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Table 2 Computational evaluation of peptides selected for experimental verification

From: Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars

Peptide

Sequence

ORT49035.1_103_123

VDLRDAKGVQVGDGNVQINRF

AAS80314.1_349_385

SFNNLGSGDQFNTPGGTQNINKGGNEVSGGNFYGSVQF

AEB69175.1_5_29

KSRFDQRGQKVIGQQINVAGDATLP

RDW70414.1_382_421

GAPANNTSNSIQHNNSGSGHQNSGSGQQNIGTNTGSGQQ

Peptide

PCFG

pHMM

PLAAC

PASTA2

AmyloG

ArchC

FPR\(\downarrow\)

FPR\(\downarrow\)

FPR\(\downarrow\)

[PEU]\(\downarrow\)

[0-1]\(\uparrow\)

[0-1]\(\uparrow\)

ORT49035.1_103_123

\(\le\) 0.0004

< 0.0004

0.022

− 2.5

0.63

0.379

AAS80314.1_349_385

< 0.0004

< 0.0004

< 0.0004

− 1.6

0.78

0.555

AEB69175.1_5_29

0.007\(- 0.07\)

< 0.0004

0.022

− 3.7

0.43

0.488

RDW70414.1_382_421

< 0.0004

\(0.01{-}0.35\)

<0.0004

− 0.9

0.26

0.599

  1. Top: List of peptides selected for experimental verification. Bottom: results of computational methods. For PCFG, pHMM (both with score averaging) and PLAAC we provide FPR against NLReff at which at least a part of the peptide is detected; for PASTA2—Pasta Energy Units; for AmyloGram (AmyloG) and ArchCandy (ArchC)—score ranged from 0 to 1. Arrow indicates if higher or lower value is more positive. Values exceeding the default or suggested thresholds are shown in bold (the thresholds are \(1e{-}2\) for PCFG, pHMM and PLAAC, -5 PEU for PASTA2, 0.5 for AmyloGram, and 0.56 for ArchCandy). For PCFG, we provide the range of values for grammars of different maximum number of symbols; For pHMM—the range of values for profiles made from different accurate MSAs