Target identity
Resolve the intended protein and biological context before assigning structures, pockets, ligands, or models to the project.
SBDD and pocket design
Qualify the structural hypothesis before designing around it.
Connect target identity, protein structure, binding-site evidence, pocket selection, candidate generation, and pose review so each design proposal can be traced back to the structural assumptions that support it.
Structure-based drug designPocket detectionTarget preparationPose reviewInteraction evidenceDesign constraints
Structure readiness before scoring
Keep target, structure, pocket, and ligand evidence in the same chain.
A protein file alone is not a design-ready target. MolexIO exposes identity resolution, structure provenance, local quality, pocket evidence, preparation choices, and pose artifacts before a candidate is interpreted as a structure-based hypothesis.
Structure qualification
Review experimental or predicted structure source, chains, residues, cofactors, missing regions, and relevant confidence evidence.
Pocket detection
Compare candidate binding sites using geometry and available supporting evidence while keeping pocket druggability separate from ligand drug-likeness.
Design constraints
Represent the selected site, interaction hypotheses, excluded regions, and retained scaffold context used to guide proposals.
Inspectable poses
Review 3D placement, contacts, clashes, and scoring context rather than treating a rank or image as proof of binding.
Connected triage
Carry structural candidates into ADMET, off-target, synthesis, MPO, and project-library workflows without breaking lineage.
Exact structure trackedChain, structure source, and selected pocket remain attached to the run.
Pose is an artifactDownloadable coordinates and interaction context support review beyond a score.
Readiness is conditionalMissing or weak structural evidence is reported rather than silently inferred.
A qualified SBDD workflow
Build from identity to a testable structural proposal.
- 01
Resolve
Confirm the target, construct, structure source, chain, ligands, and biologically relevant context.
- 02
Prepare
Review the structure and document preparation assumptions required by the selected computation.
- 03
Select the pocket
Compare sites, define the working binding region, and record why it was selected.
- 04
Design and challenge
Generate or evaluate candidates, inspect poses, and add orthogonal evidence before advancement.
Scientific boundary
A plausible pocket and pose remain hypotheses.
Protein flexibility, protonation, water networks, induced fit, cofactors, construct differences, and structure quality can change the interpretation. Pocket scores do not establish druggability, and docking does not establish binding affinity. MolexIO preserves these assumptions so structural ideas can be challenged and experimentally tested.
Questions before use
Structure-based design FAQ
Is a predicted pocket proof of druggability?
No. It is one source of evidence and should be reviewed with dynamics, chemistry, biology, and experiments.
Can a predicted protein structure support SBDD?
It can support hypothesis generation when local confidence and pocket suitability are reviewed, but it is not automatically equivalent to an experimental complex.
Does a docking pose establish binding?
No. It is a computational placement hypothesis requiring orthogonal validation.
Make the structural assumptions part of the decision.
Review target readiness, pocket evidence, candidate design, and pose artifacts in one connected project.