Caput Designdraft
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Service arm A

Protein design and evaluation

You need a new protein that binds a target and have no candidates yet. Or you have candidates and want to see, on structural criteria, which ones are worth testing.

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Projects that fit this work

  • An experimental structure exists for the target, or a reliable model can be prepared.
  • The surface you want engaged is known, or can be determined through surface analysis.
  • You have test capacity in-house, or the external laboratory item can be added.
  • A requirement to discriminate against close paralogs can be defined up front.

What we need from you to start

  • The target name or UniProt ID; the PDB ID if there is one.
  • The epitope, hotspot or region of interest, if known.
  • A list of paralogs to compare against, if selectivity is required.
  • An expectation for how many candidates to work on.

The work itself

ServiceInputOutputScope limit
De novo binder designTarget structure (PDB) or UniProt IDRanked candidate sequence library and predicted complexesThe models are predictions; they contain no binding measurement.
Epitope-directed designTarget plus the epitope (the surface patch you want engaged) or hotspotCandidates that engage the specified surface, residue-level contact mapA predicted interaction is not a measured interaction.
Protein–protein interface analysisComplex structureBinding energy estimate, buried surface area, packing quality, contact listEnergy estimates are not affinity measurements.
Paralog selectivity assessmentTarget and list of paralogs (related proteins that resemble it)Epitope conservation rate, residue-level difference tableA sequence and structure assessment, not measured selectivity.
Molecular dynamics stability analysisComplex structureRMSD/RMSF, contact persistence and a stability summary over the simulated windowBehaviour within the simulated window, not a measured in-cell lifetime. (Claim C10)
Mutational effect prediction (ΔΔG)Structure and mutation listPer-position stability and binding effectA prediction, not a measurement.
Solubility and aggregation propensitySequence or structureRisk region map, formulation notesA risk estimate, not an experimental formulation result.
Antibody/nanobody modelling and epitope mappingSequence or structureModel, predicted epitope, interface analysisThe model and predicted-epitope labels are kept explicit.
Experimental design consultationCandidate listWhich candidates to test, in what order and formatRunning the experiment is not included; this is consultation.

Deliverables

The files you receive at the end of a project

For every file: what it is, what it does not show, and which projects produce it. This list is the content of the delivery package, not a sample report.

  • Candidate sequences

    Every project
    candidates.fasta
    What it contains
    Ranked candidate sequences, each with an identifier
    What it does not show
    The ranking follows computational criteria; it does not guarantee the experimental order.
    What does the file look like?Format example
    >BARNASE_1BRS_A | gosterim dizisi, tasarlanmis aday DEGILDIR
AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNRE
GKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR

    In a real delivery each record is a designed candidate sequence carrying its rank. The sequence above is taken from the barnase chain in the 3D demonstration, purely to show the format.

  • Complex models

    Every project
    complexes/*.pdb
    What it contains
    Predicted target–binder complex for every candidate
    What it does not show
    These are predicted structures, not experimentally solved ones.
    What does the file look like?Format example
    complexes/
  candidate_001.pdb
  candidate_002.pdb
  ...
  candidate_NNN.pdb

    One structure file per candidate. File names match the candidate identifiers.

  • Evaluation table

    Every project
    metrics.csv
    What it contains
    Per-candidate interface confidence scores, binding energy estimate, buried surface area, packing quality
    What it does not show
    Interface confidence metrics and energy estimates are selection criteria, not affinity measurements.
    What does the file look like?Format example
    candidate_id,interface_confidence,binding_energy_estimate_kcal_mol,buried_surface_area_A2,packing_quality
<kimlik>,<0-1>,<kcal/mol>,<A^2>,<0-1>

    Column structure only. No sample numbers: an invented metric value could be read as a real result.

  • Contact list

    Every project
    interface_contacts.csv
    What it contains
    Residue-level contact list in the target's own numbering
    What it does not show
    Contacts are read from the model; this is not an experimentally verified interaction list.
    What does the file look like?Real example
    target_chain,target_resi,target_resn,target_atom,partner_chain,partner_resi,partner_resn,partner_atom,min_distance_A
A,83,ARG,NH2,D,39,ASP,OD1,2.5
A,83,ARG,O,D,29,TYR,OH,2.65
A,102,HIS,NE2,D,39,ASP,OD2,2.81
A,60,GLU,OE2,D,34,LEU,N,2.84
A,59,ARG,N,D,35,ASP,OD1,2.88

    These rows are real: computed from PDB 1BRS at a 4.5 Å cutoff. The full file has 43 rows.

  • Selectivity table

    Scope dependent
    selectivity.csv
    What it contains
    Epitope conservation table against the paralogs you name
    What it does not show
    A sequence and structure based prediction, not measured selectivity.
    What does the file look like?Format example
    candidate_id,paralog,epitope_identity,conserved_positions,differing_positions
<kimlik>,<UniProt>,<0-1>,<liste>,<liste>

    Column structure. You decide which paralogs are compared.

  • Stability summary

    Scope dependent
    md_summary.pdf
    What it contains
    RMSD/RMSF and contact persistence for the selected candidates
    What it does not show
    Scope dependent: not produced in every package or for every candidate.
    What does the file look like?Format example
    1. Simulasyon kurulumu (sure, kosullar, kuvvet alani)
2. RMSD / RMSF egrileri
3. Temas surekliligi tablosu
4. Yorum ve sinirlar

    Report sections. Duration and conditions are stated per project.

  • Method report

    Every project
    report.pdf
    What it contains
    Method summary, ranking rationale and methodological limits
    What does the file look like?Format example
    1. Hedef ve kapsam
2. Yontem ozeti (kullanilan adimlar)
3. Siralama gerekcesi
4. Aday bazinda bulgular
5. Metodolojik sinirlar

    Report sections. The “methodological limits” section appears in every report.

  • Benchmark report

    Scope dependent
    benchmark.pdf
    What it contains
    Small-molecule work: retrospective discrimination result for the target class
    What it does not show
    Specific to the small-molecule arm; not a mandatory part of the protein package.
    What does the file look like?Format example
    1. Hedef sinifi ve secilen referans seti
2. Bilinen aktif / yem bilesik ayirici testi
3. Sonuc ve yorum

    Report sections.

Out of scope

These items are listed deliberately: we write down what is not included so the quote holds no surprises.

  • Measuring binding experimentally — separate scope, external laboratory.
  • Protein production and purification — separate scope, external laboratory.
  • Cell or animal experiments.
  • Any guarantee of binding or committed success rate.
  • Regulatory filing preparation.

Terms used on this page

New to the field? Start here. The explanations are deliberately short.

target
The protein you are working on — the molecule you want to engage, block or detect.
binder
A protein designed to stick to the target. Think of it as the key in a lock-and-key pair.
epitope
The specific patch on the target’s surface where you want the binding to happen.
interface
The surface where two proteins touch. Whether a design works shows up largely here.
residue
A single amino acid in the protein chain — one link in the chain.
paralog
A related protein that resembles the target. You usually want the design not to bind these by mistake.
selectivity
How well a design binds the target while leaving similar proteins alone.
affinity
How tightly two molecules hold on to each other. It is measured in the lab, not computed.
computational
Work done on a computer. It is not an experiment; it shows which candidate is worth testing.
complex
The structure formed by two or more molecules bound together.
UniProt
The public database of protein sequences and their basic annotations.
PDB
The public database of experimentally solved protein structures.
molecular dynamics
Simulating how a structure moves over time — it shows whether a complex holds together.
RMSD / RMSF
Measures of how far a structure drifts (RMSD) and which parts wobble most (RMSF) during a simulation.
ΔΔG
An estimate of whether a single mutation makes a protein more stable or less.
aggregation
Protein molecules clumping together — a common problem in production.
nanobody
A single-chain binding protein, much smaller than a conventional antibody.
de novo
From scratch — designing without an existing candidate or template to start from.
BLI / SPR
Two laboratory methods that actually measure binding — where a computational prediction gets checked.

Describe your target briefly and we will settle the scope together.

The first message never asks for confidential sequences, unpublished structures or sensitive files. Technical detail follows an appropriate confidentiality process.

Let us discuss your project