Ref J1
Computational Service
Confidence Reported
Scoped After Feasibility Review
Service Overview
Linear peptides reach targets that small molecules struggle with — extended protein interfaces, extracellular receptors, shallow enzyme sites — and fail for predictable reasons: proteolysis, rapid renal clearance and poor membrane permeability. We design and optimise linear peptide sequences against a defined target site, then engineer against those failure modes with non-natural residues, terminal modifications, backbone changes and half-life extension strategies chosen deliberately rather than applied as a package.
Key Features & Advantages
Designed Against The Interface
Sequences are designed in the structural context of the target site using backbone generation and sequence design, so binding rests on modelled geometry rather than motif similarity.
Protease Stability Engineered
Cleavage sites are predicted and addressed through D-amino acids, N-methylation, unnatural residues or terminal capping, with each change assessed for its effect on binding.
Synthesis Realism Maintained
Difficult sequences — aggregation-prone stretches, multiple cysteines, problematic couplings — are flagged during design so the proposals can actually be made.
Half-Life Strategy Considered
Where systemic exposure matters, lipidation, PEGylation and albumin-binding approaches are evaluated as part of the design rather than added afterwards.
Where This Service Is Used
1Targeting a protein–protein interface too extended for a small molecule
2Designing receptor agonists or antagonists based on a natural ligand
3Optimising a peptide lead for protease stability and half-life
4Designing competitive inhibitors derived from a binding partner sequence
5Creating targeting peptides for conjugate or delivery applications
Methods and Techniques Applied
1Target site analysis with hot-spot identification and definition of the binding requirements
2Backbone generation and sequence design against the site, or optimisation of a starting sequence
3Structure prediction of designed peptides and complex modelling with the target
4Molecular dynamics assessment of complex stability and conformational preference
5Protease cleavage site prediction and stability engineering with natural and non-natural residues
6Property prediction covering solubility, aggregation, charge and, where relevant, permeability
What We Need From You
1Target structure and the site or interface to be engaged
2Any known binding peptides, natural ligand sequences or SAR data
3Route of administration and required duration of exposure
4Synthesis constraints: length limits, available non-natural residues, conjugation requirements
What You Receive
1Ranked peptide sequences with modifications specified residue by residue
2Structural models of the designed peptide in complex with the target
3Predicted stability, solubility and aggregation profiles per sequence
4Protease liability analysis with the mitigations applied
5Synthesis notes and a recommended testing order for the designed panel
What We Compute and Report
1Designed sequences with every modification specified residue by residue
2Complex models with the target and per-interface confidence
3Predicted protease cleavage sites before and after stability engineering
4Solubility, aggregation propensity and net charge across the sequence
5Simulation-based stability metrics for the peptide–target complex
Questions We Are Asked Before Scoping
Do you synthesise the peptides?
▸No. We design and prioritise; synthesis is carried out by your supplier or a partner. Designs are specified precisely enough to order directly.
Can peptides be made orally available?
▸Rarely as linear sequences. Oral exposure generally requires cyclisation, constraint and often permeation enhancers, which is why cyclic and macrocyclic design exist as separate services.
How reliable is de novo peptide binder design?
▸It has improved considerably but remains a numbers game: a designed panel is expected to contain a minority of binders. We size panels accordingly rather than promising that a specific sequence will work.
Interpretation and Limitations
Computational predictions prioritise hypotheses; they do not independently establish binding, biological activity, therapeutic efficacy, safety or clinical validity. Performance depends on input quality, target class, the structural evidence available and the applicability domain of the selected methods. Scores used for ranking are comparative devices and should not be read as measured quantities. All deliverables are for research use only and are not intended for diagnostic or therapeutic use.
Is This the Right Service for You?
Choose this when
An extended interface or extracellular receptor is the target
A natural ligand sequence is the starting point for an agonist or antagonist
Proteolytic stability and half-life are the limiting problems for an existing peptide
Consider another service when
Conformational entropy or oral exposure is the main barrier
Cyclic Peptide Design The bioactive conformation is helical and needs locking
Stapled & Constrained Peptide Design What Goes Wrong, and How We Handle It
These are the failure modes that produce confident-looking results which do not survive the next experiment. Each one is designed against rather than discovered afterwards.
Stability modifications that quietly abolish binding
Every non-natural residue or backbone change is assessed against the complex model before it is recommended.
Sequences that cannot be synthesised cleanly
Aggregation-prone stretches, difficult couplings and multiple cysteines are flagged during design, not discovered during synthesis.
Half-life strategy bolted on at the end
Lipidation, conjugation or albumin-binding options are evaluated while the sequence can still accommodate them.
A Worked Example
Blocking a receptor interface with a designed peptide
The situation
The interface was too extended for a small molecule and the natural ligand was degraded within minutes in plasma.
What the work involved
Hot-spot residues were identified from the complex, sequences were designed against them, cleavage sites were predicted, and D-amino acid and N-methylation options were scored for their effect on the modelled binding.
What came back
Twenty-four sequences with modifications specified residue by residue, ranked by predicted binding retention against predicted protease resistance.
Illustrative of the shape this work takes. Details are generalised, no client or target is identified, and scope and outcome vary with the system in question.
Service Workflow
1
Scientific Consultation
We discuss the objective, the decision it supports and the data you hold. Nothing is quoted before we understand what the result has to answer.
2
Feasibility Review
We check that the data, target class and available structural evidence can support the proposed approach, and say plainly where they cannot.
3
Technical Proposal
Scope, methods, deliverables, timeline and price are confirmed in writing, together with the limitations we expect to report.
4
Computation and QC
The analysis runs on pinned tool versions in a containerised environment, with quality checkpoints and method comparison where that is informative.
5
Report and Follow-Up
You receive the ranked results, the documented methods, the limitations and a proposed validation plan, plus support in interpreting them.
Service Process
1
Online Consultation
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2
Solution Matching
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3
Service Contract
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4
Project Execution
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5
Data Delivery
Specifications & Turnaround
Note: ICDMO delivers computational (in silico) services. Results prioritise hypotheses for testing; they do not by themselves establish binding, biological activity, efficacy or safety. All deliverables are for research use only and are not intended for diagnostic or therapeutic use. Downstream experimental work is scoped separately and executed through qualified partners.
Get a Custom Quote
Our scientific team responds within 24 hours with a detailed technical proposal and pricing tailored to your project.
Contact Us Online ConsultationStandard Deliverables
✓Sequence-verified final product
✓Full QC documentation
✓Certificate of Analysis (CoA)
✓Electronic data files
✓Project completion report
Why ICDMO?
Computational CDMO Focus
Reproducible, Versioned Pipelines
Confidence & Limitations Reported
Experiment-Aware Recommendations
Response Within One Business Day