Recognizing pitfalls in virtual screening: a critical review

T Scior, A Bender, G Tresadern… - Journal of chemical …, 2012 - ACS Publications
The aim of virtual screening (VS) is to identify bioactive compounds through computational
means, by employing knowledge about the protein target (structure-based VS) or known …

Integrating virtual screening and combinatorial chemistry for accelerated drug discovery

F López-Vallejo, T Caulfield… - … Chemistry & High …, 2011 - ingentaconnect.com
Virtual screening is increasingly being used in drug discovery programs with a growing
number of successful applications. Experimental methodologies developed to speed up the …

Expanding the medicinally relevant chemical space with compound libraries

F López-Vallejo, MA Giulianotti, RA Houghten… - Drug discovery today, 2012 - Elsevier
Analysis of marketed drugs and commercial vendor libraries used in high-throughput
screening suggests that the medicinally relevant chemical space may be expanded to …

[HTML][HTML] Consensus diversity plots: a global diversity analysis of chemical libraries

M González-Medina, FD Prieto-Martínez… - Journal of …, 2016 - Springer
Background Measuring the structural diversity of compound databases is relevant in drug
discovery and many other areas of chemistry. Since molecular diversity depends on …

Molecular scaffold analysis of natural products databases in the public domain

AB Yongye, J Waddell… - Chemical biology & drug …, 2012 - Wiley Online Library
Natural products represent important sources of bioactive compounds in drug discovery
efforts. In this work, we compiled five natural products databases available in the public …

Visualization of molecular fingerprints

JR Owen, IT Nabney, JL Medina-Franco… - Journal of chemical …, 2011 - ACS Publications
A visualization plot of a data set of molecular data is a useful tool for gaining insight into a
set of molecules. In chemoinformatics, most visualization plots are of molecular descriptors …

Balancing novelty with confined chemical space in modern drug discovery

JL Medina-Franco, K Martinez-Mayorga… - Expert Opinion on …, 2014 - Taylor & Francis
Introduction: The concept of chemical space has broad applications in drug discovery. In
response to the needs of drug discovery campaigns, different approaches are followed to …

Epigenetic relevant chemical space: a chemoinformatic characterization of inhibitors of DNA methyltransferases

E Fernández-de Gortari, JL Medina-Franco - Rsc Advances, 2015 - pubs.rsc.org
DNA methylation is an epigenetic mechanism mediated by a family of proteins called DNA
methyltransferases (DNMTs). The misregulation of the covalent modification of DNA through …

A chemical space odyssey of inhibitors of histone deacetylases and bromodomains

FD Prieto-Martínez, E Fernández-de Gortari… - RSC …, 2016 - pubs.rsc.org
The interest in epigenetic drug and probe discovery is growing as reflected in the large
amount of structure-epigenetic activity information available. Therefore, the significance of …

Molecular similarity analysis

JL Medina‐Franco, GM Maggiora - Chemoinformatics for drug …, 2013 - Wiley Online Library
Although the concept of similarity has been around since the beginning of human history, its
application to chemical systems did not emerge until after theories of chemical matter were …