The Swagger UI is at swagger-ui/index.html.

This page allows searching for structure motifs in the PDB and CSM corpus.

Some production features are not implemented, some things to consider:

No visualization of uploaded files
All low-confidence regions (pLDDT <70) are ignored
Frontend is slow on result sets with hundreds/thousands of hits, the hit limit is set to 5,000 but can be increased in the options panel

Custom query
Serine protease
Aminopeptidase
Zinc Fingers
Enolase superfamily
RNA G-tetrad
NOS bridge
M-CSA motifs

Custom query - Step 1: Define reference structure

Select structure by PDB entry ID:

Upload 3D structure (mmCIF, no-gzip):

Select file

attach_file

Custom query - Step 2: Extract motif

PDB entry ID: {{query.pdbId}}

Select label sequence identifiers as motif (format: [label_asym_id]_[struct_oper_id (1 for identity operation)]-[label_seq_id] - separate by whitespace) - e.g. 'B_1-57 B_1-102 C_1-195':

M-CSA Motifs

Select M-CSA Motif:

PDB entry ID: {{query.pdbId}} - reference: {{query.reference}}

Label sequence identifiers: {{id}}

Position-specific exchanges: {{e}} none

options

Position-specific exchanges - for format see enolase example:

Backbone distance tolerance:

Side-chain distance tolerance:

Angle tolerance:

RMSD cutoff (leave empty or type 0 to allow all hits):

Accepted hit limit (leave empty or type 0 to allow all hits):

Atom pairing scheme:

Motif pruning strategy:

Results content type:

submit query

message: {{error.message}}

Query

PDB entry id: {{result.result.query.entry_id}}

Label identifiers: {{c.label_asym_id}}_{{c.struct_oper_id}}-{{c.label_seq_id}}

Position-specific exchanges: {{e.residue_id.label_asym_id}}_{{e.residue_id.struct_oper_id}}-{{e.residue_id.label_seq_id}} {{e.allowed}} none

Parameters

Backbone tolerance: ±{{result.result.query.parameters.backbone_distance_tolerance}} Å

Side-chain tolerance: ±{{result.result.query.parameters.side_chain_distance_tolerance}} Å

Angle tolerance: ±{{result.result.query.parameters.angle_tolerance * 20}}°

RMSD filter: {{result.result.query.parameters.rmsd_cutoff | number: 2 }}

Limit result set to: {{result.result.query.parameters.limit}} hits

Atom pairing scheme: {{result.result.query.parameters.atom_pairing_scheme}}

Motif pruning strategy: {{result.result.query.parameters.motif_pruning_strategy}}

Results content type: {{result.result.query.results_content_type}}

Hits

Evaluated candidates: {{result.result.number_of_paths}} candidates in {{result.result.number_of_target_structures}} structures

Accepted hits: {{result.result.number_of_hits}}

Timings

Build paths: {{result.result.timings.paths_time}} ms ({{result.result.timings.paths_time / result.result.query.residue_ids.length | number: 2}} ms/op)

Load structures: {{result.result.timings.score_hits_time}} ms ({{result.result.timings.score_hits_time / result.result.number_of_target_structures | number: 2}} ms/op)

Backend: {{result.result.timings.query_time}} ms

Frontend without render: {{result.result.timings.total_time - result.result.timings.query_time}} ms ({{(result.result.timings.total_time - result.result.timings.query_time) / result.result.number_of_hits | number: 2}} ms/op)

Total request: {{result.result.timings.total_time}} ms

{{id.label_asym_id}}_{{id.struct_oper_id}}-{{id.label_seq_id}} | score {{subhit.score | number: 2}} | align | view AlphaFold DB entry view PDB entry

Custom query - Step 1: Define reference structure

Custom query - Step 2: Extract motif

M-CSA Motifs

{{query.title}}

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Query

Parameters

Hits

Timings

{{id}}

3D View

RMSD Distribution