PROFtmb

PROFtmb predicts per-residue topology and discriminates transmembrane beta-barrel (TMB) proteins, identifying strand orientations, periplasmic hairpins, and extracellular loops to support analysis of Gram-negative bacterial proteomes.

Key Features:

• Per-Residue Prediction: Provides a four-state per-residue labeling distinguishing upward-facing strands, downward-facing strands, periplasmic hairpins, and extracellular loops.
• Z-Value Calculation: Calculates a Z-value per protein that quantifies the likelihood of containing a membrane barrel structure.
• Whole-Protein Discrimination: Reports whole-protein discrimination performance of 70% accuracy at 60% coverage on an 8-fold cross-validated testing set.
• Comprehensive Database: Includes source code and training data and reports whole-proteome predictions from 78 Gram-negative bacterial genomes.

Scientific Applications:

• TMB Identification and Characterization: Identifies and characterizes transmembrane beta-barrel proteins in Gram-negative bacteria.
• Topology and Functional Region Analysis: Provides per-residue topology labels for studying strand orientation, periplasmic hairpins, and extracellular loops in structural and functional analyses.
• Proteome-wide Screening: Enables whole-proteome screening to discover novel TMBs across Gram-negative bacterial genomes for comparative and proteomic studies.

Methodology:

Implements a profile-based Hidden Markov Model (HMM) tailored to transmembrane beta-barrel structural features; performance was evaluated by cross-validation with reported per-residue accuracy of 86% and an 8-fold cross-validation assessment for whole-protein discrimination (70% at 60% coverage).