Empowering pharmacoinformatics by linked life science data

Goldmann, Daria; Zdrazil, Barbara; Digles, Daniela; Ecker, Gerhard

doi:10.1007/s10822-016-9990-4

Cited by 2 publications

References 59 publications

(71 reference statements)

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Computational Methods Used in Hit-to-Lead and Lead Optimization Stages of Structure-Based Drug Discovery

Heifetz¹,

Southey²,

Morao³

et al. 2017

Methods in Molecular Biology

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GPCR modeling approaches are widely used in the hit-to-lead (H2L) and lead optimization (LO) stages of drug discovery. The aims of these modeling approaches are to predict the 3D structures of the receptor-ligand complexes, to explore the key interactions between the receptor and the ligand and to utilize these insights in the design of new molecules with improved binding, selectivity or other pharmacological properties. In this book chapter, we present a brief survey of key computational approaches integrated with hierarchical GPCR modeling protocol (HGMP) used in hit-to-lead (H2L) and in lead optimization (LO) stages of structure-based drug discovery (SBDD). We outline the differences in modeling strategies used in H2L and LO of SBDD and illustrate how these tools have been applied in three drug discovery projects.

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Computational Methods Used in Hit-to-Lead and Lead Optimization Stages of Structure-Based Drug Discovery

Heifetz¹,

Southey²,

Morao³

et al. 2017

Methods in Molecular Biology

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Ligand- and Structure-Based Drug Design and Optimization using KNIME

Mazanetz

Goode

Chudyk

2020

CMC

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In recent years there has been a paradigm shift in how data is being used to progress early drug discovery campaigns from hit identification to candidate selection. Significant developments in data mining methods and the accessibility of tools for research scientists have been instrumental in reducing drug discovery timelines and in increasing the likelihood of a chemical entity achieving drug development milestones. KNIME, the Konstanz Information Miner, is a leading open source data analytics platform and has supported drug discovery endeavours for over a decade. KNIME provides a rich palette of tools supported by an extensive community of contributors to enable ligandand structure-based drug design. This review will examine recent developments within the KNIME platform to support small-molecule drug design and provide a perspective on the challenges and future developments within this field.

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Empowering pharmacoinformatics by linked life science data

Cited by 2 publications

References 59 publications

Computational Methods Used in Hit-to-Lead and Lead Optimization Stages of Structure-Based Drug Discovery

Computational Methods Used in Hit-to-Lead and Lead Optimization Stages of Structure-Based Drug Discovery

Ligand- and Structure-Based Drug Design and Optimization using KNIME

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