Boltzmann Ensemble Covalent Ligandability
Rank covalent sites by the joint presence of pocket fit, cysteine reactivity and sulfur exposure across a modeled conformational ensemble.
BioTwin / Unique capabilities
Work with more of biology. Find more ways forward.
Keep shape, changing states and possible paths in the question. BioTwin combines 8DB's native structures and mathematical operations with biological methods to help your team find routes a narrower workflow can miss. Explore the operation, see what decision it changes, and follow the evidence into the next step.
01 / Three concrete differences
Three ways a different question can change the decision.
A useful model preserves the distinction your decision depends on. These BioTwin methods keep the state, path or permitted change explicit, then give you an operation that can test it.
01 /
It fits. Can it get in?Separate cavity capacity from entry clearance. Find out whether an attractive pose has a geometric route in, or whether a different state or better structural evidence needs attention.
02 /
Which change could produce the response you want?Set an objective, search bounded changes in a protein response model, and check the result forward. Use the reachable response to guide which physical intervention deserves investigation.
03 /
Do the useful conditions happen together?Score pocket fit, cysteine reactivity and sulfur exposure within each conformer. Prioritize a modeled opportunity where the conditions coexist, rather than combining favorable averages from different states.
Find the operation your program needs
Start with the question holding up your program. Each method page explains the operation, how it differs from familiar approaches and what it can change about the next decision. Current support ranges from computational studies to emerging research directions.
38 capabilities
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01 / 5 capabilities
Protein states and binding opportunities
Topological Cryptic-Pocket Discovery
Localize candidate cryptic openings with persistent homology, then test access and conformational availability before treating them as binding sites.
Protein State Control
Frame a protein intervention around the state, transition and functional response to change, then compare possible actuators and capture mechanisms.
Programmable Allostery
Search for bounded structural-network perturbations that produce a chosen protein response, then check the proposed change in a forward model.
Certified Molecular Fit and Access
Separate geometric fit from access using clearance fields and explicit uncertainty, including cavities that can hold a probe but cannot admit it.
02 / 1 capability
RNA structure and targeting
RNA G-Quadruplex Targeting (rG4)
Connect RNA G-quadruplex formation, structural selectivity and concrete ligand-design questions, with evidence kept separate at each stage.
03 / 9 capabilities
Molecular dynamics, topology and multiscale models
Interval Molecular Dynamics and Certified Readouts
Propagate bounded input uncertainty through supported harmonic dynamics and readouts to see whether a conclusion survives the admitted variation.
Multiscale Ensemble Compression
Reduce weighted conformer descriptors while checking that the structural differences needed for a downstream decision survive.
Temporal Renormalization and Slow-Mode Survival
Coarse-grain rapidly exchanging states and test whether the slower relaxation behavior needed for a molecular question survives.
Disulfide-Aware Bonded Braidoids
Carry disulfide connectivity and assignment confidence into molecular-topology and covalent-site comparisons.
Topology-Gated Molecular Dynamics
Check a selected molecular-topology readout during simplified dynamics and reject moves that change the declared constraint.
Sheaf-Based Cross-Representation Consistency
Compare molecular representations through explicit maps and localize disagreements that could change a structural conclusion.
QBath Molecular Environment Models
Investigate reduced molecular-environment models with explicit coupling and memory assumptions, judged by the observable they preserve.
Coupled Structural Operators and Dynamic Vulnerability
Combine selected structural descriptors within a network operator, then test whether their interaction reveals a useful intervention hypothesis.
Kinetic Landscape Queries
Query state populations, transition routes and timescales to ask what a proposed intervention would need to change.
04 / 10 capabilities
Covalent chemistry and molecular design
Mechanism-Relative Covalent Reach
Investigate alternative attachment sites and chemical routes against a fixed functional objective when the first covalent handle is unsuitable.
Kinetic Amplification and Reversible-Covalent Regimes
Compare capture, adduct reversal, production and clearance to test whether a covalent mechanism can sustain the intended effect.
Target-specific covalent design
Compare recognition, reaction conditions and exposure to prioritize candidate designs and their next laboratory tests.
Tether Conformer Reach and Productive Geometry
Assess a linker from its actual attachment points, conformations and obstacles to determine which architectures merit a productive-geometry test.
Multivalent Register Engagement
Model binding-head spacing, periodic-target mismatch and strain to test when additional heads can contribute to simultaneous engagement.
Non-Cysteine Covalent Design
Investigate residue and warhead alternatives when cysteine-directed engagement is unsuitable for the target.
Ensemble Reaction-Barrier Ranking
Compare matched reaction chemistry across modeled conformers to test whether a candidate ranking survives structural variation.
Paralog and Mutation-Aware Covalent Selectivity
Turn a proposed covalent selectivity mechanism into a matched paralog or variant counterscreen.
Constraint-Guided Protein Interface Analysis
Check proposed protein interfaces against supported structural and experimental constraints, and identify what excludes an alternative.
Plasma Competition and Covalent Capture
Model target capture alongside competing extracellular reactions and losses to identify the design parameter worth testing.
05 / 4 capabilities
Recruitment, clearance and conditional interventions
Zymogen Turnover and State-Pool Occupancy Control
Test whether coupling, activation and turnover allow a proposed zymogen intervention to achieve its intended effect under the model.
E3 Recruiter and Molecular-Glue Mechanism Design
Connect an E3 recruiter or molecular-glue proposal to the distinct evidence needed for recruitment, degradation and function.
Extracellular Lysosomal Degradation · ASGPR-LYTAC
Compose a supplied extracellular target binder, GalNAc cluster and linker into an ASGPR-LYTAC construct for evaluation.
Logic-Gated Drug Activation
Specify the conditions under which a proposed drug should activate, including the environments where it should remain off.
06 / 5 capabilities
Cell states, resistance and biological context
Cell-State Arrest and Release
Identify the biological barrier a cell-state intervention must overcome, and the experiment that can test it.
Resistance Min-Cut and Protein–RNA Co-Targeting
Investigate modeled signaling escape routes before choosing a protein–RNA co-targeting hypothesis.
IDP Charge Patterning and PTM-Conditioned Boundaries
Revisit a disordered-protein intervention when charge patterning or post-translational modification changes its sequence context.
Isoform-Specific Target Assessment
Determine whether an isoform distinction changes the target, intervention or assay your program should use.
Spatial Multiomics Neighborhood Analysis
Investigate a research direction connecting spatial cell neighborhoods to local intervention constraints.
07 / 4 capabilities
Delivery, exposure and compartments
GalNAc Targeting and Hepatic Activation Modeling
Distinguish receptor-mediated liver uptake from hepatic activation, with a model and measurements suited to each mechanism.
Local Effect-Space Confinement
Assess whether a modeled local-exposure advantage remains useful after local and systemic target effects are considered.
Mechanistic Barrier and PBPK Modeling
Investigate the absorption, barrier or compartment-exposure assumption that could determine a program’s next experiment.
Subcellular Drug Partitioning
Model how small-molecule properties could change mitochondrial or lysosomal exposure beyond the whole-cell measurement.
Research questions that cross method boundaries
Some of the most interesting questions require a combination. These are proposed research compositions: their component evidence remains separate, and a joined workflow needs a candidate-specific evaluation.
- State-selective covalent capture · Connect conformational access, site chemistry and reaction-barrier questions around a defined target state. Boltzmann Ensemble Covalent Ligandability
- Selective extracellular covalent design · Compare recognition, reaction conditions and exposure to prioritize candidate designs and their next laboratory tests. Target-specific covalent design
- State-directed allosteric lock design · Investigate a desired response, candidate perturbation and the geometry of an intervention. Programmable Allostery
- Compartment-matched target clearance · Compare intracellular E3 recruitment with extracellular lysosomal clearance as distinct mechanistic routes. E3 Recruiter and Molecular-Glue Mechanism Design
- Context-specific cell-state release · Connect necessary biological gates, bypass pathways and exposure requirements. Cell-State Arrest and Release
- Isoform- and modification-aware intervention design · Examine whether transcript context and protein modification change a proposed interface or mechanism. Isoform-Specific Target Assessment
Which constraint is holding up your program?
Bring the target, the obstacle and the decision you need to make. We can identify the relevant BioTwin operations and define a focused comparison with your current approach.
What would another route make possible?
Tell us where your current investigation stops. Let’s explore which scientific distinction could open the next step.