Peptide Library Generation
Generate combinatorial peptide libraries for screening and optimization
Back to PepFun HomeBasic Parameters
100
7
Amino Acid Pool
A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
Click amino acids to toggle them in the pool:
A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
Selected: 20 amino acids
—
Scaffold Pattern optional
Enable scaffold mode to fix certain positions while randomizing others.
Use
X for variable positions.
Examples:
Fixed letters are kept as-is. Peptide Length is ignored when scaffold is active.
XXXGXXX
KXXXXXXR
XXXPXXX
CXXXXXXC
RXXXXX
Generation Options
Exclude Existing Sequences optional
Upload a previous library file to avoid regenerating the same sequences —
useful for building cumulative libraries without duplicates.
Drop file here or click to browse
Accepts: CSV, TSV, FASTA, JSON
1
Download your previous library as CSV / FASTA / JSON
2
Upload it here before generating
3
All sequences in that file are excluded from the new batch
FASTA — sequences on non-
> linesCSV / TSV — column named
sequence (or first column fallback)JSON — array of strings,
{"sequence":"..."} objects, or PepFun export formatSequence Space
Set parameters above to see the available sequence space.
About Library Generation
A peptide library is a collection of diverse sequences used for screening, optimization, and bioactive peptide discovery.
Use Cases
Drug Discovery
Screen for therapeutic peptides
Screen for therapeutic peptides
Lead Optimization
Improve existing peptide candidates
Improve existing peptide candidates
SAR Studies
Structure-activity relationships
Structure-activity relationships
Machine Learning
Training datasets for predictive models
Training datasets for predictive models
Building Cumulative Libraries
Need more than 10,000 sequences? Run multiple batches and stack them:
1
Generate batch 1 → Download as CSV / FASTA
2
Upload that file in "Exclude Existing Sequences"
3
Generate batch 2 — guaranteed no overlap with batch 1
No server-side state required — each user manages their own library files
Performance note:
Property calculation adds ~5–20ms per peptide.
For 10,000 peptides with properties, expect 1–3 minutes.