AtlasCBS: Atlas of Chemico-Biological Space

Cele Abad_Zapatero
AtlasCBS. Real screen of the AtlasCBS on the line web application based at the EBI site in the UK. The application is now available as a module within the software StarDrop(TM) from Optibrium Ltd, UK (www.Optibrium.com).
Cover. Click for entire text of the book. Update on the concept of Ligand Efficiency Indices (LEIs)

Recently, I just published an invited review with the title Ligand Efficiency Indices for Effective Drug Discovery: a unifying vector formulation. The ideas presented have been developing since 2007 and growing from the early definitions of SEI, BEI, to a unifying vector formulation where SEI, BEI are the x and y components (respectively), of a Ligand Efficiency vector named vLEI (bold denotes vector). Details can be found in the recently published paper that can be found in the 'Efficiency based drug design' and 'News and Views' tabs. A direct link to the publication can be found here also (below).

Cover. Click for entire text of the book.

A chapter in a book entitled 'Software and Techniques for Bio-Molecular Modeling' edited by Dr. Azat Mukhametov and published by the Austin Publishing Group. This book is an interesting new addition to the references of techniques, concepts and software in molecular modeling for drug discovery. Chapter 2 describes the lates developments on the AtlasCBS concept, in particular the use of KNIME workflows to produce atlas-like plots and planes using simple KNIME modules.

The entire text of the book, courtesy of the Austin Publishing Group can be found HERE or by clicking the cover image. (PDF 10mb)

AtlasCBS is a novel concept to guide the drug discovery process. The idea and the mathematical background were published in 2010 (Link).

The algebraic framework is based on two complementary ligand efficiency indices (LEIs): BEI-like based on affinity per size, and SEI-like based on polarity. These two variables are plotted in a Cartesian plane
SEI-like, x;
BEI-like, y;

This simple change in variables permits to examine at a glance the combination of three variables, namely, affinity, size and polarity and assess the efficiency of the compounds towards their target. Examples and further details are given in a recently published paper:

Cortes-Cabrera, A., Morreale, A., Gago, F. and C. Abad-Zapatero. AtlasCBS: a web server to map and explore chemico-biological space. J. Comp. Aided Mol. Design. 2012. DOI 10.1007/s10822-012-9587-5.

Recently published book: See Flyer 'Ligand Efficiency Indices for Drug Discovery: Towards and Atlas-Guided Paradigm'

The application is at:
AtlasCBS EBI user site:

The AtlasCBS framework has now been incorporated into the software package StarDrop™ (www.Optibrium.com).
An upcoming article in Future Medicinal Chemistry will discuss the inclusion of the AtlasCBS framework and the Ligand Efficiency Variables (LEIs) within the context of ‘alternative variables in drug discovery’. It is my belief that the best way proceed is within the framework of Multiple Parameter Optimization (MPO). The article is entitled ‘Alternative variables in drug discovery: promises and challenges’. The co-authors are Edmund Champness and Matthew Segall of Optibrium, Ltd.

Abad-Zapatero C, Champness EJ & Segall M. Alternative variables in drug discovery: promises and challenges. Future Med. Chem. 6(5), 577-593.

My colleagues (A. Cortes-Cabrera, A. Morreale, F. Gago) and I encourage you to use the application and send us your comments and suggestions about problems that you might encounter and ideas for further improvements.
We look forward to hearing from you.

Thank you so much,