The Interweaving of Cheminformatics and HTS

Kümmel, Anne; Parker, Christian N.

doi:10.1007/978-1-60761-839-3_17

Cited by 6 publications

(4 citation statements)

References 114 publications

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“…A challenge of chemical genomics is that biological assays are increasingly monitoring multiple parameters and thus are becoming more complex to be analyzed. Additionally, investigating the effects of compound combinations including synergies or helping delineate possible mechanisms of action also poses unique challenge (Kümmerl and Parker, ).…”

Section: Discussion: Going Forwardmentioning

confidence: 99%

“…As Kümmerl and Parker () point out, HTS is a multidisciplinary science. HTS requires the development of biologically relevant and specific assays, low cost, efficient and facile scale‐up to throughput mode, high‐quality readouts that are understandable, and pharmacological relevance to support down‐stream lead discovery processes.…”

Section: High Throughput Screening and Chemoinformticsmentioning

confidence: 99%

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Chemoinformatics and chemical genomics: potential utility of in silico methods

Valerio

Choudhuri

2012

J of Applied Toxicology

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Computational life sciences and informatics are inseparably intertwined and they lie at the heart of modern biology, predictive quantitative modeling and high-performance computing. Two of the applied biological disciplines that are poised to benefit from such progress are pharmacology and toxicology. This review will describe in silico chemoinformatics methods such as (quantitative) structure-activity relationship modeling and will overview how chemoinformatic technologies are considered in applied regulatory research. Given the post-genomics era and large-scale repositories of omics data that are available, this review will also address potential applications of in silico techniques in chemical genomics. Chemical genomics utilizes small molecules to explore the complex biological phenomena that may not be not amenable to straightforward genetic approach. The reader will gain the understanding that chemoinformatics stands at the interface of chemistry and biology with enabling systems for mapping, statistical modeling, pattern recognition, imaging and database tools. The great potential of these technologies to help address complex issues in the toxicological sciences is appreciated with the applied goal of the protection of public health.

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Section: Discussion: Going Forwardmentioning

confidence: 99%

Section: High Throughput Screening and Chemoinformticsmentioning

confidence: 99%

Chemoinformatics and chemical genomics: potential utility of in silico methods

Valerio

Choudhuri

2012

J of Applied Toxicology

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“…In the lack of previous information regarding target´s structure nor known active compounds, there is no choice but to rely on a brute force hit identification process, such as HTS (High Throughput Screening), over a whole chemical compound library. 7,8 But as data about known ligands or crystallographic structures from protein targets becomes available, such information can be used for selecting a small portion of some virtual compound database that shows a higher likelihood of interaction with a given target than a randomly chosen compound. 9 Such enrichment is the goal of Virtual Screening (VS) applications.…”

Section: Introductionmentioning

confidence: 99%

3D-Pharma, A Ligand-based Virtual Screening tool using 3D Pharmacophore Fingerprints

Domingues,

Martins-José,

LOPES

2024

Preprint

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In this work, we introduced 3D-Pharma, a new Ligand-Based Virtual Screening method that uses fingerprints of pharmacophore triplets at atomic resolutions to build very simple and predictive models. Within 3D-Pharma the molecules are described by multiple representations that comprehend several prototropic species and conformations (multiple species, multiple mode approach). All the multiple representations of a compound are concatenated into a unique fingerprint that accounts for most of its chemical and conformational diversity. The biological activity of an ensemble of active molecules are represented by a single modal fingerprint or model, validated through a new exhaustive 10-fold cross-validation scheme, which improves robustness and internal consistency of the models, as well as its predictive power. We benchmark our method with 10 datasets of active compounds and decoys gathered from DUD database and compare its performance against seven state-of-the-art LBVS methods. To generate the models, we used three external and independent datasets of bioactive compounds (Drugs, PDB Ligands and WOMBAT). We concluded that 3D-Pharma overperforms all other state-of-the-art LBVS tools analyzed, in terms of global accuracy as well as scaffold hopping and early recovery capacities. Furthermore, the models produced by 3D-Pharma are simple, robust, consistent and predictive.

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“…Spotfire by TIBCO, Vortex by DOTMATICS) are available to conduct these data analysis and mining tasks, but these are relatively expensive, have fixed sets of features and are not necessarily suited for academic structures and small biotech companies. As a consequence, there is a need for freely available and easily customizable software capable of visualizing and analyzing HTS results with an eye toward more extensive and chemical analysis using advances in cheminformatics for HTS data analysis (Ku¨mmel and Parker, 2011).…”

Section: Introductionmentioning

confidence: 99%