Videos tagged 'StarDrop Tutorials'
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Matched Series Analysis
In this worked example, we use StarDrop's Nova module to identify new derivatives that are likely to improve activity at their target, given the SAR already generated on a project. If you'd like to try this example for yourself, PDF instructions and data files for StarDrop can be found in the t...
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Reaction-based Library Enumeration
Reaction-based enumeration method offers you a user-friendly, flexible workflow for virtual library design, starting from a reaction you like to apply to your chosen set of reagents. The method is part of StarDrop’s Nova module, complementing the compound idea generation methods based on chemistr...
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Automatic QSAR Model Building and Validation
This example explores the application of the Auto-Modeller module to build a QSAR model of potency against the Muscurinic Acetylcholine M5 receptor, based on public domain Ki data. The resulting model is applied to novel compound to predict their properties and visualise the SAR.
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Tutorials: Optimising P450 Metabolic Stability
In this example we will explore the feasibility of pursuing a fast-follower for Buspirone, a 5-HT1A ligand used as an anti-anxiolytic therapeutic, which has a known liability due to rapid metabolism by CYP3A4. This example illustrates the use of StarDrop’s P450 metabolism models to explore struct...
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Tutorials: NK2-H2L
The objective in this example is to identify one or more high quality chemistries for progression to detailed in vitro and in vivo studies, based on initial screening data for potency; ideally the compounds chosen for progression should not only be potent, but also have appropriate ADME propertie...
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Guided Multi-Parameter Optimisation of 2D and 3D SAR
This worked example uses a combination of 2D and 3D methods to understand and optimise a virtual library of Heat Shock Protein 90 (HSP90) inhibitors. The objective in this example is to use the SeeSAR™ module to develop an understanding of the 3D structure-activity relationships (SAR) and then us...
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Tutorial: Guiding Selection and Design in Hit-to-Lead
The objective in this example is to identify one or more high quality chemistries for progression to detailed in vitro and in vivo studies, based on initial screening data for potency; ideally the compounds chosen for progression should not only be potent, but also have appropriate ADME propertie...
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Tutorial: R-Group Analysis
The objective in this example is to take a look at an R-Group analysis of two data sets to identify functionalities which are influencing potency. In the second half we consider an example where we have different series, based around multiple scaffolds, where the substitution points are equivalen...
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Tutorial: Hit List Triage with Card View
This example uses StarDrop's Card View to explore the results from a kinase project in which a large screening campaign has resulted in a hit list. The project team wish to evaluate the list to identify the chemotypes within and focus their resources on a small number of series that have demonstr...
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Tutorial: Guided MPO of 2D and 3D SAR
This example uses a combination of 2D and 3D methods to understand and optimise a virtual library of Heat Shock Protein 90 (HSP90) inhibitors. The library, created by a de novo design process, is based around an amide substitution on a beta resorcylic acid core. The objective in this example is t...
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Tutorial: Matched Series for SAR Analysis
This worked example considers a publically available set of PPARγ pIC50 data which contains a number of chemical series. Matched Series Analysis is used to identify when a substitution from one series has a high likelihood of improving the binding of another series at PPARγ. This approach is then...
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Tutorial: MPO Explorer - Profile Builder
In this example we will use the Profile Builder in StarDrop’s MPO Explorer module to derive a multi-parameter scoring profile, based on a data set initially described by Wager et al. [ACS Chem. Neurosci. 1 p. 435 (2010)]. Wager et al. used this data set to develop a multi-parameter optimisation m...
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Tutorial: MPO Explorer: Sensitivity Analysis
In this example, we will use the Sensitivity Analysis tool in StarDrop’s MPO Explorer module to check if the ranking of compounds in a data set is sensitive to any of the criteria or importance values in a scoring profile. This is important to consider because, if the compounds we would choose ar...
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Tutorial: Scaffold Hopping with Library Enumeration
In this example we are going to use the library enumeration feature in StarDrop’s Nova module, in combination with R-group analysis, to generate a virtual library representing a potential new lead series. This will be based on a previous series and explore the impact of a change of scaffold and v...
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Tutorial: Optimising P450 Metabolic Stability
In this example we will explore the feasibility of pursuing a fast-follower for Buspirone, a 5-HT1A ligand used as an anti-anxiolytic therapeutic, which has a known liability due to rapid metabolism by CYP3A4. This example illustrates the use of StarDrop’s P450 metabolism models to explore struct...
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Tutorial: Addressing Toxicity Risk in Multi-Parameter Optimisation
In this example we will illustrate how knowledge-based predictions of toxicity can be used within a MPO environment to guide the selection and design of compounds with a good balance of properties and reduced risk of toxicity. We will explore a library of compounds with COX2 inhibition data, with...
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Tutorial: Comparing chemical series with Probabilistic Scoring
This example is taken from a project in which screening of a diverse library resulted in hits from multiple chemistries. Without the resources to follow-up all of the hit chemistries, the project team wished to focus on a small number of series which were most likely to yield high quality leads w...
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Tutorial: Multi-Parameter Optimisation of 3D SAR
In this example we will explore the multi-parameter optimisation of a series of CDK2 inhibitors, combining a 3D insight into the structure-activity-relationship (SAR) gained from StarDrop’s torch3D™ module and predictions of ADME and physicochemical properties, using StarDrop’s unique Probabilist...
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Tutorial: Automatic QSAR Model Building and Validation
This tutorial walks through the process of building and validating a QSAR model of Muscarinic Acetlycholine M5 receptor potency using StarDrop's Auto-Modeller.
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Tutorial: Automatic Generation of New Compound Ideas
The objective in this tutorial is to evolve the chemistry around three lead compounds which have good ADME properties but which have insufficient inhibition of the target, the Serotonin transporter. Using Nova and Probabilistic Scoring we look at how we can generate new ideas for compounds to imp...
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Tutorial: Matched Series Analysis
The objective in this worked example is to identify new derivatives that are likely to improve activity at their target, given the SAR already generated on a project. This example uses a publically available set of Human Chymotrypsin Ki data and searches the ChEMBL pIC50 knowledge base (generated...