As SEURAT was built to provide access to your companies discovery data from the viewpoint of many disciplines (structural biology, medicinal chemistry, computational chemistry, biology, preclinical and legal) it inherently supports a wide range of functions and views. Listed below are some of the key features of SEURAT:
Practical Features (What your users will care about)
- Database flexibility; Seurat can work with pretty much any drug discovery database through configurations changes to its "meta-data" database mapping file (not code changes). You can then?:
- Load your own or third party results into the SEURAT native database from SDF or CSV files
- Use SEURAT to read your structure, assay and property data from your corporate database
- Do both of the above in unison
- Data flexibility: Seurat can display a wide range of data from different sources and in different forms
- Assay results from the database and from industry standard files including complex assays with standard deviation and concentration information
- Crystal structure data using PyMol launched directly from the Seurat GUI
- PK reports and any other report that can be accessed by a valid URL.
- Comes with a pre-built set of quick searches that can be chosen from a menu to cover each users first steps within SEURAT without the need for training
- Your team can build template searches that can be shared by all members of a project team leading to a reduced learning curve for team members that come later to a project.
- Even more complex searches combining constraints on structure, assay (cutoff value, date) and lot information can be built in a facile manner through the intuitive Template Form GUI
- Almost every facet of report layout can be interactively altered from within the Assay Display GUI. This list includes but is not limited to:
- Title, width, height, color, order and visibility (hidden or not) of columns.
- Height, color, order and visibility (hidden or not) of rows.
- Color of cells can be set by specific cell selection, gradient over a column you wish to color and/or a gradient over a range of values from a column different to the one you wish to color
- Font size and content (User Defined Columns) of cells.
- Almost any type of data can be added to an existing set of results as new columns in the Assay Display GUI in a step-by-step fashion:
- Your (and Seurat's) favorite property predicitions
- Additional assay results from your corporate database, Seurat's native database and/or third party data (like PUBCHEM) loaded into Seurat
- Specific value of database columns you specify in Seurat's "meta-data" configuration file.
- User defined columns; this is where you supply the values interactively
- Almost any type of compound can be added to an existing set of results as new rows in the Assay Dispaly GUI in a step-by-step fahsion:
- Add corporate compounds that fall outside your initial search by supplying a list of identifiers. All existing columns in the Assay Display will be automatically populated for these new columns where possible
- Add third party compounds (like from PUBCHEM or a compound vendor) that you have loaded into the Seurat native database or your own database once again through a list of identifiers
- Add compounds from the Seurat hypothetical compound database populated over time by your chemists.
- SAR analysis can easily be initiated from the SAR Tool:
- Select an analysis using Auto R-groups, SAR By bond or manual R-group placement
- View matching (and non matching) results in a standard tabular and novel matrix layout
- Your chemsits can try out and record hypothetical compounds through the Simple Molecule Property Calculator (SMPC) tool which:
- Provides real time feedback on Lipinski property values as you sketch and edit your compound structure.
- Allows the compound to be registered into a fully structure searchable (sub, super and similarity) database so that your ideas are not lost
- Allows each hypothetical compound to be tested against a model at an aggregate level for a pass or fail (currently only the Lipinksi model is implemented)
- Seurat Visualization Suite: Users can search for patterns and correlations, visually compare scaffolds and construct visual models which can be saved and tested against future data points
- Dynamically filterable on all columns
- Supports 6 dimensions of data through axes, color, size, label and order.
- All visualizations are synchronized for selection, filtering and visual effects.
- Details can be optionally displayed at any time for current selections
- Simple linear regression information can be requested for scatter plots.
- Heat maps and the matrix of scatter plots support scaffold level comparisons of the inherently multiplexed data in discovery projects
- Available Screening Compounds (ASC) tool; Allows 2.1 million vendor compounds to be searched on a combination of 10 physical properties (HBD, HBA, MW...), the count of the presence of 100 chemical flags being below a desired threshold and structure
- Human Kinome Tree Viewer: See the selectivity of your compounds in Kinase space by plotting their activity on the Human Kinome Tree.
- Search the Registry of Toxic Effects of Chemical Substances (RTECS) Tool
- Search for Common Functional Group Replacements in the Kinase space covered by the GVK database as determine by a disconnected MCS algorithm
Technical Features (Software and Hardware considerations)
- Pure Java application so that it can be run on any platform that supports Java 1.5. To date Seurat has been successfully deployed undex AIX, Linux, Windows XP and Mac (client only for the Mac)
- Database flexibility; Supports PostgreSQL 8. 1, Oracle 9 (and above)
- Small memory footprint; Seurat server only requires 256 megabytes of memory for a typical installation that supports 50 to 80 users