Returns chemical components that are similar to the given chemical component. Results include stereoisomers, components sharing a common scaffold, and molecules with ≥60% PARITY score-based similarity.

Returns aggregated interaction counts for protein-ligand interactions, derived from all PDB structures containing the given chemical component. The response reports how frequently a ligand atom interacts with specific amino-acid residues across the PDB, grouped by interaction type.

Returns the protein chains in PDB entries that interact with the given chemical component and are mapped to UniProt, including the associated UniProt metadata for these proteins.

Returns the amino-acid sequence for a specific PDB Entry and Chain ID (label_asym_id).

Returns MOLE tunnel annotations for a PDB entry. When assembly_id is omitted, the PDBe-preferred assembly is used.

Returns a list of FunPDBe functional annotation resources available for a given PDB Entry, including their origin (e.g: “3Dcomplex”, “WEBnma”, “canSAR”), the annotation labels they provide (e.g: “Surface_residue”, “pocket_1”, “LP/P”), evidence ontology codes (e.g: ECO_0000053), release dates (e.g: 01/06/2017), and source URLs (e.g: https://prankweb.cz).

Returns all FunPDBe functional annotations and related metadata for each annotated residue or functional site of a given PDB entry ID for a specific FunPDBe annotation resource. Includes the evidence ontology codes (e.g: ECO_0000053), release date (e.g: 01/06/2017), and source URLs (e.g: https://prankweb.cz). Raw scores, confidence scores and confidence classification labels are also provided for each residue level annotation when possible.

Returns information for all bound molecules for a given PDB entry ID, including carbohydrate polymers. Details include each Bound Molecule IDs (e.g: “bm1”, “bm2”), composition (covalently bound ligands with unique CCD IDs) and internal connectivity, or which bound are covalently bound together (e.g: [“F1”, “F6”] means bound ligands identified by author_residue_number “1” and “6” in chain_id “F” are covalently bound).

Returns composition and high-level interactions for a specific Bound Molecule ID (e.g., “bm1”) of a PDB entry ID. This includes its full composition (all covalently linked ligands with their CCD IDs), internal connectivity between those ligands (e.g: [“F1”, “F6”] means bound ligands identified by author_residue_number “1” and “6” in chain_id “F” are covalently bound), and all detected interactions between the bound molecule and surrounding residues or ligands (e.g., covalent, hydrogen-bond, polar, van der Waals, hydrophobic, and atom-plane interactions) calculated for the preferred assembly of the PDB entry.

This call provides interactions for a bound ligand found in the entry.

Returns residue-level sequence conservation data for a specified PDB entry ID and PDB entity ID, including per-residue conservation scores and amino-acid probability distributions.

Returns UniProt mappings for a specific PDB Entity ID, including matched UniProt accessions, residue-level alignment ranges, and metadata identifying the corresponding Best Chain ID for the mapping.

Returns secondary-structure annotations for a specified PDB Entity ID, including helices and strands, plus per-residue structural predictions from external tools (e.g., disorder, folding propensity, flexibility), each with associated scores, labels, and source metadata.

Returns ligand-binding site annotations for a specified PDB entity, including metadata such as Best Chain ID, Scaffold ID, and the total number of protein residues that interact with each ligand (based on ARPEGGIO). For each ligand, the endpoint provides its CCD ID, name, and a list of interacting residues grouped by the Bound Molecule ID they interact with.

Returns protein–protein interface annotations for a specified PDB Entity ID, identifying all residues that form PISA-detected contacts with interacting partner proteins. For each partner, the endpoint provides its UniProt accession, name, and the corresponding interface residue ranges, along with metadata such as the entity’s Best Chain ID.

Returns residue-level functional and biophysical annotations for a specified PDB Entity ID, aggregated from multiple PDBe-KB partner resources (e.g., SASA, hydrophobicity, disorder, flexibility, EM local resolution). Data returned includes annotation type, per-residue scores, confidence metrics, group labels, and the originating resource URL, as well as the Best Chain ID for the entity.

Returns sequence and structural domain annotations for a specified PDB Entity ID, including domain boundaries, identifiers, and names from CATH, SCOP 1.75, Pfam and InterPro domain resources, along with metadata such as the entity’s Best Chain ID.

Returns detailed chain-level annotations for a specified PDB Entity ID, including all of their polymer chains, their residue ranges, and per-residue validation information, along with metadata such as Best Chain ID and author-provided chain identifiers (Obs: chainId in additionalData response refers to struct_asym_id not the author-provided auth_asym_id).

Returns UniProt sequence-variation annotations for a specified PDB Entity ID, remapped to the entity’s residue positions. The response includes each mapped UniProt accession and its variant features, such as variant type, alternative sequence, position, associated evidence, cross-references, clinical or functional annotations, and any available structural-impact metadata.

Returns information for all assemblies of a specified PDB ID, with details provided for each constituent entity within every biological or author-defined assembly. For each assembly, the endpoint reports the molecular weight, entity types and names, chain mappings (note: the in_chains field lists struct_asym_id values rather than author-assigned chain identifiers), and the number of copies of each entity.

Returns all modeled non-water ligand instances for a PDB entry, including molecular weight, chain identifiers, residue numbers, chemical component IDs and names, PDB Entity IDs, conformer counts, Bound Molecule IDs, and functional annotations (cofactor-like, drug-like or reactant-like).

Returns summarised detailed information about each molecule (or entity in mmcif-speak) in a specified PDB entry, including entity type; molecule names mapped from UniProt; the synonym field (equivalent to _entity.pdbx_description) for polymeric entities; DrugBank-derived synonyms for ligands; sequence data; chain assignments; copy numbers; source organism and sample preparation details; and ligand or chemical component information.

List all residues in a PDB entry, excluding waters, including both modelled and unmodelled residues. For each residue, the response provides the entity ID, chain identifiers, mmCIF- and PDB-style residue numbers with insertion codes, chemical component names, the fraction of expected atoms that are modelled, and details of any alternate conformers present

Returns all interface residue contacts calculated by PISA (Proteins, Interfaces, Structures and Assemblies) for a specified PDB entry ID. The results include interaction types (e.g., salt bridges and hydrogen bonds), interatomic distances, and details of the participating atoms and residues from both interacting chains. Results can optionally be filtered by assembly_id and interface_id.

This call returns a summary for the chemical component identified by the given hetcode, including its chemical structure identifiers, physico-chemical descriptors, synonyms, PDB chemical component metadata, functional annotations, and cross-references to external resources.

This call returns a list of PDB entries that contain the given chemical component as defined in the PDB Chemical Component Dictionary. The list includes PDB entries where the component appears either as a standalone chemical component or as part of a larger entity.

These scores are harmonic means of percentile-based quality metrics for macromolecular structures: - geometry_quality: from geometric percentiles (Ramachandran, clashscore, sidechains). - data_quality: from diffraction–data percentiles (R-free, RSRZ). - overall_quality: combines geometry and data percentiles. If any contributing percentile is 0, the harmonic mean is 0. If all percentiles are unavailable, the score is null. experiment_data_available indicates whether experimental diffraction data were used

Provides a validation summary listing key geometric and electron-density–based metrics. For each category (e.g., bonds, angles, RNA suite, Ramachandran, sidechains, RSRZ), the report includes: - number of residues/instances checked - number of outliers - percent outliers - and, where applicable, RMSZ values. Categories with no relevant residues return null percentages.

Lists all geometric and model–data outliers detected by MolProbity, grouped by category (e.g., clashes, sidechains, RSRZ, bond/angle outliers, RNA suite/pucker, chirality, planes, symmetry clashes). Atoms or residues involved in each outlier are reported using unit-id notation The types_of_outliers section summarizes, per residue, which types of outliers it participates in.

Provides ligand-level validation results, combining Mogul geometric analysis (bond and angle RMSZ and atom outliers) with experimental fit metrics (OWAB, RSCC, RSR, LLDF, occupancy). Each returned ligand entry includes its location identifiers (entity, chain, residue, model) plus a flag indicating whether the ligand is an experimental outlier.

Provides a ranked list of PDB structures mapped to the given UniProt accession based on an internal quality score (based on data quality, model quality and resolution ). Each structure entry includes the experimental method, taxonomic origin, resolution, PDB ID and chain, entity and assembly identifiers, observed UniProt alignment segments, model residue ranges, and computed coverage of the UniProt sequence.

Retrieve a list of non-overlapping PDB chains that cover the largest number of observed residues for a given UniProt accession.

Retrieve detailed information on interface residues for a given UniProt accession, including the amino acid sequence for polymeric entities and the total sequence length. The response provides the type of data included and an array of residue-level details, with information such as the starting position in a processed protein sequence when applicable. This endpoint enables analysis of residues involved in protein interfaces, offering sequence context alongside structural and functional annotations.

Retrieve information on interaction partners for a given UniProt accession, including their names, annotations such as antibody roles, the PDB structures where interactions are observed, and whether the interaction is self-directed. This endpoint provides structural and functional context for protein interactions.

Retrieve comprehensive information on PDB structures mapped to a given UniProt accession. The response includes the UniProt sequence and length, along with detailed structure annotations such as entity and chain identifiers, residue coverage in UniProt and PDB numbering, observed regions, mutations, modifications, experiment type, resolution, ligand and entity counts, and supporting metadata like titles, ranking scores, and additional structure-specific information. This endpoint provides an integrated view of how PDB structures align with and represent the UniProt sequence

This call provides PDBe-KB annotations for a given UniProt accession, with optional filtering by annotation category. The response includes the UniProt sequence and length, along with detailed annotation records describing residue ranges in UniProt and PDB numbering, residue codes, associated PDB entries, and supporting metadata such as accession identifiers, scores, confidence levels, and resource links. Information on processed protein start positions is also provided, offering a unified view of structural and functional annotations across the sequence.

Retrieve PDBe-KB sequence conservation data for a UniProt accession. The response provides residue-level conservation scores, per-residue amino acid probability profiles, sequence identifiers, the length of the UniProt sequence, and colors for visualizing main and sub-tracks.

Retrieve variation details for a given UniProt accession. The response includes the protein sequence and length, UniProt identifiers, and a list of variant features with information on alternative sequences, associated diseases, evidences, genomic locations, consequence types, and predictions from tools such as PolyPhen and SIFT. Additional metadata includes clinical significance, source information, cross-references, and relevant URLs, enabling comprehensive analysis of protein sequence variations.

Retrieve text mined annotations for a given UniProt accession. The response includes associated PDB structures, and residue-level annotations. The residue start and end positions follow either UniProt or PDB numbering. Each annotation details the provider, additional supporting data such as citations, entity type, textual evidence, annotator, and AI-generated confidence scores, enabling comprehensive exploration of machine-predicted functional and structural insights.

Provides unified SIFTS residue-level mappings between PDB protein chains (auth_asym_id or struct_asym_id) and all major sequence and domain resources, including UniProt, Pfam, InterPro, CATH, SCOP, GO, Ensembl, and HMMER. Supports both PDB-to-identifier and identifier-to-PDB queries, returning the mapped residue segments and associated annotations for each resource.

Retrieve information about macromolecular complexes, including participants, stoichiometry, oligomeric state, symmetry, representative structure, structural instances, bound macromolecules, and subcomplex/supercomplex relationships. Queries using UniProt/Rfam accessions or PDB IDs can return multiple matching complexes. Currently, queries using pdb_complex_id return richer annotations and more detailed assembly information than other identifier types.

Retrieve an aggregated summary of small-molecule ligands observed across different structural instances of a given macromolecular complex. The response includes ligand names, functional annotations (such as cofactor-like, drug-like, and reactant-like), and occurrence counts based on PDB entries, chains, and ligand instances.

Retrieve related subcomplexes and supercomplexes based on macromolecular composition. Subcomplexes contain a subset of the query complex's components, while supercomplexes contain additional components. The response includes PDB Complex IDs, representative structures, relationship types, and shared or additional macromolecular participants.

Retrieve PISA-calculated structural and energetic properties for different structural instances of a given macromolecular complex, including accessible and buried surface areas, dissociation free energy, dissociation entropy, dissociation area, and solvation energy gain. The response also includes the 5th and 95th percentile values for these properties across the available structural instances.

This call returns all PDB entries and RNA chains that map to the specified Rfam accession, including the matched regions.

Retrieve the pre-generated AI summary for a four-character PDB entry. Use this for an entry overview instead of writing a new summary. Returns the available summary sections and abstract key points, preserving inline reference markers and listing their PDBe source URLs and fields. A summary may not exist for every entry.

Retrieves the Solr search schema for the PDBe search service. You can use this tool to understand the structure and fields available in the PDBe search index. Once you have the schema, you can use it to construct more effective search queries and run the query using the run_pdbe_search_query tool. This tool returns a detailed schema of the Solr search index used by PDBe. The schema includes information about all the fields available for searching, along with their types, whether they are stored or indexed, and any relevant descriptions. Expected Output Format: A text representation of the search schema, formatted as a table with the following columns: - Field Name: The name of the field in the Solr schema. - Type: The data type of the field (e.g. string, integer, date). - Stored: Indicates whether the field is stored in the index (true/false). - Indexed: Indicates whether the field is indexed for searching (true/false). - Description: A brief description of the field and its purpose. The output will be structured in a way that is easy to read and understand, allowing users to quickly grasp the available search fields and their characteristics.

Executes a search query against the PDBe Solr search service. This tool exposes common Solr query parameters directly so users can construct fielded queries, filter queries, field lists, facets, grouping, sorting, and pagination against the PDBe search index. IMPORTANT: query is passed to Solr as the raw q parameter. Use Solr query syntax such as *:*, pdb_id:1cbs, text:*kinase*, boolean clauses, ranges, and boosts as needed. IMPORTANT: the text field is a copy field that contains the full searchable text aggregated from the document. Use text:*<term>* when you want a broad wildcard text search. Expected Input Parameters: - query (string): Raw Solr query string passed as q. - fl (string or list of strings, optional): Solr field list. The legacy filters parameter is also accepted as an alias. - filters (list of strings, optional): Backwards-compatible alias for fl. - fq (string, object, list of strings, or list of objects, optional): Solr filter query or queries to narrow down the search results. Objects are converted to fielded filters, e.g. {"experimental_method": "X-ray diffraction"} becomes experimental_method:"X-ray diffraction". - sort (string, optional): The sorting criteria for the search results. - start (integer, optional): The starting index for pagination of results. - rows (integer, optional): The number of results to return. - facet (boolean, optional): Enable Solr faceting. - facet_fields (string or list of strings, optional): Field facets, sent as facet.field. - facet_queries (string or list of strings, optional): Query facets, sent as facet.query. - facet_limit, facet_mincount, facet_sort (optional): Common facet controls. - group (boolean, optional): Enable Solr grouping. - group_field (string or list of strings, optional): Grouping field, sent as group.field. - group_limit, group_offset, group_sort (optional): Common grouping controls. - params (object, optional): Additional Solr parameters to pass through for advanced use.

Example Input:
{
    "query": "text:*kinase*",
    "fl": ["pdb_id", "title", "deposition_date"],
    "fq": ["experimental_method:\"X-ray diffraction\""],
    "facet": true,
    "facet_fields": ["experimental_method"],
    "sort": "deposition_date desc",
    "start": 0,
    "rows": 10
}

Expected Output Format:
A text representation of the search results, formatted in a readable manner. The output will include:
- Metadata about the search results (e.g. number of documents found, start index).
- A list of documents matching the search query, with each document's fields and values clearly presented.
The output will be structured to facilitate easy interpretation of the search results, allowing users to quickly identify relevant information.
        

Compose or restore a molecular workspace in the shared viewer. Supply the latest complete workspace from tool results or App context, expected_revision, and atomic operations. Supports adding/removing scenes and structures, component or annotation layers, and changing layer visibility. IDs must match exactly. No operations validates and restores a saved workspace. No global server state is stored. The host must route matching workspace IDs to an existing App for cross-call updates; otherwise a new viewer opens. The App displays supplied coordinates, transforms, residue mappings and annotations; it does not calculate scientific measurements.

Build a guided molecular story with 2–20 ordered scenes and open it in Mol* 5.13.1. Each scene has a unique id, title, description and complete builder specification using the same schema as build_mvs. Set component opacity inside representation.opacity, never directly on a component. Ground all narrative claims and selections in PDBe evidence. Returns one native multi-state MVSJ with timed playback, scene navigation and download. The host can update the originating viewer or open a new result. Default duration is 6500 ms per scene and camera transition is 1500 ms. Stop after a compiled result. On validation failure, correct the input and retry once; never repeat identical input. Compilation does not establish coordinate availability or verify biological claims.

Build a custom single-scene molecular visualization with MolViewSpec and open it in Mol* 5.13.1. Supply a complete builder specification, including existing choices for follow-up changes; the host routes each result to an existing viewer or a new one. Supports chains, residue ranges, ligand instances, representations, colors, opacity, inline annotations, labels, tooltips, focus and camera. Set component opacity inside representation.opacity, never directly on a component. Ground selections in PDBe data; use label_seq_id for polymer residues and auth_seq_id with insertion code for non-polymers. Water is excluded from broad all selections unless include_water=true. Supports density isosurfaces and clipping; structure transforms/instances, multiple structures per scene, annotation tables, primitives and serialized MolQL selectors. No raw MVS trees, executable code or PyMOL text. Returns the complete normalized builder in structuredContent for follow-ups; full MVSJ is delivered to the App with download support. A compiled result completes the build; do not rebuild while waiting for viewer loading. Compilation does not verify biological claims or coordinate availability.

Compare two protein label chains using PDBe's precomputed superposition matrices and SIFTS residue correspondence. Requires a shared UniProt accession and PDBe segment containing both chains. Opens aligned proteins first; ligands and residue annotations are opt-in through include_ligands/include_annotations or the workspace controls. Includes PDBe/SIFTS correspondence and CSV export. The viewer applies PDBe's transforms; no additional fitting, RMSD, per-residue displacement or inferred binding sites are calculated.

Open an experimental PDB structure in an interactive 3D viewer. Inspect chains, ligand instances and residues. Displays the first coordinate model; defaults to the deposited asymmetric unit. A successful result completes the viewing request; stop calling this tool and let the App load coordinates.

Internal App-only helper; never call this in response to a user's request to open, view, inspect, or show a structure or PDB entry, including when they provide only an entry ID. For every initial structure-viewing request, call ebi-pdbe-open_structure. This helper is only for the App to load optional PDBe-supplied residue annotations into a workspace that is already open. Returns annotation records and track layers only, not coordinates or an MVS scene.

Explore PDBe-reported interactions for an exact ligand instance in the shared Molecular Workspace. First call with a PDB ID to list instances; then provide author chain and author residue number (plus CCD and insertion code when available) to retrieve that instance's supplied interaction records. The App displays source classifications and distances without calculating or reclassifying contacts. Contact lines are shown only when atom and assembly/model mapping is unambiguous; otherwise use the table.