Small Molecule Discovery¶
- Biomolecular Modeling
- Tutorials
- Biomodeling Floes - Documentation
- OEBioModeler
- Build Sidechains
- Cap Chain Breaks
- DU to Mol
- Enumerate Pockets on Design units
- Extract Biological Units
- Minimize Design Unit
- Mutate Residue(s)
- Protonate DU and structures
- Residue State Changer
- Rotamers of a Residue
- Subset DesignUnit
- Subset DesignUnit Within
- Superpose DUs
- Swap Metal(s)
- Update DU Content
- SiteHopper
- OEBioModeler
- Release Notes
- Cheminformatics
- Classic Floes - OpenEye Applications in Orion
- Tutorials
- How To Guides
- Frequently Asked Questions
- OpenEye Classic Floes - Documentation
- OEClassic
- BROOD - 3D Fragment Replacement
- EON - Shape Alignment and Electrostatic Similarity Scoring
- Fingerprint Search - Small Scale 2D Similarity
- FreeForm - Aqueous Ligand Configurational Free Energies with SZYBKI
- FreeForm - Bound Ligand Configurational Free Energies with SZYBKI
- FreeForm - Ligand Solvation Energies with SZYBKI
- GamePlan - Ligand Design with Water Analysis using SZMAP
- OEDocking - Dock into an Active Site for Virtual Screening
- OMEGA - 3D Conformer Ensemble Generation
- OMEGA - Conformer Generation for Macrocycles
- OMEGA - Generate a Single 3D Conformer
- POSIT - Ligand Guided Small Molecule Posing
- ROCS - Shape Based Alignment for Virtual Screening
- ROCS Query Model Builder
- ROCS, FastROCS - Import Shape Query to Record
- Receptor In DU
- SPRUCE - DesignUnit Format Type Updater
- SPRUCE - Import Prepared PDB Files
- SPRUCE - Protein Preparation from PDB Codes
- SPRUCE - Protein Preparation from PDB Files
- SZYBKI - Ligand Minimization in a Flexible Active Site
- SZYBKI - Ligand Minimization in a Rigid Active Site
- SZYBKI - Small Molecule Hydrogen-Only Minimization
- SZYBKI - Small Molecule Minimization
- Substructure Search - Small Scale Substructure Matching
- OEClassic
- Release Notes
- Database Preparation & Science Floes
- Format Conversion
- Orion ETL Floes - Documentation
- Release Notes
- v2.0.0 November 2021
- v1.2.9 November 2021
- v1.2.8 October 2021
- v1.2.7 October 2021
- v1.2.6 June 2021
- v1.2.5 June 2021
- v1.2.4 November 2020
- v1.2.3 August 2020
- v1.2.2 April 2020
- v1.2.1 March 2020
- v1.2.0 February 2020
- v1.1.1 October 2019
- v1.1.0 August 2019
- v1.0.0 July 2019
- v0.1.29 April 2019
- v0.1.28 February 2019
- v0.1.27 February 2019
- v0.1.26 February 2019
- v0.1.25 January 2019
- v0.1.24 December 2018
- v0.1.23 November 2018
- v0.1.22 November 2018
- v0.1.21 October 2018
- v0.1.20 October 2018
- v0.1.19 October 2018
- v0.1.18 September 2018
- v0.1.17 September 2018
- v0.1.16 September 2018
- v0.1.15 September 2018
- v0.1.14 September 2018
- Generative Chemistry
- Generative Structure Floes - Documentation
- Release Notes
- Large Scale Floes
- Tutorials
- How-to Guides
- Run Giga Docking on Billions of Molecules
- Estimate the cost of a Giga Docking Run
- Determine if Giga Docking Will Give Good Results with a Given Receptor
- Edit a Receptor
- Generate a Giga Docking Hit List Datast of More Than 10K Molecule
- Prepare Molecules in a CSV File for GigaDocking and FastROCS
- Edit a Receptor
- Restart a Giga Docking Job That Stopped Due to Cost
- Get Access To Full Vendor Giga Docking Collections Prepared by OpenEye
- Floe Reference Material
- Explanations
- Release Notes
- Molecular Dynamics Affinity Package
- Introduction
- MD Affinity Tutorials
- MD DataRecord
- MDOrion Floes - Documentation
- Binding Free Energies
- General MD
- Protein-Ligand MD
- Analyze Protein-Ligand MD [MDAnalysis]
- Bound Protein-Ligand MD [MDPrep] [MDRun]
- Convert MD Analysis results to Cluster-Centric Dataset [Utility]
- Extract Short Trajectory MD Results for Download [Utility]
- Ligand Bound and Unbound Equilibration for NES [MDPrep] [MDRun]
- MD API Dataset Converter [Utility]
- Short Trajectory MD with Analysis [MDPrep] [MDRun] [MDAnalysis]
- oemdaffinity.cubes - Cube Documentation
- Analysis
- Cluster Ligand Traj OEMol
- Compute BintScore for Initial Pose and Trajectory
- Concatenate Trajectory MMPBSA Energy Components
- Conf Trajs To Ligand Traj
- Generate Ligand Floe Report HTML from Protein-Ligand MD Traj Analysis.
- MD Conformer Gathering Data
- MDExtractDataCube
- MDFloeReportCube
- MDFloeWriteClusterCentricDataset
- Make Cluster Protein and Ligand average and median OEMols
- NMax Waters
- Population Analysis of Traj Clusters
- Prepare the Traj Analysis Dataset for Reporting
- STMD Result to File
- STMD Result to Tarball File
- Traj to OEMol Cube
- Trajectory Interaction Energies
- Trajectory Poisson-Boltzmann and Surface Area Energies
- FEC Analysis
- Free Energy
- MD Simulations
- RBFE Analysis
- Relative Free Energy
- Analysis
- Release Notes
- Molecular Dynamics Core Package
- Permeability Floes
- Quantum Mechanics Psi4 Floes
- Psi4 QM Floes
- Psi4 Floes
- Psi4 QM Atom Indices Torsion Scanning
- Psi4 QM Complete Molecule Torsion Scan
- Psi4 QM Conformer Ensemble
- Psi4 QM Fragmentation and Torsion Scanning
- Psi4 QM Geometry Optimization
- Psi4 QM Interaction Energy
- Psi4 QM Local Minima Search
- Psi4 QM Property Calculation
- Psi4 QM SMARTS Torsion Scan
- Psi4 QM Tautomer Floe
- Psi4 QM UI Atom Selection Torsion Scanning
- Psi4 QM Vacuum Entropy Floe
- Psi4 Updater Floes
- Psi4 Floes
- How-To Guides
- Frequently Asked Questions
- Psi4 QM Cubes
- Release Notes
- Bibliography
- Psi4 QM Floes
- Reagent Enumeration
- Snowball - The Primary OpenEye Cube Library
- snowball - Cube Documentation
- 2D Depiction
- 2D Similarity
- 3D Similarity
- Cheminformatics
- Atom-Bond Typing
- Atropisomerism
- Dipole Moment Calculation
- InChI
- Maximum Common Substructure Search
- Molecular Complexity
- Molecular Descriptor
- Molecule Alignment
- Molecule Annotation and Tagging
- Molecule Filtering
- Molecule Manipulation
- Molecule Naming
- Molecule Processing
- Molecule Property Calculation
- SMILES
- Substructure Search
- Conformations
- Debugging
- Floe Report
- Library Design
- Ligand Based Design
- Ligand Modeling
- Ligand Preparation
- Logic
- MMDS
- Models
- Protein Ligand
- SiteHopper
- Spruce
- Structure Based Design
- Surface
- Unclassified
- Utility
- Add Boolean Field
- Add Design Unit Field
- Add Query Style
- Check Design Unit
- Convert Conformers to Mols
- Convert Shape Query to Record
- Dataset Reader Optional
- Dataset Size Router
- Exception Handler
- Failure Report
- Field Type Conversion Cube
- Find Ligand
- Find Protein
- Find Receptor
- Find ShapeQuery
- Molecule Counter
- Named Collection Reader
- Named Dataset Reader
- Named File Reader
- Pass Query molecules to top of output
- Pass Query to top of output
- Process Every N records
- Process N records
- Protein Preparation Issues Detector
- Protein Preparation Report
- Shard Reader Optional
- Single File Reader
- String Parameter to String Field
- Success Counter
- Success Counter Shard
- Release Notes
- v0.23.1 December 2021
- v0.20.1 June 2021
- v0.20.1 November 2020
- v0.19.3 August 2020
- v0.19.1 August 2020
- v0.18.2 April 2020
- v0.17.2 November 2019
- v0.16.6 September 2019
- v0.16.0 July 2019
- v0.15.0 June 2019
- v0.14.0 June 2019
- v0.13.6 March 2019
- v0.13.4 November 2018
- v0.13.3 September 2018
- v0.13.0 August 2018
- snowball - Cube Documentation