e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design

Pihan, Emilie; Colliandre, Lionel; Guichou, Jean-François; Douguet, Dominique

doi:10.1093/bioinformatics/bts186

Cited by 111 publications

(92 citation statements)

References 15 publications

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“…Table 2 summarizes the variable degree of overlap between these resources and DrugCentral (MOL V2000 subset, 3935 unique APIs). The overlap matrix was computed for DrugCentral, in comparison with the following drug-focused resources: the NIH Center for Chemical Genomics (NCGC) pharmaceutical collection (11), DrugBank (12), the IDAAPM database (13), the phase 4 drugs subset from the ChEMBL 21 release (1) and the e-Drug3D database (14). Although the NCGC pharmaceutical collection is larger than DrugCentral, since it contains compounds undergoing clinical trials, its last published update was in 2012 and, as such, it does not include 240 FDA approved and 46 APIs approved elsewhere, after 2012.…”

Section: Database Contents and Data Sourcesmentioning

confidence: 99%

“…The e-Drug3D database (14) contains 3D conformations for Drugs@FDA entries, and provides information on commercially available drug fragments to facilitate computational drug repurposing and fragment based drug design. DrugCentral also covers biologics, peptides and inorganic drugs from Drug@FDA, whereas e-Drug3D focuses on small molecules having molecular weight below 2000 atomic mass units.…”

Section: Database Contents and Data Sourcesmentioning

confidence: 99%

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DrugCentral: online drug compendium

et al. 2016

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DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online. Its complementarity with other online resources is facilitated by cross referencing to external resources. At the molecular level, DrugCentral bridges drug-target interactions with pharmacological action and indications. The integration with FDA drug labels enables text mining applications for drug adverse events and clinical trial information. Chemical structure overlap between DrugCentral and five online drug resources, and the overlap between DrugCentral FDA-approved drugs and their presence in four different chemical collections, are discussed. DrugCentral can be accessed via the web application or downloaded in relational database format.

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Section: Database Contents and Data Sourcesmentioning

confidence: 99%

Section: Database Contents and Data Sourcesmentioning

confidence: 99%

DrugCentral: online drug compendium

et al. 2016

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“…121 Historically, fragment libraries have used substructures derived from drugs as one of the sources of ideas. 122 Pihan et al 123 have provided a set of commercially available fragments based on substructures of drugs. However, Morley et al 86 have analyzed a number of fragment libraries using principal moments of inertia (PMI) plots and suggest that they have limited shape diversity when compared to fragments derived from compounds tested in humans.…”

Section: Synthesis Related Aspectsmentioning

confidence: 99%

Design Principles for Fragment Libraries: Maximizing the Value of Learnings from Pharma Fragment-Based Drug Discovery (FBDD) Programs for Use in Academia

et al. 2016

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Fragment-based drug discovery (FBDD) is well suited for discovering both drug leads and chemical probes of protein function: it can cover broad swaths of chemical space and allows the use of creative chemistry. FBDD is widely implemented for lead discovery in industry, but is sometimes used less systematically in academia. Design principles and implementation approaches for fragment libraries are continually evolving, and the lack of up-to-date guidance may prevent more effective application of FBDD in academia. This Perspective explores many of the theoretical, practical, and strategic considerations that occur within FBDD programs, including the optimal size, complexity, physicochemical profile, and shape profile of fragments in FBDD libraries, as well as compound storage, evaluation, and screening technologies. This compilation of industry experience in FBDD will hopefully be useful for those pursuing FBDD in academia.Rules are for the obedience of fools and the guidance of wise men.Harry Day, Royal Air Force (1898-1977

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“…Die Gruppe der Chinolinderivate 1a zeigten das am gleichmäßigsten verteilte Tar- [19] ). Entsprechend dieser Befunde scheint es in der Tats innvoll, fürg enerelle Screeningbibliotheken auf einfache Grundgerüste zurückzugreifen, um Tr efferraten zu erhçhen und eine rasche Leitstrukturfindung zu ermçglichen.…”

Section: Inden 1980er Jahren Beobachten Evans Et Ald Ass "[…]unclassified