#13 Off-target Prediction and Toxicity Screening Feature Improvements

Dear Users,

Off-target Prediction and Toxicity Screening results have been improved. The Off-target Prediction CSV files now contain the number of hits for this peptide in healthy samples and across all samples including cell lines and cancer (total samples). Additionally, the Off-target Prediction result contains information about different peptide modifications found. The Toxicity Screening CSV files now also contain more granular information on where the respective peptide was identified (positive) versus total healthy samples of a specific category:

Off-target Prediction CSV file

#11 Off-target Prediction (07.02.25)

Dear user!

We are excited to introduce a major new feature: Off-Target Prediction! This powerful tool allows you to search our database for peptides that may be recognized by TCR/TCRm drug candidates, helping you identify potential safety risks before moving into clinical development with greater precision. Three different workflows further allow for assessment of risks from different angles:

Our database provides a default peptide similarity prediction (1) based on the well established BLOSUM62 scoring matrix, ensuring reliable and efficient peptide comparison. 

For users seeking a more tailored approach, we also support X-SCAN matrices (2) (or similar types of affinity based experimental data) and custom scoring matrices (3), allowing you to fine-tune similarity assessments to your specific research needs.

The output of the analysis workflow provides a ranked list of the 500 peptides identified to be most similar to your query. Additionally, a graphical representation of the results offers intuitive insights into sequence relationships. This output can seamlessly integrate with downstream analyses, such as our Toxicity Screening, enabling deeper exploration of peptide properties.

#10 Inline Intensity Plots (31.10.24)

Dear user!

After a testing period we decided to also directly include the intensity plots of the peptide-centric target validation directly into the user interface. This way, you don’t have to click on the download link anymore and all figures are displayed directly.

#9 New feature – Positional Search and Peptide Information (7.10.24)

Dear User! 

We are excited to announce a new feature for protein/gene-centric target validation that enables you to obtain positional information of peptides within proteins and search for overlapping peptides.

#8 New features – Positional Plots and Enhanced Search Functionality of Target Validation (17.07.24)

Dear Customer! 

We are excited to announce two new features: 

– positional plots for protein/gene-centric target validation and 

– enhanced search functionality of tables.

Positional Plots:

When searching for a certain protein or gene, we now also display a positional plot that shows the relative intensity of peptides from the first matched Uniprot ID in tumor versus healthy samples. As such you can now evaluate if certain epitopes of a gene are preferentially presented in disease samples.

#7 New feature – Protein/Gene-Centric Target Validation (24.05.24)

Dear Customer! 

We are excited to announce our new feature “Protein/Gene-centric Target Validation”. 

This new feature enables you to search the database using UniProt identifiers or gene names, similar to how you search for peptides (see screenshot below). With this feature, exploring the different epitopes of genes and their presentation in health and disease is much easier than ever before. Filtering for HLA alleles further supports the search investigations. 

By clicking on peptides, Uniprot identifier and gene names, you can now easily browse through the data.

#6 Feature Improvement – Cancer Cell Line Plot for Target Validation (27.02.24)

Dear Customer! 

We want to inform you that we have implemented a new plot for cancer cell lines:

#5 Feature Improvement – Additional Plot for Target Validation (09.02.24)

Dear Customer! 

We want to inform you that we have implemented a new plot for primary cells and tissue:

Previous Announcements

#4 New Database Release – v1.6

Dear Customers!

We’re happy to announce that as of now, our database is on version 1.6. The new release introduces new samples for Target Validation and Toxicity Screening, leading to a total amount of 4.160 samples, 1.4+ mio distinct peptides and 74k+ distinct proteins.

Please feel free to contact us if you experience problems.

Kind regards
Alithea Bio Development Team

#3 Change Request – CSV Output of Toxicity Screening (15.12.23)

Dear Customer! 

We want to inform you that the structure of the csv file you can download from toxicity screening now follows the strucure of the heatmap and contains aggregated values. 

Example csv output: 

“Peptide”, “Adrenal Gland”, …. (all remaining category names)

“PEPTIDE”, “1799.3970133463542”, …. (all the mean normalized intensities for each remaining category)

“NEXTPEPTIDE”, … (mean normalized intensities for the next peptide) 

This feature is available since 15.12.2023 17:14 CET. 

Kind regards
Alithea Bio Development Team 

#2 Feature Improvement – Toxicity Screening Category Filtering (11.12.23)

Dear Customer! 

We want to inform you that the total sample count of the categories (x-axis labels) in Toxicity Screening now also respects filtering. For example, the sample count for Adrenal Gland is 27 (cf screenshot #1). With the filter set to A*11:01, the total is 6 (screenshot #2).

#1 Feature Improvement – Protein Information in Target Validation (28.11.23)

Dear Customer! 

We want to inform you that Target Validation results now display related protein information like Uniprot Identifier, gene and protein name and the position of the peptide within the protein (see highlighted area in screenshot).