rapid and accurate …

The accurate identification of the specific points of interaction between G protein-coupled receptor (GPCR) oligomers is essential for …

We describe a general method to use Monte Carlo simulation followed by torsion-angle molecular dynamics simulations to create ensembles …

Recent Talks

Introducing EasyVVUQ, a Python library designed to make it easy to apply a range of VVUQ techniques to your existing simulation …

Recent Posts

Overview of my work using atomic models to interpret SAXS and SANS data.

Molecular dynamics provides quantitative and qualitative insight into this flexible protein.

RT is a major anti-HIV drug target where ligand binding can change the dynamics far from the binding site.

Projects

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CCP-SAS

Verified Exascale Computing for Multiscale Applications.

CompBioMed

European HPC Centre of Excellence focussed on the use and development of computational methods for biomedical applications..

EOSC Hub

The contact point for European researchers and innovators to discover, access, use and reuse a broad spectrum of resources for advanced data-driven research.

INSPIRE

Combining molecular simulation and machine learning to guide precision cancer therapy.

VECMA

Verified Exascale Computing for Multiscale Applications.