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Computational protein design and molecular modelling

We design protein binder candidates for your target.

We start from the target structure and deliver candidate sequences, predicted complex models and an evaluation report that states what each metric means. Experimental validation is a separate scope you can add.

Let us discuss your projectExplore the 3D example
Files delivered
  • Candidate sequences
  • Complex models
  • Evaluation table
  • Contact list
  • Method report

metrics are not estimates. We make no binding claim for any candidate without experimental validation.

SourceThe barnase–barstar interface · PDB 1BRSA demonstration prepared on a publicly available structure, not a design output of the team.

In short

If the field is new to you, the work is this

What do we do?

We produce proposals for new proteins designed to stick to a protein of yours. The lock-and-key picture helps: your protein is the lock, we design keys that fit it.

How do we do it?

All of it happens on a computer. Starting from the three-dimensional shape of your protein, we try thousands of possibilities and filter down to the most promising ones.

What do I get at the end?

A ranked list of candidates, three-dimensional models showing how each one sits on your protein, tables of the criteria used, and a report explaining why the leaders lead.

Will these candidates actually work?

Only the lab can say. We show which ones are worth trying; the trying itself is separate work, and we can arrange that too if you want.

Workflow

From the target structure to the delivered files

Each link produces the input for the next. The last link is optional and happens at an external laboratory.

  1. 01

    Target

    The protein to work on is fixed, together with the surface to engage if there is one.

  2. 02

    Design

    Candidate binder sequences are generated for that target.

  3. 03

    Evaluation

    Candidates are examined on structural criteria: interface, contacts, stability, selectivity.

  4. 04

    Ranking

    Candidates are ranked on those criteria, with the rationale written down.

  5. 05

    Delivery

    Sequences, models, tables and the method report are handed over together.

  6. 06

    Validation

    Optional: binding measurement at an external laboratory.

Everything up to here is computational

Services

Two arms of work, one setup

Which work we run ourselves and which we coordinate with a named external laboratory — that is the distinction you need when weighing a quote.

Computational

Protein design and evaluation

From the target structure to candidate sequences and predicted complexes, with interface, selectivity and stability analyses.

  • De novo binder design
  • Epitope-directed design
  • Protein–protein interface analysis
  • Paralog selectivity assessment
  • Molecular dynamics stability analysis

See the detail — 9 items

Computational

Structure-based small-molecule work

Docking, pocket and druggability assessment, virtual screening and structure-based optimisation support.

  • Molecular docking
  • Binding-site and druggability analysis
  • Virtual screening for hit discovery
  • Structure-based optimisation support

See the detail — 4 items

External laboratoryItems coordinated with an external laboratory

The work below is run as a service purchase. The provider and scope are stated in writing before the quote.

  • Experimental binding measurement (BLI/SPR)
  • Recombinant protein production
  • ADMET profiling
  • Solid form prediction

3D demonstration

The barnase–barstar interface: the workflow shown on real data

This is not a candidate designed by the team. It is a demonstration, on a publicly available and experimentally solved protein–protein complex, of how the workflow steps look.

SourceRCSB PDB 1BRSBuckle AM, Schreiber G, Fersht AR. Biochemistry. 1994;33(30):8878–89.

Ribbon model of the barnase protein — the still image shown before the demonstration starts.

Nothing 3D is downloaded until you press start. The structure file is 390 KB; the viewer library loads separately.

  1. 01

    Target

    What is on screen
    A single protein chain: barnase (chain A). The whole surface is visible; no region is marked yet.
    In your project
    Every project starts by fixing the target structure. Without an experimental structure we prepare a modelled one from the UniProt entry, and the report says that it is a model.
  2. 02

    Region of interest

    What is on screen
    19 residues on barnase that come within 4.5 Å of barstar are highlighted. The list was computed from this file, not picked by hand.
    In your project
    In your project this region is the epitope or hotspot you want engaged. You specify it, or we settle it together through surface analysis.
  3. 03

    The binding protein

    What is on screen
    The second chain is added: barstar (chain D), in its own colour. Barstar is not a designed candidate; it is the natural inhibitor of barnase.
    In your project
    In your project this position is taken by the designed candidate binders. For each candidate you receive a sequence and a predicted complex model, ranked on computational criteria.
  4. 04

    The interface

    What is on screen
    Both chains together, with the contacting residues marked on each side. The three closest contacts are drawn as measurement lines with their distances (2.5 / 2.65 / 2.81 Å). No motion here depicts binding taking place; the structure stands as crystallography solved it.
    In your project
    Interface analysis is the core of the report: contact list, buried surface area, packing quality and a binding energy estimate. These numbers are not affinity measurements; they indicate which candidate is worth testing.
  5. 05

    Deliverables

    What is on screen
    The same complex, next to the file actually produced from this demonstration: a 43-row contact list.
    In your project
    At the end of a project you receive candidate sequences, predicted complex models, a metrics table, the contact list and the method report — including the ranking rationale and the limits.
Limits of this demonstration
  • This structure is not a design output of the team; it is a publicly available experimental structure.
  • The demonstration runs no live computation: no docking, design or simulation happens in the browser.
  • The highlighted region is a geometric contact list, not an indicator of affinity or of a successful design.
  • The crystal contains three copies of the complex; only biological assembly 1 (chains A and D) is shown here.

A contact was counted where the minimum heavy-atom distance is 4.5 Å or less. Computed on this file, for model 1 and the A–D chain pair.

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.

Process

From the first call to delivery

Because timing and scope differ per project, no calendar is stated here; both are put in writing in the scoping call.

  1. 01

    Scoping call

    The target, the epitope of interest, the selectivity requirement and the delivery expectation are agreed.

  2. 02

    Target preparation

    Structure selection, preparation and definition of the region to be worked on.

  3. 03

    Design and filtering

    Candidate generation, filtering and ranking on interface confidence metrics.

  4. 06

    Report and delivery

    Files, the method report and the methodological limits are delivered together.

Packages

Validation is optional

Experimental validation is not part of the standard computational package. It can be added as a separate item; the external laboratory cost appears as its own line in the quote.

Design Package

Computational design and evaluation outputs. No experimental measurement.

Quote for your project

Scope is agreed in the first call; the amount follows in writing once scope is set.

  • Computational design and evaluation
  • Candidate sequences and predicted complex models
  • Interface, selectivity and stability analyses
  • Method report with the methodological limits
  • Measuring the candidates experimentally is not part of this package

Let us agree the scope

Design + Validation

External laboratory

The Design Package together with binding measurement at an external laboratory.

Quote for your project

Scope is agreed in the first call; the amount follows in writing once scope is set.

  • Everything in the Design Package
  • Binding measurement by BLI/SPR at an external laboratory
  • Measured binding data or a binding classification
  • Expression yield information
  • The computational ranking compared against the experimental result
  • External laboratory cost shown as a separate line in the quote

Let us agree the scope

The number of candidates, which analyses are included and the revision scope are set per project. That is why we do not publish a list price.

FAQ

What people ask before the first call

There is no experimental structure for my target. Can we still start?

Usually yes. We start from the UniProt entry and prepare a model structure. In that case the whole study rests on a modelled structure, and we say so explicitly in the report and in the limits section. The quality of that structure directly affects how confidently the design can be read.

What exactly do I receive?

Candidate sequences, predicted complex models, a per-candidate metrics table, a residue-level contact list, a selectivity table if requested, and the method report. The report carries both the ranking rationale and the methodological limits. The file list is itemised on the Approach and deliverables page.

Is experimental measurement included?

Not in the standard computational package. Experimental binding measurement is a separate scope, coordinated as a service purchase from a named external laboratory. The provider and the scope appear as a separate line in the quote.

Do the scores in the report mean the design will bind?

No. Interface confidence metrics and binding energy estimates are criteria for deciding which candidates are worth testing; they are not affinity measurements. We make no binding claim for any candidate without experimental validation.

How do we share confidential information?

Do not share it in the first enquiry. The form asks only for a short, non-confidential summary. Technical detail, sequences and unpublished structures are taken after an appropriate confidentiality process. You can tick the box to ask for that process first.

How do scope and price become definite?

In the scoping call we put in writing the target, the region of interest, the selectivity requirement, how many candidates will be worked on and which analyses are included. The price follows that scope as a quote; we do not publish a fixed list price.

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.
PDB
The public database of experimentally solved protein structures.
UniProt
The public database of protein sequences and their basic annotations.
BLI / SPR
Two laboratory methods that actually measure binding — where a computational prediction gets checked.
molecular dynamics
Simulating how a structure moves over time — it shows whether a complex holds together.
docking
Computing how a small molecule might sit in a pocket on the target.
druggability
How suitable a pocket is for being targeted by a drug-like molecule.
RMSD / RMSF
Measures of how far a structure drifts (RMSD) and which parts wobble most (RMSF) during a simulation.
ångström (Å)
A length unit at atomic scale — one ten-billionth of a metre; atoms sit a few Å apart.
virtual screening
Filtering a large set of compounds on a computer to surface the most promising ones.
de novo
From scratch — designing without an existing candidate or template to start from.

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