Enum: SecondaryStructureType

Per-residue secondary structure assignment. The permissible values correspond to the canonical DSSP 8-state (SS8) classification, which is also the secondary-structure track vocabulary used by protein language models such as ESM3. The single-letter DSSP code is recorded in the dssp_code annotation.

URI: valuesets:SecondaryStructureType

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Permissible Values

Value	Title	Meaning	Description	Exact Mappings	Broad Mappings	Aliases	Dssp Code	Ontology Gap	Ss8 Class
ALPHA_HELIX	alpha helix	SO:0001117	Right-handed alpha helix (3.6 residues/turn, i to i+4 hydrogen bonding)		uniprot_core:Helix_Annotation		H		H
THREE_TEN_HELIX	3-10 helix	SO:0001119	3-10 helix (3 residues/turn, i to i+3 hydrogen bonding)		uniprot_core:Helix_Annotation		G		G
PI_HELIX	pi helix	SO:0001118	Pi helix (4.1 residues/turn, i to i+5 hydrogen bonding)		uniprot_core:Helix_Annotation		I		I
BETA_STRAND	beta strand	SO:0001111	Extended beta strand participating in a beta sheet		uniprot_core:Beta_Strand_Annotation		E		E
BETA_BRIDGE	isolated beta bridge		Residue in an isolated single-pair beta bridge		uniprot_core:Beta_Strand_Annotation		B	true	B
TURN	hydrogen-bonded turn	SO:0001128	Hydrogen-bonded turn reversing backbone direction over <=4 residues	uniprot_core:Turn_Annotation			T		T
BEND	bend		Region of high backbone curvature without regular hydrogen bonding				S	true	S
COIL	coil / loop	SO:0100012	Irregular, unstructured backbone region (loop / random coil)			loop, random coil, blank	C		C

Slots

Name	Description
secondary_structure	Per-residue secondary structure state

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/valuesets

LinkML Source

name: SecondaryStructureType
instantiates:
- valuesets_meta:ValueSetEnumDefinition
description: Per-residue secondary structure assignment. The permissible values correspond
  to the canonical DSSP 8-state (SS8) classification, which is also the secondary-structure
  track vocabulary used by protein language models such as ESM3. The single-letter
  DSSP code is recorded in the ``dssp_code`` annotation.
title: Secondary Structure Type
from_schema: https://w3id.org/valuesets
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: DRAFT
rank: 1000
permissible_values:
  ALPHA_HELIX:
    text: ALPHA_HELIX
    description: Right-handed alpha helix (3.6 residues/turn, i to i+4 hydrogen bonding)
    meaning: SO:0001117
    annotations:
      dssp_code:
        tag: dssp_code
        value: H
      ss8_class:
        tag: ss8_class
        value: H
    title: alpha helix
    broad_mappings:
    - uniprot_core:Helix_Annotation
  THREE_TEN_HELIX:
    text: THREE_TEN_HELIX
    description: 3-10 helix (3 residues/turn, i to i+3 hydrogen bonding)
    meaning: SO:0001119
    annotations:
      dssp_code:
        tag: dssp_code
        value: G
      ss8_class:
        tag: ss8_class
        value: G
    title: 3-10 helix
    broad_mappings:
    - uniprot_core:Helix_Annotation
  PI_HELIX:
    text: PI_HELIX
    description: Pi helix (4.1 residues/turn, i to i+5 hydrogen bonding)
    meaning: SO:0001118
    annotations:
      dssp_code:
        tag: dssp_code
        value: I
      ss8_class:
        tag: ss8_class
        value: I
    title: pi helix
    broad_mappings:
    - uniprot_core:Helix_Annotation
  BETA_STRAND:
    text: BETA_STRAND
    description: Extended beta strand participating in a beta sheet
    meaning: SO:0001111
    annotations:
      dssp_code:
        tag: dssp_code
        value: E
      ss8_class:
        tag: ss8_class
        value: E
    title: beta strand
    broad_mappings:
    - uniprot_core:Beta_Strand_Annotation
  BETA_BRIDGE:
    text: BETA_BRIDGE
    description: Residue in an isolated single-pair beta bridge
    annotations:
      dssp_code:
        tag: dssp_code
        value: B
      ss8_class:
        tag: ss8_class
        value: B
      ontology_gap:
        tag: ontology_gap
        value: 'true'
    title: isolated beta bridge
    broad_mappings:
    - uniprot_core:Beta_Strand_Annotation
  TURN:
    text: TURN
    description: Hydrogen-bonded turn reversing backbone direction over <=4 residues
    meaning: SO:0001128
    annotations:
      dssp_code:
        tag: dssp_code
        value: T
      ss8_class:
        tag: ss8_class
        value: T
    title: hydrogen-bonded turn
    exact_mappings:
    - uniprot_core:Turn_Annotation
  BEND:
    text: BEND
    description: Region of high backbone curvature without regular hydrogen bonding
    annotations:
      dssp_code:
        tag: dssp_code
        value: S
      ss8_class:
        tag: ss8_class
        value: S
      ontology_gap:
        tag: ontology_gap
        value: 'true'
    title: bend
  COIL:
    text: COIL
    description: Irregular, unstructured backbone region (loop / random coil)
    meaning: SO:0100012
    annotations:
      dssp_code:
        tag: dssp_code
        value: C
      ss8_class:
        tag: ss8_class
        value: C
      aliases:
        tag: aliases
        value: loop, random coil, blank
    title: coil / loop