Receptor Workbench

Build structural protocols that medicinal chemists can trust for compound prioritization.

Select biologically relevant structures, assess task suitability, prepare receptor packages and validate the protocol before using it to rank compounds.

Screenshot of the MedMap receptor workbench platform interface
Evaluate a Receptor ProtocolReview a Multi-Structure Strategy

Validate the structural context before using it to rank compounds.

Why Receptor Choice is Scientific

The best-resolution PDB is not always the best receptor for your task.

Selection factor
Why it matters
Biological state

The structure must represent the conformational or activation state relevant to the project hypothesis.

Ligand confidence

Known ligand identity, binding mode and covalent status affect pocket interpretation and validation.

Pocket completeness

Missing loops, side chains, waters, cofactors or metals may invalidate downstream calculations.

Mutation / construct context

Engineered constructs, truncations or mutations may not represent the intended target state.

Downstream task

Fine docking, FEP, selectivity analysis and covalent design may require different receptor choices.

Preparation readiness

Protonation, waters, cofactors, charges and box definition must be traceable and task-appropriate.

Selection Workbench

From receptor selection to a directly calculable structure package

Diagram annotating the selection workbench interface with seven numbered steps and arrows, from project input through to platform output
1.

Project Input: target/gene, UniProt, disease/pathway, known ligands.

2.

Downstream tasks and receptor preference.

3.

User constraints and must-have structural conditions.

4.

Candidate structure recall and target matching.

5.

Pocket completeness and high-risk structure count.

6.

Recommended receptor pack and overall readiness.

7.

Directly calculable structure packages and explanatory report.

Multi-Receptor Strategy

Manage conformations, roles and protocol eligibility in one project

Receptor role
Intended use
Example decision
Primary

Primary ranking / lead optimization

Use for the main compound ranking workflow

Secondary conformation

Conformational robustness

Retain candidates that are not dependent on one pocket state

Selectivity receptor

Selectivity or family member comparison

Identify structural drivers of selectivity

Off-target

Risk evaluation

Flag compounds with undesired structural compatibility

Preparation & Protocol Validation Workflow

A favorable score is not evidence that a protocol is valid

  1. 1Protein input
  2. 2Preparation
  3. 3Reference ligand
  4. 4Pocket & box
  5. 5Redocking
  6. 6RMSD diagnostics
  7. 7Eligibility
Diagnostic
Suggested display
Reference ligand

Name / residue name / structure identity

Reference heavy atoms

Count

Pose heavy atoms

Count

Mapping method

Graph-mapped / template-based RMSD

RMSD

Value + threshold

Docking mode

Noncovalent / approximation / covalent-aware

Status

Pass / Review / Fail

Reason / limitation

Human-readable explanation

If RMSD cannot be calculated, do not substitute docking energy. Report the failure state and the reason.

Recommended receptor package

A receptor package with intended use, validation evidence and known limitations

Primary

KRAS-G12C Receptor Package

Intended Use: Primary ranking/lead optimization

Prepared Files & Settings

kras_g12c_prepared.pdb

Prep: Protonated (pH 7.4)

Docking Box & Reference Ligand

Box Size: 18 × 18 × 18 Å

Ref: G12C-Inhibitor (32 atoms)

Diagnostics

RMSD: 1.72 Å

Status: Pass

Task Suitability

DockingFEPCovalent-Aware

Limitations & Review Notes

Flexible loop regions in pocket B require manual alignment check

Protocol History

Version: v2.4 (Current Active)

History: v1.0 Invalidated (Box size mismatch)

From molecular ideas to the next experimental decision

Discuss a focused project review, pilot scope or complete optimization program with MedMap.

Evaluate a Receptor Protocol