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Project Management

Effective data organization is crucial for managing antibody campaigns. AbLead uses Projects to group related sequences and structures.

Creating a Project

  1. Navigate to the Dashboard.
  2. Click File > Import Project.
  3. Enter a descriptive Project Name.
  4. (Optional) Add Notes (a description of the project, etc.).

Importing Sequences

To analyze antibodies, you must import sequence data and optionally associate it with structural models (PDB or mmCIF files).

Sequence Format Requirements

Your sequence file must contain the amino acid sequences for the Light and Heavy chains. Minimally the Fv, but full length sequences are recommended. The system automatically detects and supports multiple formats (including FASTA, CSV, FASTQ, GenBank, EMBL, SwissProt, and Clustal).

  • Split Chains: Identify Light and Heavy chains separately.

  • Matching Names (FASTA, FASTQ, etc.): Use the same base name for both chains, appending _LC for Light Chains and _HC for Heavy Chains. This allows the system to automatically pair them into Fvs.

  • CSV Sequence Format (name,seq1,seq2): For CSV files, format each entry with three comma-separated columns: name,seq1,seq2 (headers such as Name,Sequence1,Sequence2 or Name,HC,LC are optional). The system automatically evaluates seq1 and seq2 using sequence annotation models to determine which sequence is Heavy Chain (HC) and Light Chain (LC).

Example (FASTA): 

>Ab001_LC
ESALTQPASVSGSPGQSITI...
>Ab001_HC
EVQLVQSGAEVKKPGASVKV...

Example (CSV): 

name,seq1,seq2
Ab001,EVQLVQSGAEVKKPGASVKV...,ESALTQPASVSGSPGQSITI...
Ab002,DIQMTQSPSSLSASVGDRVT...,EVQLVESGGGLVQPGGSLRL...

Structure Association Logic (PDB & mmCIF)

AbLead automatically associates optionally uploaded or built structure files (PDB or mmCIF) with your Fv sequences based on exact name matching.

  • Rule: If an Fv sequence has the basename Ab001, the system looks for an associated structure file named Ab001.pdb, Ab001.cif, or Ab001.mmcif in your uploaded files.
  • Effect: If a match is found, structural surface properties (SPH, SPP, SPN, SPCD) are calculated. If not, only sequence-based metrics are reported. The associated structure file is also used in the Liabilities analysis.
  • Chain Labels: The structure file should contain both chains, with the Light Chain labeled L and the Heavy Chain labeled H. This is required for the Liabilities analysis.

[!NOTE] Format Normalization & Multi-File Upload: To ensure consistent analysis and visualization across the platform, sequence imports in non-FASTA or tabular formats (such as CSV, GenBank, EMBL, SwissProt, or Clustal) are automatically parsed and converted to FASTA format upon upload (with CSV sequence pairs automatically classified into Heavy and Light chains). Multiple sequence files can be selected and uploaded at the same time; the system automatically merges and parses all entries into a unified dataset. Similarly, all uploaded structure files (including .cif and .mmcif models) are automatically converted and saved to the database in standard PDB format.

Run Analysis

Clicking Run Analysis will run the analysis on the project. Upon completion, the Project View may be displayed, or the dialog may be closed to return to the Dashboard.

Project Sharing

Projects can be shared with other users within the same organization (same email domain) on the system directly from the Project View. If you have the appropriate permissions, clicking Share will open a dialog allowing you to add users by email and define their access level:

  • Read-Only: Shared users can view all project data, run analyses that do not save data (like exporting or viewing variants), but they cannot save any modifications, apply mutations, or delete the project.
  • Write: Shared users have full modification permissions to edit, engineer, and apply mutations to the project.
  • Grant: Shared users can additionally share the project with others and manage their permissions.

Export/Import Project (.zip)

A Project or group of projects may be exported to a .zip file by clicking File > Export Project. This will create a .zip file containing the project name, notes, and all sequences and PDB files associated with the project. An exported Project or group of projects may be imported by clicking File > Import Project (.zip). This will open a dialog allowing you to select a .zip file to import. The project or projects will be imported into the Dashboard of the current user. This feature allows for offline project sharing or storage.

Import Library

Sequence files (supporting FASTA, FASTQ, GenBank, EMBL, SwissProt, and Clustal) containing nucleotide or protein sequences can be validated and selectively imported into projects using the Import Library tool.

  1. Navigate to the Dashboard.

  2. Click File > Import Library.

  3. Enter a Library / Project Name and select the Expected Format (VHH, scFv, Fab, Standard Fv, or Auto-detect).

  4. Upload one or more .fasta, .fastq, .gb, .embl, .swiss, .dat, .aln, .clustal, .txt, .csv, or compressed .gz files (or paste raw sequences).

  5. Click Validate Library to translate nucleotide sequences and run domain checks.

  6. Use the checkboxes or the Bulk Action bar to select your desired clones.

  7. Click Export FASTA or Import Selected to Project to create a project and begin calculations.

Note: Preprocessing raw next-generation sequencing data is outside the scope of a developability and engineering dashboard like AbLead. Before uploading files to AbLead, users should run their raw sequencer outputs through standard upstream bioinformatics pipelines to:

  • Trim Adapters & Quality Filter: Remove low-quality bases and sequencing adapters (using tools like Cutadapt or Trimmomatic).
  • Merge Overlapping Reads: Align and merge R1 and R2 into a single full-length read (using standard assemblers like PEAR, FLASH, or Pandaseq).
  • Isolate Fv/VHH regions: Trim constant regions or primer sequences if necessary.

Deleting and Restoring Projects

Clicking File > Delete Project will delete the project. Clicking File > Trash shows the Trash view. Here the trash may be emptied or project(s) restored to the Dashboard.

Labels, Active Projects & Archiving

Labels are used to group and filter projects. Clicking Labels > New Label will open a dialog allowing you to create and nest custom labels. Clicking Labels > Manage Labels opens a dialog to rename or delete existing user labels (system labels are locked and uneditable). Clicking Labels > Apply Label with selected projects applies or removes selected labels.

Active Projects & Archiving

  • Active Projects: An uneditable system label (Active Projects) acts as the primary dashboard view (similar to an Inbox). All newly created or imported projects are automatically tagged with Active Projects by default.

  • Archiving: Selecting one or more projects in the active dashboard view reveals the Archive icon button ( Archive) in the main toolbar. Clicking Archive removes the Active Projects label from the selected projects, automatically deselecting and hiding them from the active dashboard view while preserving them intact.

  • All Projects View & Unarchiving: Clicking All Projects at the bottom of the labels sidebar displays all non-deleted projects regardless of label. Selecting projects while in the All Projects view displays the Unarchive / Move to Active icon button ( Unarchive) in the toolbar, allowing you to restore the Active Projects label to selected projects.

Global Projects

Global (or Public) Projects are administrator-managed reference projects made available system-wide to all registered users across all domains:

  • Identification: Global projects are marked with a blue Global badge on the main dashboard project list.

  • Access Level: Non-administrator users have Read-Only access to Global projects, allowing complete dataset inspection, visualization, sequence comparison, and data exports without modifying master records.

  • Copy Projects: Users may copy Global projects to their own Dashboard for modification by selecting the Global project(s) and using File > Export Project (.zip). Then click File > Import Project (.zip) and import the exported project(s).

Project Names and Notes

Double click empty space in project name field and or anywhere in a notes field to edit the project name or notes.

Searching Projects and Entries

The Dashboard search bar allows finding projects and individual antibody entries by name, notes, labels, or sequence regions. Additionally, a project-level search bar is available directly inside the Project View's inner toolbar to filter the results table dynamically using the exact same options:

  • 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 find all projects/antibodies with a potential N-glycosylation site in their Variable Heavy chain region.

Logout

Clicking File > Logout will log you out of the application.