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what it does

PepSee is a software tool for interactive, visual compound prioritization as well as the design of next-generation peptide therapeutics. Peptide design ideally supports a multi-parameter optimization to maximize the likelihood of success. PepSee visualizes the relevant parameters at hand, side by side with the sequence data. Color-coded display stimulates SAR exploration.
The main features of PepSee comprise:

  • comfortable sequence & data import (from Excel, FASTA, PLN, Text, even PDF)
  • automated as well as manual sequence alignment
  • various data coloring and plotting options
  • organizing and annotating your compounds
  • interactive design of novel peptides

over Excel

The vast majority of peptide analytics and design today is done in Excel. But as soon as the length and number of sequences grows and more and more data accumulates, Excel is not adequate anymore. Here is a comparison:

feature Excel PepSee
assembling tabular data
easily focus on the rows and columns of interest
live data plots
compounds organized in groups
automated alignments that can still manually be tweaked
highlighting/filtering based on sequence motifs
various color-coding options for the sequence data


Dr. Torsten Hoffmann, COO Silence Therapeutics, former CSO Zealand Pharma and CSO Proteros biostructures
PepSee is filling an enormous gap in peptide therapeutics analysis and design.

Dr. Frosty Loechel, Evotec
I was doubtful in the beginning — but you guys really delivered with PepSee.

Keld Fosgerau, PhD, CSO, Gubra aps
It was a great pleasure to have contributed to this creative project with you guys.

Jan Holst Jensen, PhD, CEO and Founder of BiochemFusion
A sheer pleasure! — And PepSee works beautifully with our database tools.

Marie Skovgaard, PhD, Director Medicinal Chemistry at Zealand Pharma A/S
In retrospect working with Excel now seems like living in the stone age.

Jakob Lind Tolborg, Consultant
Spotting relations between sequence patterns and assay data is a central challenge in peptide drug discovery. In the past scientists had only Excel to do this, but with PepSee, looking back at Excel now feels like black and white TV.

use cases

unfold to read about a number of example applications in PepSee

  • The most common use case is naturally:
    I want to import my data to see sequence and properties of interest side by side.
  • When it comes to the analysis, the most pressing need is:
    I want to understand the SAR, so show me where changes result in a certain effect!
  • As a prerequisite to spotting certain patterns of interest you have:
    In order to see commonalities/differences I need to align my sequences.
  • As a researcher you rarely work alone and even if you do, you certainly want to present your work:
    For my peer group I need an easy way to present my data.
    plot &


Academic researchers may use PepSee for publication purposes free of charge: Windows 64bit Mac OS X

Commercial customers: please request a free trial license here!


PepSee is by design easy to use and pretty self-explanatory. Still, in order to give you a jump-start, we have prepared for you a tutorial-style guide through it's various functionalities. as well as an

To import your data from Excel, please use the same format as is in this sample data file. For an introduction of PepSee and various show cases we recommend you to take a look at this

webinar video

citing toolname

In publications please cite PepSee with the respective version number as follows:

PepSee version 2.8; BioSolveIT GmbH, Sankt Augustin, Germany, 2019,


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