Antibody Discovery Suite
The Antibody Discovery Suite comprises the 3D Antibody Modeling Floes and the Specifica AbXtract™ - NGS Antibody Discovery Floes.
The 3D Antibody Modeling floes generate and analyze models for target antibodies. Antibody model generation floes rely on ImmuneBuilder to build models and use SPRUCE to prepare them for downstream modeling applications.
The AbXtract floes provide next-generation sequencing (NGS) antibody discovery in the Orion molecular design platform. AbXtract can process tens of millions of sequences to characterize sequences and extract sequence- and functional-based features to identify promising leads.
- 3D Antibody Modeling Package
- 3D Antibody Modeling Tutorial
- Antibody MD Simulations Tutorial
- Understanding Antibody Surfaces and Annotations
- Antibody SiteHopper-based Clustering Tutorial
- OpenEye 3D Antibody Modeling - Documentation
- Antibody CDR Loop Ensemble Generation
- Antibody Experimental Structure Prep
- Antibody MD Simulations with Conformational Analysis
- Antibody Mutate Residue(s)
- Antibody SiteHopper-based Clustering
- Antibody Structure Relaxation
- Antibody Subset System
- Antibody Surface Patch Generation
- Export Dataset to Fasta
- Humanize Fv Antibodies
- Import Antibody FASTA Files
- Renumber and Restyle Antibody
- Sequences to 3D Models for Fv Antibodies
- Sequences to 3D Models for Nanobodies
- Release Notes
- Bibliography
- AbXtract™ - NGS Antibody Discovery
- Introduction to AbXtract
- Tutorials
- Tutorial 1: NGS Pipeline with Custom Interactive Selection (PacBio), In-Vitro Library
- Tutorial 2: NGS Pipeline with Automated Top Lead Selection (PacBio), In-Vitro Library
- Tutorial 3: NGS and Sanger Pipeline with Automated Top Lead Selection (PacBio), In-Vitro Library
- Tutorial 4: NGS and Sanger Pipeline with Automated Top Lead Selection (Illumina), In-Vitro Library
- Tutorial 5: NGS Pipeline with Automated Top Lead Selection (PacBio), Patient Library
- Tutorial 6: NGS UMIs Extract and Annotation Floe
- Video Tutorials Featuring AbXtract
- How to Guides
- How to Use the Floe Report and NGS Select to Select Population of Interest
- How to Use the Floe Report and SANGER Select to Pick Population of Interest
- How to Condense a Dataset with Too Many Records
- I Performed Enrichment. How Do I Know which Population of My Given Sequence was Found?
- How to Reduce the Number of Fields in the Output
- How to Download the CSV of the Dataset of Records
- How to Visualize Custom Experimental Metrics
- How to upload data from an AIRR-compatible file
- How to export any dataset to an AIRR-compatible file
- Frequently Asked Questions
- Abxtract Floes - Documentation
- AbXtract/AIRR File to Orion Dataset - AbXtract
- Archive To Files
- Automated Top Lead Selection - AbXtract
- Cluster (AbScan) Antibody Binding Regions - AbXtract
- Condense Dataset by Region of Interest by Most Abundant - AbXtract
- Convert floe report to html files
- Custom NGS Select by Seq ID of Additional NGS Representatives by Group - AbXtract
- Custom SANGER Select of Additional NGS Representatives by Group - AbXtract
- Export AIRR Fields for Dataset - AbXtract
- Liability Quantification Across CDRs - AbXtract
- Logomaker for Antibody CDRs - AbXtract
- Modify Sample Name/Barcode Group for Downstream Processing - AbXtract
- Multiple Round Relative Abundance and Enrichment Calculation by Region of Interest (ROI) - AbXtract
- NGS IgMatcher, Annotation Only - AbXtract
- NGS Pipeline - AbXtract
- NGS Pipeline Efficiency - AbXtract
- NGS Pipeline with Automated Top Lead Selection - AbXtract
- NGS UMIs Extract and Annotation - AbXtract
- NGS and Sanger Pipeline - AbXtract
- NGS and Sanger Pipeline with Automated Top Lead Selection - AbXtract
- Overlap Among Different Datasets - AbXtract
- Quick Sanger from ABI Traces - AbXtract
- Quick Sanger from DNA or Amino Acid Sequence Files - AbXtract
- Single Round Relative Abundance and Enrichment Calculation by Region of Interest (ROI) - AbXtract
- Subset the Number of Fields for Export - AbXtract
- Key Fields
- Liability Metric Fields
- Biophysical Metric Fields
- Identifier Fields
- Overlap Fields of NGS to SANGER or NGS
- Enrichment, Abundance and Relative Abundance Fields
- Scaffold / Germline Call Fields
- Clustering Fields
- Annotation Fields
- Sequence Quality Fields
- Special Fields to Add to Upload (Use in Analyze Tool Only)
- AIRR Fields
- 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