Literature DB >> 22798082

AtlasCBS: a web server to map and explore chemico-biological space.

Alvaro Cortés-Cabrera1, Antonio Morreale, Federico Gago, Celerino Abad-Zapatero.   

Abstract

New approaches are needed that can help decrease the unsustainable failure in small-molecule drug discovery. Ligand Efficiency Indices (LEI) are making a great impact on early-stage compound selection and prioritization. Given a target-ligand database with chemical structures and associated biological affinities/activities for a target, the AtlasCBS server generates two-dimensional, dynamical representations of its contents in terms of LEI. These variables allow an effective decoupling of the chemical (angular) and biological (radial) components. BindingDB, PDBBind and ChEMBL databases are currently implemented. Proprietary datasets can also be uploaded and compared. The utility of this atlas-like representation in the future of drug design is highlighted with some examples. The web server can be accessed at http://ub.cbm.uam.es/atlascbs and https://www.ebi.ac.uk/chembl/atlascbs.

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Year:  2012        PMID: 22798082     DOI: 10.1007/s10822-012-9587-5

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  16 in total

1.  Ligand efficiency: a useful metric for lead selection.

Authors:  Andrew L Hopkins; Colin R Groom; Alexander Alex
Journal:  Drug Discov Today       Date:  2004-05-15       Impact factor: 7.851

Review 2.  Finding the sweet spot: the role of nature and nurture in medicinal chemistry.

Authors:  Michael M Hann; György M Keserü
Journal:  Nat Rev Drug Discov       Date:  2012-04-30       Impact factor: 84.694

3.  Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation.

Authors:  Cele Abad-Zapatero; Ognjen Perišić; John Wass; A Patrícia Bento; John Overington; Bissan Al-Lazikani; Michael E Johnson
Journal:  Drug Discov Today       Date:  2010-08-19       Impact factor: 7.851

Review 4.  Navigating chemical space for biology and medicine.

Authors:  Christopher Lipinski; Andrew Hopkins
Journal:  Nature       Date:  2004-12-16       Impact factor: 49.962

5.  The PDBbind database: methodologies and updates.

Authors:  Renxiao Wang; Xueliang Fang; Yipin Lu; Chao-Yie Yang; Shaomeng Wang
Journal:  J Med Chem       Date:  2005-06-16       Impact factor: 7.446

6.  A web-based platform for virtual screening.

Authors:  Paul Watson; Marcel Verdonk; Michael J Hartshorn
Journal:  J Mol Graph Model       Date:  2003-09       Impact factor: 2.518

7.  Time-Trajectories in Efficiency Maps as Effective Guides for Drug Discovery Efforts.

Authors:  Serge Christmann-Franck; Daniel Cravo; Cele Abad-Zapatero
Journal:  Mol Inform       Date:  2011-03-14       Impact factor: 3.353

Review 8.  Ligand Efficiency Indices (LEIs): More than a Simple Efficiency Yardstick.

Authors:  Cele Abad-Zapatero; Daniel Blasi
Journal:  Mol Inform       Date:  2011-03-17       Impact factor: 3.353

9.  Retrospective Mapping of SAR Data for TTR Protein in Chemico-Biological Space Using Ligand Efficiency Indices as a Guide to Drug Discovery Strategies.

Authors:  Daniel Blasi; Gemma Arsequell; Gregori Valencia; Joan Nieto; Antoni Planas; Marta Pinto; Nuria B Centeno; Cele Abad-Zapatero; Jordi Quintana
Journal:  Mol Inform       Date:  2011-03-18       Impact factor: 3.353

10.  The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics.

Authors:  Christoph Steinbeck; Yongquan Han; Stefan Kuhn; Oliver Horlacher; Edgar Luttmann; Egon Willighagen
Journal:  J Chem Inf Comput Sci       Date:  2003 Mar-Apr
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  1 in total

1.  Progress on open chemoinformatic tools for expanding and exploring the chemical space.

Authors:  José L Medina-Franco; Norberto Sánchez-Cruz; Edgar López-López; Bárbara I Díaz-Eufracio
Journal:  J Comput Aided Mol Des       Date:  2021-06-18       Impact factor: 4.179

  1 in total

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