• OEApplications 2023.1
    • Release Highlights 2023.1.0
      • Supported Platforms
      • Related Application Versions
      • General Notices
    • Detailed Release Notes 2023.1
      • AFITT 2.6.3
      • BROOD 3.2.1
      • EON 2.4.1
      • Zap TK 2.4.5
      • OEDOCKING 4.2.1
      • OEDocking TK 4.2.1
      • OMEGA 4.2.2
      • Omega TK 4.2.2
      • MolProp TK 2.6.2
      • PICTO 5.0.0
      • OEDepict TK 2.5.2
      • pKa-Prospector 1.2.1
      • QUACPAC 2.2.2
      • Quacpac TK 2.2.2
      • ROCS 3.6.0
      • Shape TK 3.6.0
      • SiteHopper 2.0.3
      • Sitehopper TK 2.0.3
      • SPRUCE 1.5.2
      • Spruce TK 1.5.2
      • Szmap TK 1.6.6
      • SZYBKI 2.6.0
      • Szybki TK 2.6.0
    • Previous Release Highlights
      • Release Highlights 2022.2.2
      • Release Highlights 2022.2.1
      • Release Highlights 2022.1
      • Release Highlights 2021.2
      • Release Highlights 2021.1
      • Release Highlights 2020.2.2
      • Release Highlights 2020.2
      • Release Highlights 2020.1.1
      • Release Highlights 2020.1
      • Release Highlights 2020.0
      • Release Highlights 2019.Nov
      • Release Highlights 2019.May
      • OEApplications 2018.Nov
  • Getting Started
    • Installation and Platform Notes
      • Licenses for OpenEye Software
      • Installation
      • Example and Tutorial Data
      • MPI
      • Uninstallation
    • Release Cycle
    • Legal Notices
      • Copyright and Trademarks
      • Sample Code
      • Citation
      • Technology Licensing
  • AFITT 2.6.3.0
    • Overview
    • Applications
    • Utility Programs
    • FLYNN
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
      • Usage Notes
    • Coot Integration
      • Overview
      • Using FLYNN
      • Using WriteDict
      • Using RotFit
      • Installing Coot Interface
    • Utilities
      • AlignGrid
      • RotFit
      • Rscc
      • WriteDict
    • Theory
      • Fragment Fitting
    • Release History
      • AFITT 2.6.3
      • AFITT 2.6.2
      • AFITT 2.6.1
      • AFITT 2.6.0
      • AFITT 2.5.3
      • AFITT 2.5.2.0
      • AFITT 2.5.1
      • AFITT 2.5.0
      • AFITT-CL 2.4.1
      • AFITT-CL 2.4.0
      • AFITT-CL 2.3.0
      • AFITT-CL 2.2.0
      • AFITT-CL 2.1.1
      • AFITT-CL 2.1.0
      • AFITT-CL 2.0.1
      • FLYNN 2.0.0
    • Citation
  • BROOD 3.2.1.0
    • Introduction
      • Applications
      • Utility Programs
      • Installing the BROOD Database
    • vBROOD
      • Overview
      • Build and Run
      • Build a New Query
      • Run BROOD
      • Filtering
      • View Results
      • Viewing Results in VIDA
    • BROOD
      • Overview
      • Input Files
      • Example Commands
      • Command Line Help
      • Parameters
      • Output Files
    • CHOMP
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Utilities
      • Overview
      • Command Line Help
      • Example Commands
      • Required Parameters
      • Optional Parameters
    • Overview
    • Human Complement C3a Receptor Example
      • Specifying the database
      • Loading a molecule
      • Editing the query
      • Selecting properties
      • Setting up the BROOD search
      • Opening and viewing results
      • Exploring the Results
    • Fragment Joining Tutorial
      • BROOD database
      • Loading two molecules
      • Loading the protein
      • Choosing a query
      • Setting up a search
      • Examining the Log files
      • Viewing results in a protein site
    • Generating a Database with Crystallographic Conformations
      • Preparing data sources
      • Generating a database
      • Advanced topic: editing the fragments at an intermediate step
    • Theory
      • Fragment similarity searching
      • Clash detection and selectivity
      • Strain energy
      • Fragment joining
      • Cyclization
      • Molecular complexity
      • Aromatic fragment comparison
      • Shape-based belief model
      • Abbott bioavailability score
      • CHOMP Theory
    • BROOD Fragment Database
      • ChEMBL31 Fragment Database
      • ChEMBL31_lite Fragment Database
      • brood-database-chembl-3.0.0
    • Release History
      • BROOD 3.2.1
      • BROOD 3.2.0
      • BROOD 3.1.7
      • BROOD 3.1.6
      • BROOD 3.1.5
      • BROOD 3.1.4.0
      • BROOD 3.1.3
      • BROOD 3.1.2
      • BROOD 3.1.1
      • BROOD 3.1.0
      • BROOD 3.0.0
      • BROOD 2.0.0
      • BROOD 1.1.2
      • BROOD 1.1.1
      • BROOD 1.1.0
      • BROOD 1.0.1
      • BROOD 1.0.0
      • BROOD 0.9.b2
      • BROOD 0.9.b1
    • Citation
  • EON 2.4.1.0
    • Introduction
      • Overview
      • Applications
    • EON
      • Overview
      • Example Commands
      • Report File
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Theory
    • Release History
      • EON 2.4.1
      • Zap TK 2.4.5
      • EON 2.4.0
      • Zap TK 2.4.4
      • EON 2.3.7
      • Zap TK 2.4.3
      • EON 2.3.6
      • Zap TK 2.4.2
      • EON 2.3.5
      • Zap TK 2.4.1
      • EON 2.3.4.0
      • Zap TK 2.4.0
      • EON 2.3.3
      • EON 2.3.2
      • EON 2.3.1
      • EON 2.3.0
      • EON 2.2.0
      • EON 2.1.0
      • EON 2.0.0
    • Citation
  • OEDocking 4.2.1.0
    • Introduction
      • Overview
      • Applications
      • Utility Programs
    • Tutorials
      • Overview
      • Receptor preparation tutorial
      • CombineReceptors tutorial
      • FRED tutorial
      • HYBRID tutorial
      • POSIT tutorial
      • POSIT MPI tutorial
    • Theory
      • Receptors
      • FRED Theory
      • HYBRID Theory
      • POSIT Theory
    • FRED
      • Overview
      • Input Preparation
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • HYBRID
      • Overview
      • Input Preparation
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • POSIT
      • Overview
      • Input Preparation
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • MakeReceptor
      • Overview
      • GUI Layout
      • Setting up a Receptor
    • Utilities
      • ReceptorInDU
      • OEB2DUReceptor
      • DockingReport
      • ScorePose
      • ReceptorToolbox
      • combine_receptors
      • DU2OEBReceptor
    • Release History
      • OEDOCKING 4.2.1
      • OEDocking TK 4.2.1
      • OEDOCKING 4.2.0
      • OEDocking TK 4.2.0
      • OEDOCKING 4.1.2
      • OEDocking TK 4.1.2
      • OEDOCKING 4.1.2
      • OEDocking TK 4.1.2
      • OEDOCKING 4.1.0
      • OEDocking TK 4.1.0
      • OEDOCKING 4.0.0.2
      • OEDOCKING 4.0.0.0
      • OEDocking 3.5.0
      • OEDocking 3.4.0
      • OEDocking 3.3.1
      • OEDocking 3.3.0
      • OEDocking 3.2.0
      • OEDocking 3.0.1
      • OEDocking 3.0.0
      • POSIT 3.1.0
      • POSIT 1.0.3
      • POSIT 1.0.2
      • POSIT 1.0.1
      • POSIT 1.0.0
      • FRED 2.2.5
      • FRED 2.2.4
      • FRED 2.2.3
      • FRED 2.2.2
      • FRED 2.2.1
      • FRED 2.2.0
    • Citation
  • OMEGA 4.2.2.0
    • Introduction
      • Overview
      • Applications
      • Utility Programs
    • FILTER
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
      • Filter Files
    • OMEGA
      • Overview
      • GPU-Omega
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
      • Additional specifications
    • Utilities
      • Flipper
      • MakeFraglib
      • Oeb2SdConf
    • Theory
      • OMEGA Theory
      • Macrocycle Conformations
      • Filtering Theory
    • Release History
      • OMEGA 4.2.2
      • Omega TK 4.2.2
      • MolProp TK 2.6.2
      • OMEGA 4.2.1
      • OMEGA 4.2.0
      • Omega TK 4.2.0
      • MolProp TK 2.6.0
      • OMEGA 4.1.2
      • Omega TK 4.1.2
      • MolProp TK 2.5.7
      • OMEGA 4.1.1
      • Omega TK 4.1.1
      • MolProp TK 2.5.6
      • OMEGA 4.1.0.0
      • Omega TK 4.1.0
      • MolProp TK 2.5.5
      • OMEGA 4.0.0.6
      • OMEGA 4.0.0
      • OMEGA 3.1.2
      • OMEGA 3.1.1
      • OMEGA 3.1.0
      • OMEGA 3.0.1
      • OMEGA 3.0.0
      • OMEGA 2.5.1
      • OMEGA 2.4.6
      • OMEGA 2.4.3
      • OMEGA 2.4.1
      • OMEGA 2.4.0
      • OMEGA 2.3.3
      • OMEGA 2.3.2
      • OMEGA 2.3.1
      • OMEGA 2.3.0
      • OMEGA 2.2.2
      • OMEGA 2.2.1
    • Citation
  • PICTO 5.0.0.0
    • Introduction
      • Overview
      • Applications
    • PICTO
      • Overview
      • Sketcher
      • SMARTS
      • Implicit/Explicit Hydrogens
      • Atom Labeling, Aromatic Displays, Aromatic Modeling, and other Displays
    • Release History
      • PICTO 5.0.0
      • OEDepict TK 2.5.2
      • PICTO 4.6.0
      • OEDepict TK 2.5.1
      • PICTO 4.5.4
      • OEDepict TK 2.5.0
      • PICTO 4.5.3
      • OEDepict TK 2.4.7
      • PICTO 4.5.2
      • OEDepict TK 2.4.6
      • PICTO 4.5.1.0
      • OEDepict TK 2.4.5
      • PICTO 4.5.0
    • Citation
  • pKa-Prospector 1.2.1.0
    • Introduction
      • Overview
      • Applications
    • pKa-Prospector
      • Overview
      • QuickStart
      • Query Molecule
      • Property Filters
      • Search Buttons
      • Results View
      • Preferences
      • Result Report
      • Menu Items
      • Appending Data
      • Selecting an Imported Database
    • Release History
      • pKa-Prospector 1.2.1
      • pKa-Prospector 1.2.0
      • pKa-Prospector 1.1.7
      • pKa-Prospector 1.1.6
      • pKa-Prospector 1.1.5
      • pKa-Prospector 1.1.4.0
      • pKa-Prospector 1.1.3
      • pKa-Prospector 1.1.2
      • pKa-Prospector 1.1.1
      • pKa-Prospector 1.1.0
      • pKa-Prospector 1.0.0
    • Citation
  • QUACPAC 2.2.2.0
    • Introduction
      • Overview
      • Applications
    • FixpKa
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • MolCharge
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • pKaTyper
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Tautomers
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • MolCharge Theory
      • Introduction
      • Marsili-Gasteiger Partial Charges
      • MMFF94 Partial Charges
      • AM1 Charges
      • AM1BCC Charges
      • ELF Conformer Selection
      • Amber ff94, ff96, ff99, ff99sb, and ff99sbc0 Partial Charges
    • Release History
      • QUACPAC 2.2.2
      • Quacpac TK 2.2.2
      • QUACPAC 2.2.1
      • Quacpac TK 2.2.1
      • QUACPAC 2.2.0
      • Quacpac TK 2.2.0
      • QUACPAC 2.1.3
      • Quacpac TK 2.1.3
      • QUACPAC 2.1.2
      • Quacpac TK 2.1.2
      • QUACPAC 2.1.1.0
      • Quacpac TK 2.1.1.2
      • Quacpac TK 2.1.1
      • QUACPAC 2.1.0
      • QUACPAC 2.0.2
      • QUACPAC 2.0.1
      • QUACPAC 2.0.0
      • QUACPAC 1.7.0
      • QUACPAC 1.6.3
      • QUACPAC 1.5.0
      • QUACPAC 1.3.1
      • QUACPAC 1.3.0
      • QUACPAC 1.1.0
    • molcharge Appendix: Complete list of -method options
    • Citation
  • ROCS 3.6.0.0
    • Introduction
      • Overview
      • Applications
      • Utility Programs
    • ROCS
      • Overview
      • Input Files
      • Example Commands
      • Report File
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • vROCS
      • Overview
      • Setup a simple run and a validation run
      • Results visualization and analysis
      • Statistics metrics
      • Saving ROCS data
      • ROCS shape query sources
      • Editing ROCS queries in vROCS
      • vROCS menus
    • Utilities
      • CheckCff
      • Chunker
      • HLMerge
      • MakeRocsDB
      • ROCSReport
    • ROCS Tutorials
      • Introduction
      • Build/edit a query using the Wizard
      • Build/edit a query manually
      • Perform a ROCS validation run
      • Perform a simple ROCS run
      • Perform a ROCS run from the command line
    • Theory
      • Shape Theory
      • Color Features
      • Color Force Field
      • Similarity Measures
    • Release History
      • ROCS 3.6.0
      • Shape TK 3.6.0
      • ROCS 3.5.1
      • Shape TK 3.5.1
      • ROCS 3.4.3
      • Shape TK 3.4.3
      • ROCS 3.4.2
      • Shape TK 3.4.2
      • ROCS 3.4.1.0
      • Shape TK 3.4.1
      • ROCS 3.4.0
      • ROCS 3.3.2
      • ROCS 3.3.1
      • ROCS 3.3.0
      • ROCS 3.2.2
      • ROCS 3.2.1
      • ROCS 3.2.0
      • ROCS 3.1.2
      • ROCS 3.1.1
      • ROCS 3.1.0
      • ROCS 3.0.0
      • ROCS 2.4.2
      • ROCS 2.4.1
      • ROCS 2.3.1
      • ROCS 2.3.0
      • ROCS 2.2.0
    • List of selected ROCS publications
    • Citation
  • SiteHopper 2.0.3.0
    • Introduction
      • Overview
      • Applications
    • SiteHopper Search
      • Overview
      • GPU Prerequisites
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • SiteHopper build
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Release History
      • SiteHopper 2.0.3
      • Sitehopper TK 2.0.3
      • SiteHopper 2.0.2
      • Sitehopper TK 2.0.2
      • SiteHopper 2.0.1
      • Sitehopper TK 2.0.1
      • SiteHopper 2.0.0
      • SiteHopper TK 2.0.0
      • SiteHopper 1.0.0
    • Citation
  • SPRUCE 1.5.2.0
    • Introduction
      • Overview
      • Applications
      • Utility Programs
      • Utilizing a Loop Template Database
    • SPRUCE
      • Overview
      • Spruce Output Naming Conventions
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Superposition
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • EnumSites
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • GetStructure
      • Overview
      • Example Commands
    • LoopDBBuilder
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • DU2PDB
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Release History
      • SPRUCE 1.5.2
      • Spruce TK 1.5.2
      • SPRUCE 1.5.1
      • Spruce TK 1.5.1
      • SPRUCE 1.5.0
      • Spruce TK 1.5.0
      • SPRUCE 1.4.0
      • Spruce TK 1.4.0
      • SPRUCE 1.3.0
      • Spruce TK 1.3.0
      • SPRUCE 1.2.0.2
      • SPRUCE 1.2.0.0
      • Spruce TK 1.2.0
      • SPRUCE 1.1.0
      • SPRUCE 1.1.0
      • SPRUCE 1.0.0
    • Citation
  • SZMAP 1.6.6.0
    • Introduction
      • Overview
      • Applications
      • Utility Programs
      • A Word About Pronunciation
    • Spruce Before Szmap
      • Overview
    • SZMAP
      • Overview
      • SZMAP Input and Output
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • GamePlan
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Utilities
      • SzmapGrid
      • GridComp
      • SzmapReport
    • VIDA Extensions
      • Introduction
      • Installing VIDA Extensions
      • WaterColor VIDA Extension
      • Water Orientation VIDA Extension
      • Color By Atom Properties
    • Tutorials
      • SZMAP Workflow
      • Protein and Ligand Preparation
      • Running SZMAP Stabilization Calculations
      • Analyzing SZMAP Results
      • Running SZMAP at Coordinates
      • Running Gameplan
    • Theory
      • Philosophy and Design
      • Technical Details
    • Release History
      • SZMAP 1.6.6
      • SZMAP 1.6.5
      • Szmap TK 1.6.5
      • SZMAP 1.6.4
      • Szmap TK 1.6.4
      • SZMAP 1.6.3
      • Szmap TK 1.6.3
      • SZMAP 1.6.2
      • Szmap TK 1.6.2
      • SZMAP 1.6.1.0
      • Szmap TK 1.6.1
      • SZMAP 1.6.0
      • SZMAP 1.5.0
      • SZMAP 1.4.1
      • SZMAP 1.4.0
      • SZMAP 1.3.0
      • SZMAP 1.2.1
      • SZMAP 1.2.0
      • SZMAP 1.1.1
      • SZMAP 1.1.0
      • SZMAP 1.0.0
    • Appendix 1: SZMAP Grids
      • Protein + Ligand Complex
      • Ligand Only
      • Protein Only
      • (Complex - Protein - Ligand) Stabilization
    • Appendix 2: SZMAP Atom Properties
      • Complex, Apo or Ligand
      • (Complex - Protein - Ligand) Stabilization
    • Citation
  • SZYBKI 2.6.0.0
    • Overview
    • Applications
    • Utility Programs
    • SZYBKI
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • FREEFORM
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Theory
      • SZYBKI Theory
      • Freeform Theory
    • Utilities
      • OptLigandInDU
      • OptimizeDU
    • Release History
      • SZYBKI 2.6.0
      • Szybki TK 2.6.0
      • SZYBKI 2.5.1
      • Szybki TK 2.5.1.2
      • Szybki TK 2.5.1.1
      • SZYBKI 2.5.0
      • Szybki TK 2.5.0
      • SZYBKI 2.4.0
      • SZYBKI 2.3.1
      • Szybki TK 2.3.1
      • SZYBKI 2.3.0.2
      • SZYBKI 2.3.0.0
      • Szybki TK 2.3.0
      • SZYBKI 2.2.0
      • SZYBKI 1.11.0
      • SZYBKI 1.10.1
      • SZYBKI 1.10.0
      • SZYBKI 1.9.0
      • SZYBKI 1.8.0
      • SZYBKI 1.7.0
      • SZYBKI 1.5.2
      • SZYBKI 1.5.1
      • SZYBKI 1.5.0
      • SZYBKI 1.3.4
      • SZYBKI 1.3.3
      • SZYBKI 1.3.2
      • SZYBKI 1.3.1
      • SZYBKI 1.3.0
      • SZYBKI 1.2.2
    • Citation
  • VIDA 5.0.4.0
    • Introduction
      • General Concepts
      • Scope
      • Layout
      • Undo / Redo
      • Mouse Map
      • User Directory
      • Help
    • Installation and Platform Notes
      • Enterprise Installation for Windows
    • File I/O
      • Opening Files
      • Closing Files
      • Saving Files
      • Importing Files
      • Exporting Files
      • Drag and Drop
      • Copy and Paste
    • 3D Display
      • User Interaction
      • Rendering
      • Stereo
      • Viewpoint
      • Bookmarks
      • Tiled Display
      • Toolbars
      • Display Widgets
      • Molecular Visualization
      • Grid Visualization
      • Grid Types
      • Reentrant Grids
      • Surface Visualization
      • Symmetry
    • 2D Display
      • Preview vs. Viewer
      • Interaction
      • Advanced Depiction Options
    • Spreadsheet
      • Basic Usage
      • Sorting
      • Displaying Data
      • Organizing Columns
      • Creating New Columns
      • Filtering
      • Statistics
      • Formatting Columns
      • Advanced Depiction Options
      • Importing/Exporting
      • Atom Spreadsheet
      • Residue Spreadsheet
    • List Management
      • Introduction
      • Browsing
      • Views
      • List Columns
      • List Manipulation
    • Processes
      • Processes
      • Pipes
    • Molecule Manipulation
      • Creating Molecules
      • Editing Molecules
    • Custom Views
      • FRED View
      • EON View
      • ROCS View
    • Selection Language
      • Introduction
      • Operators
      • Lists and Ranges
      • Properties
      • Macros/Pre-defined sets
      • Scripting with ScratchScope
    • Scripting
      • Journal File
      • Startup File
      • Scripts Directory
      • Scripting API
      • Scripting Window
      • OpenEye Toolkits
      • Customizing the User Interface
    • Extensions
      • Example Extensions
      • Extension Manager
      • Creating Extensions
      • Distributing Extensions
    • Preferences
    • Menus
      • File
      • Edit
      • View
      • Data
      • Style
      • Bookmarks
      • Tools
      • Select
      • Window
      • Help
    • Examples
      • Data
      • Scripts
    • VIDA Python API
      • General Functions
      • Scope Functions
      • User Interface Functions
      • Display Functions
      • Object Functions
      • Molecule Builder Functions
      • Data Analysis Functions
      • Deprecated Functions
    • Release History
      • VIDA 5.0.4
      • VIDA 5.0.3
      • VIDA 5.0.2
      • VIDA 5.0.1
      • VIDA 5.0.0
      • VIDA 4.4.0
      • VIDA 4.3.0
      • VIDA 4.2.0
      • VIDA 4.1.1
      • VIDA 4.1.0
      • VIDA 4.0.3
      • VIDA 4.0.0
      • VIDA 3.0.0
      • VIDA 2.1.2
      • VIDA 2.1.1
      • VIDA 2.1.0
      • VIDA 2.0.2
    • Citation
  • Glossary
  • Bibliography
Applications-
  • All OpenEye Documentation »
  • Contents »
  • pKa-Prospector 1.2.1.0 »
  • pKa-Prospector »
  • Menu Items

Menu Items¶

Saving Data¶

Under the “File” menu there are various options to save your results to PDF or CSV. “Save Selected as PDF” saves only those rows which have been selected in the results view. Shift clicking and control clicking will select range and individual rows respectively.

Session History¶

The “Session History” menu keeps track of all searches performed during a session. The search results are stored in memory so they can be retrieved quickly, without having to search again.

Query Bookmarks¶

The “Query Bookmark” menu provides a means of saving individual query molecules and current property filter settings. These bookmarks persist between sessions.

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© Copyright 2023, Cadence Design Systems, Inc. (Cadence). Last updated on May 15, 2023.