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Molecular Design Lab Primer design · Peptide analysis · MHC/HLA binding prediction Free beta
Home / Peptide Analysis
Physicochemical analysis · Sliding-window design

Peptide Analysis & Design Tool

Analyze peptide or protein sequences, estimate key physicochemical properties and generate ranked peptide candidates for general, antibody/immunogen or vaccine-oriented research workflows.

Molecular weight & pI Charge & GRAVY Instability & composition Sliding-window candidate design
1 · Sequence MKWVTFISLL... 2 · Properties MW · pI · charge GRAVY · instability 3 · Design length · step application preset Ranked candidates score · properties · flags Downstream review synthesis · MHC/HLA · lab Sequence-derived analysis supports prioritization; it does not replace experimental validation.
Peptide analysis and design are separate but connected steps: characterize the sequence first, then generate and rank candidate windows.

Analysis workspace

Sequence-derived properties

1. Peptide / Protein Sequence

Use a peptide sequence for direct characterization or a longer protein sequence if you also plan to design candidate peptide windows.
Charge depends on the selected pH.
Interpretation note. Sequence-based properties are calculated from the amino-acid composition. They are useful for candidate comparison but do not directly measure solubility, aggregation, stability or biological activity.

2. Analysis Results

Enter a sequence and click Analyze peptide.

Candidate design

Sliding-window peptide generation

3. Peptide Design

Generate overlapping peptide candidates from the source sequence and rank them using the selected application preset.

Number of amino acids in each candidate window.
How far the window moves between candidates.
Changes heuristic application-specific adjustments.
Number of ranked candidates returned.
Used when pH-dependent properties are calculated.
Enter a protein sequence above and click Design peptides.

Scientific diagrams

Window generation and sequence liabilities
Sliding-window peptide generation M A D V K L P Q E A L N K K L A D V E S T... Window 1 · length = L Window 2 · moved by step S Window 3 · next candidate Smaller step → denser overlap · larger step → fewer candidates
Sliding-window design systematically samples a protein sequence. Peptide length determines window size, while step controls overlap density.
Sequence liabilities to review C M N-G / N-S FILVWY Cys disulfide / handling Met oxidation-prone Asn motif deamidation context Hydrophobic cluster solubility / aggregation risk Flags are not automatic rejection rules Interpret them in the context of the experimental goal, sequence length and formulation strategy.
Sequence liabilities help explain synthesis and handling risks. They should guide comparison rather than act as universal pass/fail rules.

Related Molecular Design Lab

MHC / HLA Prediction PCR & qPCR Primer Design Design Assay Projects
Research use: sequence-derived properties and ranking scores are computational aids and require application-appropriate experimental validation.