What input does protein structure search require?

One experimental or predicted protein structure in PDB or mmCIF format.

What does protein structure search return?

Ranked database hits, identifiers, E-values, coverage, TM-scores, LDDT values, alignments, and downloadable files.

How should protein structures be prepared?

Confirm accession, model, chain, biological assembly, domain boundaries, residue numbering, missing regions, alternate conformations, and prediction confidence. Repair coordinates only when necessary and retain both the original file and every preparation decision.

Which structure-alignment score should I use?

Use method-native scores together rather than selecting one universal number. TM-score emphasizes length-normalized global fold similarity, RMSD reports geometric deviation over the aligned atoms, and coverage shows how much of each structure actually corresponds.

Does structural similarity prove shared function?

No. Similar folds can support different functions, and local similarity can occur without shared global architecture. Review residue-level correspondence, domains, ligands, oligomeric state, taxonomy, sequence evidence, curated annotations, and experiments.

How much does protein structure search cost?

A complete protein structure search project is generally quote-based. Current providers describe fold recognition and protein-structure analysis as customized services covering data review, method selection, modeling or comparison, validation, and interpretation rather than publishing one universal project price. The cost depends on structure or sequence count, database scope, model preparation, method comparison, manual inspection, figures, annotation, and whether experimental follow-up is included. Open-source FoldSeek, US-align, and FoldMason can remove a software-license fee, but they do not remove expert analysis or compute requirements. ProteinIQ self-service starts at $29 per month for academic Plus and $99 per month for commercial Pro, with the configured protein structure search workflow estimated in credits before submission. Done-for-you analysis is scoped separately.

Protein structure search online

What is protein structure search?

Protein structure search is the process of querying a structural database with a three-dimensional protein model to find geometrically similar entries. FoldSeek represents local tertiary interactions with a structural alphabet, enabling fast candidate retrieval before detailed score, alignment, and biological review.

Use structure search to find remote homolog candidates, fold analogs, related domains, or structurally similar proteins when sequence search is insufficient. The query may be experimental or predicted, but chain choice, domain boundaries, missing residues, and model confidence affect retrieval.

ProteinIQ directly runs FoldSeek database search against supported structural collections. Results retain database identifiers, alignment statistics, TM-score and LDDT context, coverage, E-values, and files so promising hits can be checked with detailed pairwise alignment and independent biological evidence.

When to use protein structure search

Best fit. Finding structural neighbors, remote homolog candidates, analogs, and fold-family context
Required evidence. One reviewed protein structure with appropriate chain and domain boundaries
Execution boundary. FoldSeek performs the core structure search directly; downstream homology and function claims still require independent review.

Benefits of protein structure search

Structural sensitivity. Finds remote relationships missed by sequence search
Connected evidence. Scales to large structural databases
Reusable output. Returns inspectable alignments and method-native scores

Primary limitations

Coverage limit. Database coverage limits what can be found
Method dependence. Query boundaries and quality affect ranking
Interpretive limit. Structural similarity alone does not prove function

Protein structure search methods

FoldSeek converts tertiary residue neighborhoods into a structural alphabet and applies sequence-search techniques to retrieve similar structures rapidly. Global shape-search and pairwise alignment methods use different representations and scoring objectives.

Database composition matters. Searching clustered predicted structures can reveal broad fold neighborhoods, while curated experimental structures may offer stronger ligand, assembly, and functional context.

Protein structure search applications

Protein structure search supports remote-homology discovery, structural annotation, fold classification, model-quality investigation, target comparison, and selection of templates or representatives for deeper analysis.

A match can reflect global fold, one shared domain, repetitive architecture, or local geometry. Inspect the aligned region rather than transferring annotations from the database record as a whole.

How to run protein structure search online

FoldSeek performs the core structure search directly; downstream homology and function claims still require independent review.

Prepare the query. Choose the relevant chain, domain, assembly, and conformational state, and review missing or low-confidence regions.
Choose databases. Select structural databases and thresholds that match the intended sensitivity and result volume.
Run FoldSeek. Run FoldSeek while preserving database versions, search settings, warnings, and failed inputs.
Review matches. Inspect rank, E-value, coverage, TM-score, LDDT, residue alignment, and query–target length differences together.
Validate candidates. Confirm important candidates with detailed superposition, sequence evidence, curated annotations, and experiments when the claim requires them.

How to interpret protein structure search results

Evaluate E-value, score, coverage, aligned length, TM-score, LDDT, and sequence identity together. No single threshold is universal across query lengths, databases, and scientific questions.

Structural similarity is not proof of common ancestry or shared biochemical function. Confirm domain architecture, conserved residues, oligomeric state, ligands, taxonomy, and sequence evidence before annotation transfer.

How protein structure search works

FoldSeek performs the core structure search directly; downstream homology and function claims still require independent review.

Prepare the query. Choose the relevant chain, domain, assembly, and conformational state, and review missing or low-confidence regions.
Choose databases. Select structural databases and thresholds that match the intended sensitivity and result volume.
Run FoldSeek. Run FoldSeek while preserving database versions, search settings, warnings, and failed inputs.
Review matches. Inspect rank, E-value, coverage, TM-score, LDDT, residue alignment, and query–target length differences together.
Validate candidates. Confirm important candidates with detailed superposition, sequence evidence, curated annotations, and experiments when the claim requires them.

Inputs and outputs

Check formats before running, then inspect and download the result from every workflow step.

Inputs

Structure-analysis inputs. PDB mmCIF FASTA TSV One experimental or predicted protein structure in PDB or mmCIF format.

Outputs

Reviewable results. PDB CSV TSV JSON FILES Ranked database hits, identifiers, E-values, coverage, TM-scores, LDDT values, alignments, and downloadable files.