Overview
What this category covers
Peptides reach targets small molecules cannot and fail for reasons small molecules do not: proteolysis, rapid clearance and poor permeability. This category covers linear design against a defined interface and the three main routes to fixing those failures — head-to-tail cyclisation, helical stapling and macrocyclisation into more drug-like chemical space.
What we deliver
▸Structure-guided linear peptide design with protease stability engineering
▸Cyclic peptide design with proper conformational ensemble sampling
▸Stapled and constrained peptide design with binding-face protection
▸Macrocycle design combining peptidic and small-molecule chemistry
▸Permeability and property prediction using beyond-rule-of-five appropriate models
Who this is for
▸Programmes targeting extended protein–protein interfaces
▸Teams with a peptide lead that clears too quickly or degrades
▸Groups seeking oral or cell-permeable peptide therapeutics
▸Projects designing targeting peptides for conjugates or delivery
How engagements in this category are run
Peptide projects are scoped around the failure mode that actually limits the molecule — proteolysis, clearance, permeability or conformational entropy — since each calls for a different strategy. Designs are delivered fully specified, down to non-natural residues, terminal modifications and cyclisation chemistry, so they can be ordered from your supplier directly. Panels are sized to your synthesis budget and ordered so early results discriminate between the design hypotheses.
Services
4 computational services in this category
J1
Linear Therapeutic Peptide Design
AI-driven design of linear peptide drugs targeting extracellular receptors, PPI interfaces, and enzyme active sites. Sequence optimization for potency, selectivity, and proteolytic stability…
Learn MoreJ2
Cyclic Peptide Design (Head-to-Tail)
Computational design of head-to-tail cyclic peptides for improved proteolytic stability and oral bioavailability. Conformation sampling, ring closure energetics, cell permeability prediction…
Learn MoreJ3
Stapled Peptide & Constrained Peptide Design
Design of hydrocarbon-stapled or otherwise constrained peptides to lock bioactive helical conformations. Cross-linking position optimization, helix propensity scoring.
Learn MoreJ4
Macrocycle Design (Beyond Peptides)
Design of macrocyclic molecules combining peptide and small-molecule features. Macrocyclization position screening, conformational ensemble, permeability-potency optimization.
Learn MoreIn Practice
What a project in this category looks like
Three shapes we are asked for most often. Scope is always set after a feasibility review, so timelines below are typical rather than quoted.
Making a peptide lead survive in plasma
The situation
A peptide binds well but is degraded within minutes and cleared quickly.
What we do
Cleavage site prediction, stability engineering with non-natural residues, terminal modification and backbone changes, cyclisation assessment, and half-life extension options evaluated against the binding model.
What you receive
Designed sequences with every modification specified for direct ordering, complex models, predicted stability and the trade-off against binding for each change.
Typical timeline: 3–6 weeks
Targeting an extended protein–protein interface
The situation
The interface is too large and flat for a small molecule, and the team wants a peptide or macrocycle route.
What we do
Hot-spot analysis of the interface, backbone generation and sequence design against it, complex modelling and simulation, and constraint strategy selection between linear, cyclic, stapled and macrocyclic options.
What you receive
Ranked designs across the chosen formats with complex models, predicted properties and a synthesis and testing order.
Typical timeline: 5–9 weeks
Constraining a helix without killing binding
The situation
A helical peptide binds but pays entropic cost, and previous stapling attempts abolished activity.
What we do
Binding-face identification from the complex, systematic staple position and spacing screening away from contacts, crosslink chemistry comparison, and simulation to verify the constraint stabilises the intended conformation.
What you receive
Ten to forty constrained designs with position and chemistry specified, helicity analysis before and after constraint, and the hydrophobicity change each introduces.
Typical timeline: 4–7 weeks
Questions
Asked before we scope this work
Will cyclisation make the peptide orally available?
Sometimes, and it is not automatic. Oral macrocycles need specific hydrogen-bond donor counts and conformational shielding. We predict permeability and state the risk rather than assuming the benefit.
Do you synthesise the peptides?
No. Designs are specified precisely enough to order directly from your supplier, including non-natural residues, terminal modifications and cyclisation chemistry.
How reliable is de novo peptide binder design?
It has improved but remains a numbers game: a designed panel is expected to contain a minority of binders. We size panels on that basis rather than on a best case.
More
Other service categories
Target Identification & Validation5Virtual Screening (Small Molecule)3Small Molecule Design & Optimization2ADMET & Drug-Likeness Prediction4Molecular Dynamics & Simulation3AIDD — Small Molecule Platform2Structure-Based Drug Design (SBDD)3Bioinformatics & Multi-Omics Analysis11Antibody Design & Engineering (AI)5Protein Design & Engineering (AI)4ADC & Bioconjugate Design2Compound & Biological Library Design3
Bring us the scientific question, not a service code
Share your target, dataset, sequences or objective. We will recommend a scoped computational plan, the expected deliverables, a timeline and the validation options.
Request a Feasibility Review