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MolProbity Next

Structure Validation

Upload a macromolecular structure file for comprehensive all-atom contact analysis and geometry validation. MolProbity Next provides quality assessment for proteins, nucleic acids, and their complexes, diagnosing local problems and helping guide model improvement.

Drop a structure file here, or click to browse

Accepted: PDB (.pdb, .ent) and mmCIF (.cif, .mmcif) — compressed (.gz) files supported

Asn/Gln/His flips (?)

Optional: provide CIF restraint files for custom or unknown ligands. Required for clashscore analysis of non-standard residues. Use files generated by refinement tools (eLBOW, ACEDRG, Grade) — CIF files downloaded from the PDB may not include the energy type definitions needed for all-atom contact analysis.

Full geometry reports per-residue bond/angle counts for all residues. Automatically disabled for structures over ~1000 residues unless explicitly enabled.

Enter a PDB ID to fetch from RCSB

Classic 4-character ID (e.g., 1crn) or extended ID (e.g., pdb_00001crn)

Asn/Gln/His flips (?)

Optional: provide CIF restraint files for custom or unknown ligands. Required for clashscore analysis of non-standard residues. Use files generated by refinement tools (eLBOW, ACEDRG, Grade) — CIF files downloaded from the PDB may not include the energy type definitions needed for all-atom contact analysis.

Full geometry reports per-residue bond/angle counts for all residues. Automatically disabled for structures over ~1000 residues unless explicitly enabled.

Structure will be fetched as mmCIF from RCSB PDB.

Citations

Williams et al. (2018) MolProbity: More and better reference data for improved all-atom structure validation. Protein Science 27: 293-315.

Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Cryst. D66: 12-21.

Davis et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35: W375-W383.

About MolProbity

MolProbity is a general-purpose web service for quality validation of 3D structures of proteins, nucleic acids, and complexes. It provides an expert-system consultation about the accuracy of a macromolecular structure model.

An integral step is the addition and optimization of all hydrogen atoms, enabling all-atom contact analysis to detect steric problems alongside updated dihedral-angle diagnostics.

MolProbity works best as an active validation tool — used during each rebuild/refine cycle, not just at the end to provide global statistics before deposition.

Validations Performed
  • All-atom clashscore
  • Ramachandran analysis
  • Sidechain rotamer analysis
  • C-beta deviation
  • Cis-peptide evaluation
  • CaBLAM backbone validation
  • Bond & angle geometry
  • Chirality validation
  • RNA suite & pucker analysis
  • MolProbity score
  • Predicted structure support
  • Interactive 3D visualization
2026-11-03 — Usage guidelines and hosting details on the front page
2026-11-02 — Submitting the same file again from the same browser while it is still running takes you to that job
2026-11-02 — Files with residues stacked on top of each other stop early, naming the stacked residues
2026-11-02 — Moorhen updated to 1.1.3, and its hotspot colors now clear when you reset or pick another hotspot
2026-10-29 — DNA and RNA no longer show false missing atoms (OP3, O2', or the 5' phosphate at the start of a strand)
See full changelog →
Usage Guidelines: MolProbity Next is a free, shared service for validating individual structures. Please don't script or automate submissions or send large batches; heavy use from one address is throttled. For bulk validation, run MolProbity locally with Phenix. Results are private to their link and are deleted after 7 days. Powered by CCTBX from the Phenix project.
Hosted by the Phenix project
Lawrence Berkeley National Laboratory
phenix-online.org
Richardson Laboratory
Department of Biochemistry, Duke University
kinemage.biochem.duke.edu