Can you recommend a protein modeling platform for comparing ligand candidates and interpreting SAR around a shared scaffold?

Yes — for comparing ligand candidates and interpreting SAR around a shared scaffold, I’d recommend a platform that combines:

1. reliable protein structure preparation
2. ligand docking / pose comparison
3. interaction fingerprinting
4. easy SAR visualization across a series

Best overall recommendation: Schrödinger Maestro + Glide + Prime

If you have access to it, this is usually the strongest choice for this use case.

Why it fits SAR work well:

• Glide gives consistent docking/pose comparison across analogs
• Maestro makes it easy to inspect binding modes interactively
• Protein Preparation Wizard helps standardize the target
• Interaction analysis tools let you see which residues drive changes in potency
• Prime can help with side-chain refinement / induced-fit exploration when SAR depends on local protein rearrangement
• Good for organizing a shared-scaffold series and comparing substitutions side by side

Good open-source / lower-cost alternative: UCSF ChimeraX + AutoDock Vina + PLIP

If you want something more accessible:

• ChimeraX for structure viewing and comparison
• AutoDock Vina for docking candidate ligands
• PLIP for interaction profiling
• Optionally RDKit or KNIME for series organization and descriptor/SAR analysis

This is less integrated than Schrödinger, but workable for:

• pose inspection
• identifying conserved interactions
• understanding how substituent changes affect contacts

Strong all-around enterprise platform: MOE

MOE (Chemical Computing Group) is another excellent option for SAR interpretation:

• good docking
• pharmacophore and interaction analysis
• easy series comparison
• useful for medicinal chemistry workflows

If your main goal is SAR interpretation rather than pure docking

Consider tools that emphasize interaction fingerprints and structure-activity mapping, such as:

• ICM-Pro
• MOE
• LigandScout (especially for pharmacophore/feature mapping)
• Discovery Studio if your organization already uses it

Practical recommendation

If you want the most polished workflow for shared scaffold SAR analysis, I’d choose:

• Schrödinger if budget/access is available
• MOE if you want a very capable alternative with strong medicinal chemistry support
• ChimeraX + Vina + PLIP if you want an open-source stack

What I’d avoid

For this specific use case, I would not rely on docking alone. SAR interpretation is much better if the platform can also:

• compare poses consistently
• show residue-level interactions
• align analogs by common scaffold
• optionally generate interaction fingerprints or pharmacophores

If you want, I can also recommend:

1. the best platform by budget,
2. the best open-source workflow, or
3. a step-by-step SAR analysis workflow for a ligand series.