Degrader design is a coupled, multi-stage problem—target, ligase, geometry, linker, and prioritization all interact. This service brings those stages into one computational workflow, so every design decision is made with the full picture in view.
Assess degradation suitability, accessible lysines, and structural coverage for the protein of interest.
Compare recruiters across expression, neo-substrate risk, and ternary feasibility.
Model the target–PROTAC–E3 complex and rank productive geometries.
Design linkers and stress-test binding stability with molecular dynamics.
Score and tier candidates across structure, potency, selectivity, and feasibility.
Each stage is available as a standalone engagement, and modules can be assembled into a full program. Internal links below route to the dedicated service pages for each capability.
You have a target but no degrader chemistry. We assess degradation suitability, shortlist ligases, and propose a first linker and recruiter design.
You have degraders with SAR data. We model ternary geometry, test linker stability, and prioritize the series to focus synthesis.
A degrader binds but does not degrade. We diagnose whether the bottleneck is ternary formation, lysine accessibility, or a downstream step.
The design cycle moves from scope to prioritized candidate, with explicit checkpoints so modeling and wet-lab data inform each other.
Request a Project ScopeDefine the degradation goal, the stage of the program, and the specific decision each deliverable must support.
Collect structures, sequences, ligand chemistry, and any degradation, selectivity, or binding data available.
Execute the selected modules—ligase selection, ternary modeling, linker design, or stability analysis—in sequence or parallel.
Combine module outputs into a ranked candidate shortlist with per-criterion scoring and uncertainty flags.
Provide the design package and validation plan, then fold new experimental results into a refined next round.
A ligase chosen in isolation can fail at the linker stage; a linker optimized in isolation can break ternary geometry. Our integrated workflow carries structural and energetic evidence forward so downstream decisions stay consistent.
Engagements are sized to the decision. A focused module can be scoped in days; a full pipeline with MD and prioritization runs across several weeks with milestones.
Lysine accessibility, structural coverage, and degradation feasibility for the target.
Recommended ligase, linker, and attachment points with ranked ternary geometries.
MD metrics and relative binding-energy ranks across the candidate set.
Tiered candidates, uncertainty flags, and a validation experiment roadmap.
The authors demonstrated catalytic, event-driven protein knockdown by PROTACs, establishing that substoichiometric degradation—rather than target occupancy—is the design goal that matters for potency.
The authors linked ternary-complex affinity and cooperativity to degradation potency and rate, showing that structural interface organization—not just affinity—predicts productive degradation.
The right scope depends on where your program stands—these answers clarify how the service flexes to fit.
It spans target degradation suitability, E3 ligase selection, ternary-complex modeling, linker and attachment-point design, and candidate prioritization, with each stage scoped to your program's needs.
No. You can start from any stage—whether that is target analysis, ligase selection, or candidate prioritization—and assemble only the modules your program requires.
Yes. We support both PROTAC and molecular-glue modalities, adapting the interface-modeling and degradation-suitability analysis to each mechanism of induced proximity.
Every deliverable includes a validation plan. We identify the experiments that would most reduce uncertainty and link each computational prediction to the assay that tests it.
Timelines scale with scope. A focused single-module analysis can be scoped in days, while a full pipeline with MD and prioritization typically runs several weeks. We provide a milestone plan at scoping.
Share your target, degrader chemistry, and the stage your program has reached. CD ComputaBio will propose a fit-for-purpose design scope across the modules you need. Related services: PROTAC Design and Development Service, PROTAC Structure Modification, Molecular Dynamics Simulation.
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