My ex-InhibOx colleagues (Simone Fulle, Garrett Morris, Paul Finn) and myself have recently published a topical review on “The emerging role of cloud computing in molecular modelling” in the Journal of Molecular Graphics and Modelling.   This paper starts with a gentle and in-depth introduction to the field of cloud computing.  The second part of the paper is how it applies to molecular modelling (and the sort of tasks we can run in the cloud).  The third and last part presents two practical case studies of cloud computations, one of which describes how we built a virtual library to use in virtual screening on AWS.

We hope that after reading this article the cloud will become a less nebulous affair! *pun intended*

As an addendum, I recently came across this paper “Teaching cloud computing: A software engineering perspective” (2013) on how to teach cloud computing at a graduate level.  This work is relevant, because lots of universities are presently including cloud computing in their curricula.

In this study we selected point mutations resulting in Pim-1 variants that are expressed in cancer tissues and reported in SNP databases, such as FastSNP and COSMIC. These Pim-1 variants have been comprehensively characterized to investigate the effect of single amino acid substitution on Pim-1 thermal and thermodynamic stability and structure in solution. Our results indicate that the effects of the mutation observed in cancer tissues cause local changes of tertiary structure, but do not affect binding to type I kinase inhibitors.

This work has been pioneered by researches at the Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome and served as an inspiration for one of my thesis chapters.

Congratulations to all involved in the Memoir publication in Nucleic Acids Research! 

Memoir is a web server which builds homology models for membrane proteins.  It is a web-enabled workflow combining some of OPIG’s software; MP-T, IMembrane, Medeller & Fread.  The inputs are a sequence of the membrane protein you wish to model (target) and a PDB file to use as template.

Memoir may be found here and there is also a video tutorial narrated by Jamie.  There is even a funny blooper of him practising, which I kept to celebrate this moment.

Happy modelling!