### Abstract

The conditional probability, P(σ|x), is a statement of the probability that the value of σ will be found given the prior information that a value of x has been observed. Here σ represents any one of the secondary structure types, α, β, τ, and ρ for helix, sheet, turn, and random, respectively, and x represents a sequence attribute, including, but not limited to: (1) hydropathy; (2) hydrophobic moments assuming helix and sheet; (3) Richardson and Richardson helical N-cap and C-cap values; (4) Chou-Fasman conformational parameters for helix, P(α), for sheet, P(β), and for turn, P(τ); and (5) Garnier, Osguthorpe, and Robson (GOR) information values for helix, I(α), for sheet, I(β), for turn, I(τ), and for random structure, I(ρ). Plots of P(σ|x) vs. x are demonstrated to provide information about the correlation between structure and attribute, σ and x. The separations between different P(σ|x) vs. x curves indicate the capacity of a given attribute to discriminate between different secondary structural types and permit comparison of different attributes. P (α|x), P(β|x), P(τ|x) and P(ρ|x) vs. x plots show that the most useful attributes for discriminating helix are, in order: hydrophobic moment assuming helix > P(α) > > N-cap > C- cap ≃ I(α) ≃ L(τ). The information value for turns, I(τ), was found to discriminate helix better than turns. Discrimination for sheet was found to be in the following order: I(β) > > P(β) ≃ hydropathy > I(ρ) ≃ hydrophobic moment assuming sheet. Three attributes, at their low values, were found to give significant discrimination for the absence of helix: I(α) ≃ P(α) ≃ hydrophobic moment assuming helix. Also, three other attributes were found to indicate the absence of sheet: P(β) > > I(ρ) ≃ hydropathy. Indications of the absence of σ could be as useful for some applications as the indication of the presence of σ.

Original language | English (US) |
---|---|

Pages (from-to) | 382-399 |

Number of pages | 18 |

Journal | Proteins: Structure, Function and Genetics |

Volume | 12 |

Issue number | 4 |

DOIs | |

State | Published - 1992 |

Externally published | Yes |

### Fingerprint

### Keywords

- amino acid sequence
- distributions
- protein secondary structure

### ASJC Scopus subject areas

- Genetics
- Structural Biology
- Biochemistry

### Cite this

*Proteins: Structure, Function and Genetics*,

*12*(4), 382-399. https://doi.org/10.1002/prot.340120410

**Use of conditional probabilities for determining relationships between amino acid sequence and protein secondary structure.** / Arnold, G. E.; Dunker, A.; Johns, S. J.; Douthart, R. J.

Research output: Contribution to journal › Article

*Proteins: Structure, Function and Genetics*, vol. 12, no. 4, pp. 382-399. https://doi.org/10.1002/prot.340120410

}

TY - JOUR

T1 - Use of conditional probabilities for determining relationships between amino acid sequence and protein secondary structure

AU - Arnold, G. E.

AU - Dunker, A.

AU - Johns, S. J.

AU - Douthart, R. J.

PY - 1992

Y1 - 1992

N2 - The conditional probability, P(σ|x), is a statement of the probability that the value of σ will be found given the prior information that a value of x has been observed. Here σ represents any one of the secondary structure types, α, β, τ, and ρ for helix, sheet, turn, and random, respectively, and x represents a sequence attribute, including, but not limited to: (1) hydropathy; (2) hydrophobic moments assuming helix and sheet; (3) Richardson and Richardson helical N-cap and C-cap values; (4) Chou-Fasman conformational parameters for helix, P(α), for sheet, P(β), and for turn, P(τ); and (5) Garnier, Osguthorpe, and Robson (GOR) information values for helix, I(α), for sheet, I(β), for turn, I(τ), and for random structure, I(ρ). Plots of P(σ|x) vs. x are demonstrated to provide information about the correlation between structure and attribute, σ and x. The separations between different P(σ|x) vs. x curves indicate the capacity of a given attribute to discriminate between different secondary structural types and permit comparison of different attributes. P (α|x), P(β|x), P(τ|x) and P(ρ|x) vs. x plots show that the most useful attributes for discriminating helix are, in order: hydrophobic moment assuming helix > P(α) > > N-cap > C- cap ≃ I(α) ≃ L(τ). The information value for turns, I(τ), was found to discriminate helix better than turns. Discrimination for sheet was found to be in the following order: I(β) > > P(β) ≃ hydropathy > I(ρ) ≃ hydrophobic moment assuming sheet. Three attributes, at their low values, were found to give significant discrimination for the absence of helix: I(α) ≃ P(α) ≃ hydrophobic moment assuming helix. Also, three other attributes were found to indicate the absence of sheet: P(β) > > I(ρ) ≃ hydropathy. Indications of the absence of σ could be as useful for some applications as the indication of the presence of σ.

AB - The conditional probability, P(σ|x), is a statement of the probability that the value of σ will be found given the prior information that a value of x has been observed. Here σ represents any one of the secondary structure types, α, β, τ, and ρ for helix, sheet, turn, and random, respectively, and x represents a sequence attribute, including, but not limited to: (1) hydropathy; (2) hydrophobic moments assuming helix and sheet; (3) Richardson and Richardson helical N-cap and C-cap values; (4) Chou-Fasman conformational parameters for helix, P(α), for sheet, P(β), and for turn, P(τ); and (5) Garnier, Osguthorpe, and Robson (GOR) information values for helix, I(α), for sheet, I(β), for turn, I(τ), and for random structure, I(ρ). Plots of P(σ|x) vs. x are demonstrated to provide information about the correlation between structure and attribute, σ and x. The separations between different P(σ|x) vs. x curves indicate the capacity of a given attribute to discriminate between different secondary structural types and permit comparison of different attributes. P (α|x), P(β|x), P(τ|x) and P(ρ|x) vs. x plots show that the most useful attributes for discriminating helix are, in order: hydrophobic moment assuming helix > P(α) > > N-cap > C- cap ≃ I(α) ≃ L(τ). The information value for turns, I(τ), was found to discriminate helix better than turns. Discrimination for sheet was found to be in the following order: I(β) > > P(β) ≃ hydropathy > I(ρ) ≃ hydrophobic moment assuming sheet. Three attributes, at their low values, were found to give significant discrimination for the absence of helix: I(α) ≃ P(α) ≃ hydrophobic moment assuming helix. Also, three other attributes were found to indicate the absence of sheet: P(β) > > I(ρ) ≃ hydropathy. Indications of the absence of σ could be as useful for some applications as the indication of the presence of σ.

KW - amino acid sequence

KW - distributions

KW - protein secondary structure

UR - http://www.scopus.com/inward/record.url?scp=0026629597&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0026629597&partnerID=8YFLogxK

U2 - 10.1002/prot.340120410

DO - 10.1002/prot.340120410

M3 - Article

VL - 12

SP - 382

EP - 399

JO - Proteins: Structure, Function and Genetics

JF - Proteins: Structure, Function and Genetics

SN - 0887-3585

IS - 4

ER -