Structure-guided screening built for biotech partners.
Moleculepath Bio designs small-molecule hit campaigns around your target protein structure — delivering ranked hit shortlists with binding pose rationalization, not a generic diversity screen.
The problem
Hit identification fails when structure is an afterthought.
Hit identification campaigns frequently produce large lists of low-quality actives. When library selection is disconnected from binding site geometry, the result is structural redundancy, pan-assay interference compounds, and selectivity liabilities discovered six months too late.
The structural data already exists — protein coordinates from crystallography, cryo-EM, or curated homology models. The problem is that most screening workflows do not use it. Fragment campaigns are run against generic diversity sets. Docking is applied as a post-screen filter, not as the design input. The binding site constrains which scaffolds can work — but that constraint is never enforced at the library selection stage.
Three integrated capabilities
Structure-first at every stage.
Structural Screening
The target protein structure is the first input, not an afterthought. Binding site analysis maps pocket geometry, electrostatics, and flexibility before a single compound is evaluated. Docking protocols are calibrated to the specific pocket architecture.
Fragment Library Design
Fragment sets are computationally curated to match the binding site geometry of your specific target. Libraries biased toward pocket-compatible physicochemistry outperform generic diversity sets in enrichment rate and hit quality.
Hit Triage Engine
Ranked shortlists delivered with binding pose 3D visualization, docking score distributions, ADMET filters, and a written structural rationale for top-tier compounds. Not a ranked SMILES list. Not a CSV without context.
Target classes
Scientific approach
The binding site constrains the answer before the screen begins.
Structure-based drug design: the methodology
SBDD uses the three-dimensional structure of a target protein — from X-ray crystallography, cryo-EM, or a validated homology model — to guide compound selection. Binding site geometry constrains which molecular shapes can bind, which functional groups make productive contacts, and which scaffold trajectories are feasible for a hit-to-lead campaign.
Fragment-based approaches start from small, rule-of-three-compliant molecules that probe individual sub-pockets, then elaborate them systematically using structural feedback — rather than applying a diversity screen and hoping for coverage.
Fragment elaboration: building hits that make structural sense
Fragment elaboration uses binding pose analysis to identify vectors — directions from the fragment into unexplored sub-pocket volume — that can tolerate added molecular complexity. Each elaboration step is evaluated not just on docking score, but on whether the added atoms make productive contacts with the pocket.
The result is a set of leads with explicit structural rationale at every branch point — which means fewer SAR surprises at the lead optimization stage.
Who we work with
Moleculepath is built for scientists who need structure-quality hit matter, not another ranked list.
Discovery Lead
You have a validated target with a crystal structure and need structurally diverse hit matter by the next SAR review. Your team can run biochemical assays — but doesn't have the computational chemistry infrastructure to run a full SBDD campaign in-house.
Medicinal Chemist
You need docking results with explicit binding pose rationalization, not a ranked SMILES list. You want to understand why each hit was selected before you commit synthesis resources — and you want the ADMET filters applied before delivery, not after.
BD Director, clinical-stage
You want a screening partner who co-owns the hit list quality, not just delivers a CSV. The engagement model should be a scientific collaboration — with a target briefing, a campaign design proposal, and a structured data package at the end.
Have a target? Start a conversation.
Every partner program begins with a scientific discussion about your target — its structural data, your program timeline, and whether structure-guided hit identification is the right approach.
Discuss a Target