Lead Optimization Module
Lead Optimization is the final phase of the chemistry part of the drug discovery process. During lead optimization, the structures of candidate molecules are manipulated to achieve an optimal balance between a variety of properties including target selectivity, potency, efficacy, and safety. Computational methods used in lead optimization include estimation of ADMET properties and binding affinity, identification of ligand binding hotspots, and accurate binding mode prediction.
OpenEye solutions in the Lead Optimization Module include Machine Learning, 3D-QSAR, Molecular Dynamics, Freeform, SZMAP, BROOD, Permeability, and POSIT.
- Lead Optimization Overview Tutorial
- 3D QSAR Modeling Floes
- Classic Lead Optimization Floes
- Introduction
- Tutorials
- Classic Lead Opt Floes - Documentation
- BROOD - 3D Fragment Replacement
- BROOD - 3D Fragment Similarity
- BROOD - DB File to Collection
- BROOD - Fragments Conformer Generation
- BROOD - Query Builder
- CHOMP - Generate BROOD Fragment Database
- Calculate Atropisomerism
- FreeForm - Aqueous Ligand Configurational Free Energies with SZYBKI
- FreeForm - Bound Ligand Configurational Free Energies with SZYBKI
- GamePlan - Ligand Design with Water Analysis using SZMAP
- POSIT - Ligand Guided Small Molecule Posing
- Classic Lead Optimization Release Notes
- Generative Design Hit-to-Lead Floes
- Introduction
- Generative Design Floe Tutorials, Hit-to-Lead
- Floe Reference Documentation
- Reaction & Reagent Database - Create from BULK SMILES
- Reaction & Reagent Database - Create from Dataset
- Reaction & Reagent Database - Create from ZINC Download
- Reaction & Reagent Database - Directory Listing
- Reaction & Reagent Database - Launch Product Enumerations
- Reaction & Reagent Database - Product Enumeration Summary
- Reaction & Reagent Database - Reagent Molecule Classification
- Reaction & Reagent Database - Retrieve Reaction Reagents
- Release Notes
- Legacy Release Notes
- Generative Design Lead Optimization Floes
- Introduction
- Generative Design Floe Tutorials, Lead Optimization
- Floe Reference Documentation
- Focused Library - Core Input
- Focused Library - Molecule Input
- Focused Library - Reagent Join
- Focused Library - Synthon Analogs
- Generative Structure Floe
- Generative Structure Floe - Site selection
- Generative Structure Indexing - Graft Database Generator
- Generative Structure Indexing - MMP Molecule Indexer
- Generative Structure Indexing - MMP Transform Extractor
- Release Notes
- Legacy Release Notes
- Large Scale Floes Hit-to-Lead
- Machine Learning Model Building Floes
- Introduction
- Tutorials
- Tutorials to Build Machine Learning Models
- ML Build: Regression Model with Tuner using Fingerprints for Small Molecules
- ML Build: Cheaper and Faster Machine Learning Regression Models with Tuner using Fingerprints for Small Molecules
- ML Build: Classification Model with Tuner using Fingerprints for Small Molecules
- ML Build: Regression Model with Tuner on User-Based Feature Vector Input
- ML ReBuild: Transfer Learn ML Regression Model Using Fingerprints for Small Molecules
- Tutorials to Predict Molecules based on trained Machine Learning Models
- ML Predict: Use Pretrained Regression Models to Predict Properties of Molecules
- ML Predict: Use Pretrained Classification Fingerprint Model to Predict Properties of Molecules
- ML Predict: Regression using Feature Input Floe
- Predict the Solubility of Small Molecules
- Predict hERG Toxicity of Drug-Like Molecules
- How-To Guides
- Floe Reference Documentation
- Data Processing of Small Molecules for ML Model Building
- ML Build: Regression Model with Tuner using Fingerprints for Small Molecules
- ML Build: Classification Model with Tuner using Fingerprints for Small Molecules
- ML Build: Regression Model with Tuner using Feature Input
- Solubility Prediction for Small Molecules using ML and Cheminfo Fingerprints
- ML Predict: Regression using Fingerprints for Small Molecules
- ML Predict: Classification using Fingerprints for Small Molecules
- ML Predict: Regression using Feature Input
- ML ReBuild: Transfer Learn ML Regression Model using Fingerprints for Small Molecules
- hERG Toxicity Prediction for Small Molecules using ML and Cheminfo Fingerprints
- ML Predict: XGBoost for Small Molecules
- Theory
- FAQs
- Bibliography
- Release Notes
- Legacy Release Notes
- Molecular Dynamics Affinity Package
- Introduction
- How-To Guide and Tutorials
- MD Affinity Floes - Documentation
- Analyze Protein-Ligand MD [MDAnalysis]
- Associate Force Field Offxml Files With Ligand Record [Utility]
- Bound Protein-Ligand MD [MDPrep] [MDRun]
- Compare Experimental Affinity with End Point Analysis Results [Utility]
- Compare Induced-Fit Posing (IFP) Results to Target Receptor [IFP] [IFD] [Induced-Fit Docking]
- Convert MD Analysis results to Cluster-Centric Dataset [Utility]
- Edge Mapper for RBFE calculations [FECalc]
- Equilibration and Nonequilibrium Switching [MDPrep] [MDRun] [FECalc]
- Extract Short Trajectory MD Results for Download [Utility]
- Induced-Fit Posing (Confined) [IFP] [IFD] [Induced-Fit Docking]
- Induced-Fit Posing (IFP) Prep: Pruning reference receptor for docking [IFP] [IFD] [Induced-Fit Docking]
- Ligand Bound and Unbound Equilibration for NES [MDPrep] [MDRun]
- MD API Dataset Converter [Utility]
- NES Result Utilities [Utility] [FECalc]
- Nonequilibrium Switching Recovery [Utility] [FECalc]
- Nonequilibrium Switching [MDRun] [FECalc]
- Plain Gromacs [MDRun]
- Plain Molecular Dynamics [MDRun]
- Short Trajectory MD with Analysis [MDPrep] [MDRun] [MDAnalysis] [STMD]
- Solvate and Run MD [MDPrep] [MDRun]
- Molecular Dynamics Affinity Release Notes
- Legacy Release Notes
- v 6.4.4 October 2024
- v 6.4.3 July 2024
- v 6.3.6 April 2024
- v 6.2.1 February 2024
- v 6.1.7 September 2023
- v 6.1.4 September 2023
- v 6.1.2 July 2023
- v 6.0.3 April 2023
- v 5.6.1 December 2022
- v 5.5.3 September 2022
- v 5.5.0 July 2022
- v 5.0.5 April 2022
- v 5.0.3 December 2021
- v 4.0.1 June 2021
- v3.0.1 November 2020
- v2.0.0 September 2020
- v1.0.0
- v0.9.6
- v0.9.4
- Permeability Floes
- Protein Modeling Floes
- Quantum Mechanics Psi4 Floes
- Psi4 QM Floes
- Psi4 HF3c Dipole Moment
- 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
- How-To Guides
- Frequently Asked Questions
- Release Notes
- Bibliography
- Psi4 QM Floes
- Small Molecule Modeling Floes
- Introduction
- Tutorials
- Small Molecule Modeling - Documentation
- 2D Diverse Subset
- 2D Hitlist Clustering
- 3D Diverse Subset
- 3D Hitlist Clustering
- Annotate Docking Hits by Interactions from Single Source
- DBSCAN 2D Similarity Clustering
- DBSCAN 3D Similarity Clustering
- Dataset Classification – Bemis-Murcko
- EON - Shape and Electrostatic Similarity Alignment
- Filter Docking Hits by Interactions
- Fingerprint Search - Small Scale 2D Similarity
- FreeForm - Ligand Solvation Energies with SZYBKI
- Hierarchical 2D Similarity Clustering
- Hierarchical 3D Similarity Clustering
- K-Medoids 2D Similarity Clustering
- K-Medoids 3D Similarity Clustering
- Large Scale 2D Similarity Clustering
- Large Scale 3D Similarity Clustering
- MultistatePKaModel Based Ionization States Enumeration Floe
- OEDocking - Dock into an Active Site for Virtual Screening
- OMEGA - Conformer Generation for Macrocycles
- ROCS - Shape Based Alignment for Virtual Screening
- ROCS Query Model Builder
- SZYBKI - Ligand Minimization in a Flexible Active Site
- SZYBKI - Ligand Minimization in a Rigid Active Site
- SZYBKI - Single point MMPBSA
- SZYBKI - Small Molecule Minimization
- Small Molecule Modeling Release Notes
- AI Fold Floes
- Format Conversion
- Orion ETL Floes - Documentation
- Legacy Release Notes
- v6.3.0 August 2024
- v6.3.1 September 2024
- v6.3.0 August 2024
- v6.2.0 June 2024
- v6.1.2 February 2024
- v6.0.0 September 2023
- v2.3.0 July 2023
- v2.1.3 February 2023
- v2.1.2 November 2022
- v2.1.1 September 2022
- v2.1.0 July 2022
- v2.0.2 February 2022
- v2.0.1 December 2021
- 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
- Format Conversion (ETL) Floes Release Notes
- Utility Floes
- Introduction
- Tutorials
- How To Guides
- Utility Floes - Documentation
- Build Sidechains
- Calculate Dipole Moment
- Cap Chain Breaks
- DU to Mol
- DU to PDB
- Dataset Append – Generating SMILES Field
- Dataset Deduplication – Based on Molecule, String, Integer, or Float Field
- Dataset Deduplication – Merge
- Dataset Filtering – Create Custom Filter
- Dataset Filtering – Custom or Built-in Filter Types
- Dataset Manipulation – Add Molecule Title Field
- Dataset Manipulation – Add Title to Molecule Field
- Dataset Manipulation – Concatenation
- Dataset Manipulation – Field Rename
- Dataset Manipulation – Field Type Conversion
- Dataset Subsetting – Random Splitting Or Selection
- Dataset Subsetting Based on Dataset, Numerical, String, or Regex Field
- Dataset Subsetting Based on String Keys
- Extract Biological Units
- Generate 2D Similarity Matrix
- Generate 3D Similarity Matrix
- Generate Fingerprints
- Generate User-Defined Fingerprints
- Generate and Deduplicate SMILES for One or More Datasets
- Minimize Design Unit
- Mutate Residue(s)
- OMEGA - 3D Conformer Ensemble Generation
- OMEGA - Generate a Single 3D Conformer
- Protein Loop Modeling or Re-modeling
- Protonate DU and structures
- QUACPAC - Partial Charges
- ROCS, FastROCS - Import Shape Query to Record
- Receptor In DU
- Residue State Changer
- Rotamers of a Residue
- SPRUCE - Import Prepared PDB Files
- SPRUCE - Protein Preparation
- Subset Design Unit
- Subset Design Unit Within
- Subset Design Unit to Smallest Binding Unit
- Substructure Search - Small Scale Substructure Matching
- Superpose DUs
- Swap Metal(s)
- Update DU Content
- Utility Floes Release Notes
- Historical Release Notes