Automated Sequence Alignment, An Aqueous Solubility Model, and Library Specific Properties
This month we are showcasing several new features in the Ligand Express platform. While many interactivity improvements that have been implemented, we will be highlighting only three of them here (Read our release notes to see all changes to the platform). We have introduced sequence alignments for all protein structures visualized in ourprotein viewer. On the property prediction side, we have made it easier to hone in on the properties most relevant to your research questions, allowing users to select subsets of properties to explore. That is not the only change coming to Property Prediction, a new model has joined the collection, Aqueous Solubility (logS). LogS, a key determinant of a drug’s pharmacokinetic profile, is the platforms first quantitative model.
Details on these pivotal changes can be found down below.
Automated Sequence Alignment
To better examine single nucleotide variants, we have added automated sequence alignment between a protein structure’s sequence and the canonical protein sequence. Aligning the structure’s primary sequence is a key step to linking single nucleotide variants to the 3D protein structure, with additional annotations (e.g. highlighting the position of single nucleotide variants) planned for future releases.
Specify Properties to Calculate for Molecules within Certain Libraries
To streamline the analysis of properties that are most relevant to your project it is now possible to select a subset of properties within libraries. Interested in your molecules’ ability to pass the blood brain barrier and their likelihood of being a substrate of p-glycoprotein? Select these properties when making a new library and only those properties will be computed for molecules added to the library. At anytime, properties can be added to a library and computed on the fly. Use libraries to dynamically select top performing molecules, and compare them head to head on the properties that matter most for your research question.
The aqueous solubility, logS, of organic molecules plays a large role in the behaviour of a small molecule drug. Given its important in influencing the properties of a drug, we have added a quantitative model that will rapidly predict the logS of a given molecule. The predictive model (R2 = 0.85) is the first quantitative model added to property prediction, and the first physicochemical property predicted through POEM. More properties are actively being explored, with some already scheduled for future releases.
We will continue to improve the functionality of property prediction, including additional support for filtering and selecting small molecules, as well as implement more customization options. There are also changes expected for Proteome Screening and its analysis. Follow our Linkedin page here and our Twitter page here for updates as the become available.
For all updates from this month’s release and more, please visit https://cyclicarx.com/product.
Are you a fan of the changes made to Ligand Express? All feedback is greatly appreciated! We would love to hear from you, please send any feedback to firstname.lastname@example.org.