Chemical Space: Big Data Challenge for Molecular Diversity

Chimia
Mahendra AwaleJean-Louis Reymond

Abstract

Chemical space describes all possible molecules as well as multi-dimensional conceptual spaces representing the structural diversity of these molecules. Part of this chemical space is available in public databases ranging from thousands to billions of compounds. Exploiting these databases for drug discovery represents a typical big data problem limited by computational power, data storage and data access capacity. Here we review recent developments of our laboratory, including progress in the chemical universe databases (GDB) and the fragment subset FDB-17, tools for ligand-based virtual screening by nearest neighbor searches, such as our multi-fingerprint browser for the ZINC database to select purchasable screening compounds, and their application to discover potent and selective inhibitors for calcium channel TRPV6 and Aurora A kinase, the polypharmacology browser (PPB) for predicting off-target effects, and finally interactive 3D-chemical space visualization using our online tools WebDrugCS and WebMolCS. All resources described in this paper are available for public use at www.gdb.unibe.ch.

Citations

May 3, 2018·Chemical Communications : Chem Comm·Ivan Di BonaventuraJean-Louis Reymond
May 17, 2018·Angewandte Chemie·Thissa N SiriwardenaJean-Louis Reymond
Dec 1, 2018·Future Medicinal Chemistry·Antonio-Jesús Banegas-LunaHoracio Pérez-Sánchez
Jun 7, 2019·Molecular Informatics·Mahendra AwaleJean-Louis Reymond
Aug 1, 2020·Frontiers in Cellular and Infection Microbiology·Derry K MercerAlfredo M Angeles-Boza
May 26, 2018·International Journal of Molecular Sciences·Nicholas Ekow ThomfordKevin Dzobo
Mar 3, 2020·Frontiers in Chemistry·Sven Bühlmann, Jean-Louis Reymond
Jan 13, 2021·Journal of Cheminformatics·Alice CapecchiJean-Louis Reymond
Feb 5, 2021·ACS Nano·Marcelo D T TorresCesar de la Fuente-Nunez
Dec 24, 2019·Journal of Chemical Information and Modeling·Alice CapecchiJean-Louis Reymond
Jan 13, 2021·Journal of Cheminformatics·Daniel Probst, Jean-Louis Reymond
Oct 22, 2019·Journal of Cheminformatics·Samina Kausar, Andre O Falcao
Mar 13, 2021·Chemical Society Reviews·Wenyi LiJohn D Wade
Jul 23, 2021·ACS Chemical Neuroscience·Ángel SantiagoLaura Dominguez
Dec 27, 2018·Journal of Chemical Information and Modeling·José JiménezGianni De Fabritiis
Mar 26, 2019·Journal of Chemical Information and Modeling·Mahendra AwaleJean-Louis Reymond
Dec 20, 2017·Journal of Chemical Information and Modeling·Daniel Probst, Jean-Louis Reymond
Sep 25, 2021·Science Advances·Yu LiuLeroy Cronin

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Journal of Chemical Information and Modeling
Ricardo VisiniJean-Louis Reymond
Expert Opinion on Drug Discovery
Rajan ChaudhariShuxing Zhang
© 2022 Meta ULC. All rights reserved