LigandScout 4.4. comes with several new features for the various plots, such as the Scatter Plot and the Parallel Coordinates Diagram. Now, both provide means for reversing the scale of an axis. Additionally, the Scatter Plot ’s axis can use non-linear scaling. The scatter plot further allows to show additional information for the selected molecules, enabling an easier comparison of specific ligands.

With the Radar Plot, LigandScout 4.4 includes a new plot type. Similar to the Parallel Coordinates Diagram and the Scatter Plot, it helps to visualize properties of a molecule library. Additionally, the ROC Curve Plot, has received an upgrade and is now also a detachable plot.

Further, LigandScout 4.4 introduces a novel feature-rich Molecule Editor. It provides means for drawing arbitrary molecules in 2D and allows to define custom fragments.

Through the new Show Binding Affinity Surface functionality, it is possible to analyze which ligand parts contribute positively or negatively to the binding of a ligand and an environment. The surface coloring depends on the ligand atoms’ binding affinity contribution.

LigandScout’s Alignment Perspective could always be used to align molecules and/or pharmacophores. With LigandScout 4.4, it is also possible to use reference points in order to align complete active sites with each other and/or with molecules and/or with pharmacophores.

Version 4.3 greatly expands LigandScout’s capabilities in the field Molecular Dynamics Simulations Pharmacophores for the entire trajectory or a subset can be calculated with a single click. Producing such a huge amount of data requires advanced techniques for analyzing and understanding them. To achieve this goal LigandScout 4.3 offers various user interactive and highly customizable plots (E.g. MD Pharmacophores Plots )- with more to come.

With the addition of the molecular dynamics plots the library Scatter Plot and the Parallel Coordinates Diagram have received an upgrade, too. All plots can now be resized and de-attached into separate screens.

LigandScout 4.3 also introduces a new pharmacophore feature type, namely Halogen Bonding .

Furthermore, LigandScout 4.3 introduces a completely new set of features summarized under the term Remote Execution . It is now possible to screen large compound libraries on remote High Performance Computing (HPC) clusters directly from within the graphical LigandScout user interface. Similarly, conformer generation can be done remotely. In order to use LigandScout’s remote execution features, a server software running on the requested HPC cluster is required. Please contact Inte:Ligand support for more details and installation instructions. It is also possible to run the software with virtual clusters in the Amazon Web Services Elastic Compute cloud.

Finally, with LigandScout 4.3, the search functionality in this manual has been overhauled and is now able to search for arbitrary words and terms.

With LigandScout 4.2 you can, for the first time, analyze molecular dynamics trajectories within pharmacophore dimensions. For each frame you select, you can create a structure- based pharmacophore model and analyze the interactions of your ligand within the protein. LigandScout 4.2 supports CHARMM, GROMACS, and Amber file formats.

The possibilities to determine druggable pockets within a protein and to generate structure-based pharmacophore models within a binding site that contains no ligand are some of the new key features of LigandScout 4.2, making anchored docking possible for the first time from the LigandScout Graphical User Interface. Moreover, we have implemented the best validated docking program into the LigandScout GUI: Molecular docking using AutoDock 4.2 and AutoDock Vina 1.1 are accessible directly from the active site view.

Additional new functionality includes drag and drop, e.g. molecules from your drawing software into LigandScout, expanded table multiparameter filtering and exporting capabilities, e.g. to MS Excel, a new conformer generator , a new binding site analyzer for optimizing geometric flips and/or tautomeric states of amino acid side chains, and additional pharmacophore model editing possibilities, including moving selected features freely to any 3D location in the binding site.

Some of the most recent changes include the possibility to edit molecule library files directly within LigandScout. New molecule properties can be added, existing ones can be modified, or deleted. Properties, as well as smiles molecules, can be imported from XLS (MS Excel) spreadsheats. They can be merged based on their names or any common property.

LigandScout 4.2 also introduces interactive charts for molecule libraries. The scatter-plot can depict the complete library in two-dimensional space based on up to two different properties. The parallel coordinate diagram displays a y-axis for each molecule property and connects values for each property with lines. Both charts allow for interactive selection and filtering of the library.

Last but not least, LigandScout 4.2 also adds GUI elements to the ligand-based perspective to speed-up clustering based workflows for creating ligand-based models.