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Project View

The Project View provides a summary of all antibodies in the project.

[!NOTE] Multispecific Antibodies: Because multispecific antibodies consist of arbitrary multi-chain constructs (such as bispecifics or CrossMabs), they bypass sequence-level scoring and do not display residue-level stability, surface property, humanness, or liability analysis values in the Project View. For detailed information on designing and managing multispecific constructs, refer to the Assembler documentation.

To run standard analysis and scoring on the individual binding arms of a multispecific entry, you can use the Extract Fvs feature to isolate and save them as individual Fv entries in the project. For details, see the Extract Fvs documentation.

Rather than pulling all of these analyses together manually and building a speadsheet in order to rank order a discovery set and focus on lead selection and optimization, follow my core work principle and Be Inherently Lazy. Pull together your analyses into a single analysis tool and run the tool to do the hard work for you.

Full Project View

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  • Sort & Filter: Click a header sort button to sort or its filter button to enter a filter value. Filtering is context sensitive and can filter by text or value ranges. Click the filter button again to clear a filter. Click the sort button again to sort in the opposite direction.

  • Name: The entry name associated with the analysis. Names may be double-clicked to be edited. If the entry name background is light red, it means that no PDB structure is available for that entry. If the cell contains a small eggshell square in the upper right corner, it means that the entry has engineering mutations.

    • If the entry name is styled in red font, it indicates that the calculation is outdated based on a change in a method or the introduction of a new method which would change the values in the results grid. To update the calculation and restore the font to standard black, select the entry or entries and perform an Analysis > Full Re-run Analysis.

    • If the entry is a Multispecific (has been through the Assembler), it will have a label 'Multispecific' and the analyses will not have been run. To see the individual analyses, use Extract Fvs to create individual Fv entries in the project.

    • If the entry light chain has a constant domain, and is missing or has an extra junction residue, the entry name will be flagged with a descriptive warning stating one of 'Missing R', 'Extra R', 'Missing G', 'Extra G'. Use Edit > Repair Junction to correct these issues and automatically re-run the analysis.

  • Lineage: The parent of the entry. If the entry is a variant, the parent is the antibody it was derived from. These may be set by the user, but are automatically set for Engineering builds.

  • Genetic Origin: The genetic origin and species of the antibody chains. This is determined as the closest germline sequence using sequence identity matching against the platform's embedded germlines database after ANARCI structural alignment. These values are helpful for determining genetic diversity, comparison to known germline stabilities (but that can change with a single mutation), and known germline titer (but that can change with a single mutation). Non-human sequences are shown with a light orange background. Kappa VLs are showin in light Kobicha and Lambda VLs are shown in light Lavender.

    [!NOTE] CDR3 Junction Exclusion: In the Project View, V-gene assignment and species identification ignore the CDR3 junction region (evaluating only IMGT positions 1 to 104). In contrast, the detailed Germline tool's alignment view matches V germlines across positions 1 to 108 (including the CDR3 junction). Because of this difference in region coverage, species assignment or percent identity values between the Project View and the Germline tool alignment can occasionally differ for borderline cases.

  • Nearest Neighbor: The closest sequence to that entry within the set. This is a simple depiction of set diversity. Clading provides a more detailed view of set diversity.

    • Alignment: The residues for each antibody's variable light (VL) and variable heavy (VH) chains are aligned according to the selected numbering scheme (e.g., IMGT, Kabat, AHo, or Martin).
    • Merging: The aligned VL and VH positions are merged to represent the full variable fragment (Fv).
    • Distance Calculation: The sequence distance (p-distance) is calculated between every pair of antibodies in the project using the formula: \(\text{Distance} = 100 \times (1 - \text{Percent Identity})\)
    • Comparable Length: The comparable length (denominator) is the sum of the positions present in the union of both sequences for both chains.
    • Identification: For each entry, the antibody that yields the lowest distance is identified as its Nearest Neighbor.
  • CDR Length: The measured sequence lengths, as well as the summed total, for the CDRs based on the defined region scheme.

  • Stability

    • AbLang, AbLang2, and IgBert: Summed LLM likelihood differences between the parent and most likely residues at each position for full-length sequence and framework positions only. AbLang is a broader LLM while AbLang2 and IgBert remove germline bias. Scoring is based on natural antibody distributions. See AbLang, AbLang2, and IgBert.

      [!NOTE] Single-Chain (VHH / Nanobody) Exception: Since both AbLang2 and IgBert are executed in paired-chain mode, they require both the heavy and light variable domain sequences to perform calculations. When single-chain sequences (like VHH) are analyzed, these models cannot execute and their values are reported as NC (Not Calculated) rather than defaulting to 0.00. The original AbLang model is run in single-chain mode and will still compute scores for heavy-chain-only inputs.

    • Disrupted CDR3 Salt Bridge: Identifies if the canonical HC-CDR3 salt bridge has been disrupted by mutation. This can impact fold stability.

    • Surface Properties
      These are calculated similar to the OPIG TAP method.
    • SPH: Hydrophobicity character of the surface.
    • SPP: Positive charge character of the surface.
    • SPN: Negative charge character of the surface.
    • SPCD: Fv charge interaction character of the surface.
    • Cysteines
    • Cysteine Missing: Identifies if a normal Ig fold cysteine is missing from the sequence.
    • Unusual Cysteine: Identifies cysteines in the sequence that are not in the normal Ig fold positions.
    • Unpaired Cysteine: Identifies unpaired cysteines in the sequence. After structure evaluation this count may be modified directly in the grid or in the Excel export to lower the score (lower is better). Performing a "Full Re-run Analysis" on the entry will reset the value.
    • Potential PTMs
      See LAP: Liability Antibody Profiler by sequence & structural mapping of natural and therapeutic antibodies. Detailed descriptions of these motifs are available in the Satlawa Liabilities Table.
    • Deamidation and Isomerization: If these are realized over time they could degrade antigen binding.
    • N-linked Glycosylation: Identifies potential glycosylation sites. While these could help solubilize the Fv, they may also impact affinity and efficacy if there are differences across productions.
    • Met and Trp Oxidation: Methionine and Tryptophan residues are susceptible to oxidation. If realized over time they could degrade antigen binding.
    • Hydrolysis: Creation from NP to DP during deamidation, which could then isomerize.
    • Fragmentation: Potential cleavage between defined residues.

    • Humanness
      A measure of the VL, VH, and Fv humanness of the sequence.

    • Sapiens: Calculates the mean residue probability score across the variable domain using the Sapiens masked language model. Sapiens thresholds were calibrated using clinical trial anti-drug antibody (ADA) rates from the Immunogenicity Database Collaborative (IDC) dataset, where highly tolerated human therapeutics consistently score ≥ 0.85, whereas immunogenic/chimeric antibodies fall below 0.75.

    • OASign: Calculates the percentage of 9-mers in the sequence that are present in a curated database derived from the Observed Antibody Space (OAS). A higher score indicates a more human sequence.
    • RPEMHC: An MHC-II binding affinity predictor utilizing a sliding 15-mer window over the Fv domain. The score represents the sum of 15-mer binding scores above 0.5 averaged across four major HLA alleles (HLA-DRB1*0101, HLA-DRB1*0301, HLA-DRB1*0401, and HLA-DRB1*1501). While these values are often in the Good range, they are most useful in guiding de-immunization engineering.

    [!IMPORTANT] Integrated Immunogenicity Assessment: Sapiens, OASign, and RPEMHC must be evaluated in conjunction for a complete developability profile. OASign and Sapiens quantify sequence humanness (which corresponds to T-cell receptor self-tolerance), whereas RPEMHC predicts physical peptide presentation to human MHC-II. A therapeutic candidate is only safe if it scores well on both metrics: a "Good" (Green) RPEMHC score on a sequence with low humanness (such as a mouse sequence) is still highly immunogenic in patients because there is no self-tolerance for the presented peptides.

  • Score
    The score of the entry, calculated based on the analyses performed. This value may be used for rank ordering the set. The function used in the score calculation is exposed in the Excel output. The values and weights used for the KBC score may be customized in the KBC Scoring Preferences section. Users can save, rename, and manage multiple named scoring sets (presets) to dynamically apply different weight configurations. A permanent 'KBC Default' preset serves as the read-only baseline default. In custom presets, rules are fully customizable (you can add new rules for any biological/physical attribute, edit their operator conditions, and delete existing ones). Publishing new rules or deleting a rule will automatically save changes to the database instantly. The active scoring preset for each project can be selected directly using the Scoring dropdown menu in the project view toolbar. Projects default to 'KBC Default' (ignoring any active selection in Scoring Preferences) unless a custom preset is explicitly assigned to that project. If an assigned custom preset is deleted, the project reverts automatically to 'KBC Default'.

  • Format Preferences & Presets
    Conditional formatting ranges for all standard results columns (e.g., SPH, Sapiens, pI, CDR lengths, and liabilities) can be customized by navigating to Format Preferences in the user menu. Similar to Scoring Preferences, users can configure comparison operators, threshold values for Good, Low, Med, and High severities, and save them as named formatting sets. A read-only "KBC Default" preset serves as the baseline formatting template. Active formatting presets can be assigned to a project using the Format dropdown menu in the project view toolbar. Setting a format preset dynamically colors the results dashboard grid cells and applies corresponding native conditional formatting rules to Excel exports. If a custom formatting preset is deleted, projects using it automatically revert to "KBC Default".

  • Notes
    User-editable notes for each entry. Double-click the cell in the grid to edit. Notes are saved to the database and persisted across analysis re-runs and engineering modifications. They are also included in the Excel and CSV exports.

  • Custom Metadata Columns
    Users can upload or define custom metadata columns (such as assay data, affinity measurements, or internal identifiers) directly to the project view:

    • Upload Metadata: Available under Edit > Upload Metadata.... Matches uploaded row names against existing antibody entry names. Column types (text, integer, float) are automatically inferred, and scientific notation formats (e.g., 32.4e-8) are normalized to standard scientific notation (e.g., 3.24e-7).
    • Overwrite Warnings: If the uploaded file contains columns that already exist in the project, a confirmation modal warning that "Duplicate columns will be overwritten" will appear. Click OK to overwrite the values or Cancel to not import.
    • Format & Renaming Settings: Click the settings gear icon in a custom column header to open the Format Settings modal. Here, you can rename the column title or configure the display format/notation:
      • Text: Displays values as plain text.
      • Integer: Displays values formatted as whole numbers.
      • Decimal Float: Displays values formatted as decimals (e.g., %.2f for two decimal places).
      • Scientific Notation: Displays values formatted in standard exponential notation (e.g., %e).
      • Custom: Allows you to enter a custom printf-style format string (e.g., %i or %.3f).
    • Conditional Formatting Settings: Define severity threshold values (Good, Low, Med, High) to dynamically color cell backgrounds in both the results grid and the exported Excel spreadsheet (applied as native rules):
      • Good: Green background.
      • Low: Yellow background.
      • Med: Orange background.
      • High: Red background.
      • Comparison Operators: Users can select explicit comparison operators (>=, >, <=, <, =, !=) next to each threshold, giving complete control over rules even when only a single severity level is defined.
    • Inline Editing: Double-click any custom metadata cell in the grid to edit its value directly. Cells dynamically recalculate and refresh their color and decimal formatting in real-time.
    • Deleting Columns: Click the trash/delete icon in a custom column header to permanently delete the metadata column and its associated records from the project schema.
    • Rearranging Columns: Drag and drop the column headers to rearrange the order of the columns.

  • Analysis

    • Alignment: Opens the sequence alignment viewer to compare sequences with selected reference numbering and region schemes.
    • Clading: View hierarchical clustering tree diagrams and cladograms of sequences to evaluate panel sequence diversity.
    • Liabilities: Opens the liabilities profile dashboard displaying sequence potential liabilities and structural hot-spots.
    • Germline: Opens the detailed germline alignment comparison view for selected antibody chains.
    • Humanness: Open the OASign humanness score comparison panel.
    • PFA: Opens the Positional Frequency Analysis grid viewer to inspect residue frequencies and deep-learning suggestions.
    • Covariance: Opens the covariance analysis viewer to investigate and repair broken residue-pair constraints.
    • Mutation Grid: Opens a grid highlighting mutations relative to specific parents across engineered designs.
    • Physical Properties: Opens the Fv properties grid detailing charges, pI values, and molecular weights.
    • Solvent Exposures: View structural residue solvent exposure values (relative SASA and SASA) mapped from Fv models.
    • Surface Properties: Opens the surface properties workspace to inspect SPH, SPP, SPN, and SPCD surface hotspot patches.
    • Clinical Comparison: Compares project sequence properties and coordinates with therapeutic antibodies in clinical development.
    • PLAbDab Search: Query the patent and literature antibody database for sequence similarities.
    • Observations: View structural observation flags, mutations, and design metadata.
    • Full Re-run Analysis: Triggers a clean re-run of sequence calculations and profiles, refreshing intermediate caching results.

  • Edit

    • Upload Metadata...: Upload assay values, affinity data, and custom columns to the project grid. Matches entries automatically by name.
    • Add Fvs and/or PDBs...: Add entries to the project and/or add PDBs to existing entries.
    • Assembler: Open the Assembler interface for the selected Fvs.
    • Humanization: Open the Humanization interface for the selected Fv.
    • Bulk Humanize...: Humanize multiple selected antibodies in a single batch.
    • Engineering: Open the Engineering interface for the selected Fv.

    • First Pass Optimize: Automatically scan for and design mutations to resolve severe developability liabilities in a single step. For the selected antibody entry, this runs severe liability checking rules and generates a target mutation design set under Engineering named "First Pass Optimize" using the following rules:

      • Unusual Cysteines (C): Mutated to Serine (S).
      • Deamidations (N): Mutated to Glutamine (Q).
      • Isomerizations or Fragmentations (D): Mutated to Glutamic Acid (E).
      • Language Models / CVV: Selects the highest probability or frequency alternative residue.
      • Exclusion Areas: Preserves the parent residue at structural Honegger exclusion positions and Vernier positions (setting includeParent: true so the parental residue is kept in the design set).
      • CDR Exclusions: Skips language model (AbLang/AbLang2/IgBert/CVV) liabilities that fall within CDR regions, matching the default "Select Severe" settings.

    • Engineer pI: Open the pH interface for the selected Fv.

    • Surface Mutagenesis: Opens the surface mutagenesis workspace to design variants with modified surface properties.
    • Repair Junction: Automatically correct junctions on constant-containing light chains.
    • Set Parent...: Set or clear the parent of the selected entries.
    • Bulk Edit Notes...: Update notes for multiple selected antibodies at the same time.
    • Extract Fvs: Extract variable domains (Fv pairs) from the selected antibodies.
    • PDB Files: Open the PDB Files interface to download or delete PDB files.
    • Build Models: Generate 3D structural Fv or VHH models for the selected entries.
    • Delete Selected: Delete the selected entries from the project and database.
    • Export
    • Excel: Export the selected entries to an Excel file with conditional formatting and scoring.
    • CSV: Export the selected entries to a CSV file.
    • Analysis Report: Export the selected entries to a Word document analysis report.
    • Sequences: Visualize or export the selected entries' sequences in multiple formats.
    • WIPO ST.26 (Patent)...: Create a WIPO ST.26 (Patent Sequence Listing) formatted sequence data file for patent applications.
    • Share: Open the sharing dialog to grant or manage access to the project for other users within the same organization (same email domain) (requires appropriate permissions). Sharing may also be performed from the main Dashboard.

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Conditional Formatting Rules

To help evaluate antibody developability and lead selection at a glance, the Project View applies color-coded conditional formatting based on established ranges and thresholds:

Metric / Value Good (Green: #88B46C) Low / Medium (Yellow: #F8D548 / Orange: #E29848) High / Alert (Red: #CF4A3C)
KBC Score ≤ 16.4 Orange: 25.2 < Score ≤ 34.0
Yellow: 16.4 < Score ≤ 25.2		 > 34.0
Nearest Neighbor ≥ 10.0% Yellow: 5.0% < Distance < 10.0% ≤ 5.0%
Sapiens (Humanness) ≥ 0.85 Yellow: 0.75 ≤ Score < 0.85
Orange: 0.65 ≤ Score < 0.75		 < 0.65
OASign (Humanness) ≥ 0.85 Yellow: 0.75 ≤ Score < 0.85 < 0.75
RPEMHC VL / VH ≤ 28.0 Yellow: 28.0 < Score ≤ 35.0 > 35.0
RPEMHC Fv ≤ 24.0 Yellow: 24.0 < Score ≤ 28.5 > 28.5
AbLang (Full) ≤ 78.23 Yellow: 78.23 < Score ≤ 101.82 > 101.82
AbLang FR ≤ 39.45 Yellow: 39.45 < Score ≤ 59.55 > 59.55
AbLang2 (Full) ≤ 8.74 Yellow: 8.74 < Score ≤ 13.11 > 13.11
AbLang2 FR ≤ 4.58 Yellow: 4.58 < Score ≤ 8.03 > 8.03
IgBert (Full) ≤ 9.36 Yellow: 9.36 < Score ≤ 17.11 > 17.11
IgBert FR ≤ 4.33 Yellow: 4.33 < Score ≤ 10.32 > 10.32
Covariance (CVV Full) ≤ 12.0 Yellow: 12.0 < Score ≤ 46.0 > 46.0
Covariance (CVV FR) ≤ 4.0 Yellow: 4.0 < Score ≤ 15.0 > 15.0
SPH (Hydrophobicity) ≤ 100.91 (75th percentile) Yellow: 100.91 < Score ≤ 113.34 > 113.34 (95th percentile)
SPP (Positive Charge) ≤ 0.57 (75th percentile) Yellow: 0.57 < Score ≤ 1.00 > 1.00 (95th percentile)
SPN (Negative Charge) ≤ 0.33 (75th percentile) Yellow: 0.33 < Score ≤ 1.15 > 1.15 (95th percentile)
SPCD (Charge Interaction) ≥ -2.3 (25th percentile) Yellow: -11.4 ≤ Score < -2.3 < -11.4 (5th percentile)
pI 8.0 ≤ pI ≤ 10.0 Yellow: 7.6 ≤ pI < 8.0 or 10.0 < pI ≤ 11.0 < 7.6 or > 11.0
Disrupted CDR3 Salt Bridge 0 (Intact) - ≥ 1 (Disrupted)
Cysteines / Potential PTMs 0 detected Orange: 2 detected
Yellow: 1 detected		 ≥ 3 detected
CDR-L1 Length 11 to 14 Yellow: 10 or 15 to 17 < 10 or > 17
CDR-L2 Length 8 - ≠ 8
CDR-L3 Length 9 to 11 Yellow: 7 to 8 or 12 to 13 < 7 or > 13
CDR-H1 Length 13 to 16 - < 13 or > 16
CDR-H2 Length 9 to 12 - < 9 or > 12
CDR-H3 Length 11 to 16 Yellow: 5 to 10 or 17 to 30 < 5 or > 30
CDR Length Sum 64 to 78 Yellow: 53 to 63 or 79 to 93 < 53 or > 93

Additionally, cell backgrounds are colored for specific designations: - Non-Human Origin: Light Orange (#E29848 equivalent or tinted) - Kappa Variable Light (VL): Light Kobicha - Lambda Variable Light (VL): Light Lavender

Searching Entries

A project-level search bar is available directly inside the Project View's inner toolbar to filter the results table dynamically using substrings, motifs, or region-level scopes:

  • Standard Search: Enter any name, note substring, label, or sequence subsequence (e.g., EVQLV) to find matching records.
  • PROSITE Motif Search: Enter NCBI/PROSITE regular expression motifs (e.g., N{P}[ST]{P}) to scan sequences for complex patterns.
  • Domain Modifiers: Appending a suffix scope restricts sequence searches to specific regions:
    • .Fv: Restricts sequence search to both variable domains (Variable Heavy + Variable Light).
    • .VH: Restricts sequence search to the Variable Heavy domain only.
    • .VL: Restricts sequence search to the Variable Light domain only.

Example: Searching for N{P}[ST].VH will filter the table to show only antibodies with a potential N-glycosylation site in their Variable Heavy chain region.

References