A brief history of protein sorting prediction

H Nielsen, KD Tsirigos, S Brunak, G von Heijne - The protein journal, 2019 - Springer
Ever since the signal hypothesis was proposed in 1971, the exact nature of signal peptides
has been a focus point of research. The prediction of signal peptides and protein subcellular …

Genome-scale metabolic modeling enables in-depth understanding of big data

A Passi, JD Tibocha-Bonilla, M Kumar, D Tec-Campos… - Metabolites, 2021 - mdpi.com
Genome-scale metabolic models (GEMs) enable the mathematical simulation of the
metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a …

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

NY Yu, JR Wagner, MR Laird, G Melli, S Rey… - …, 2010 - academic.oup.com
Motivation: PSORTb has remained the most precise bacterial protein subcellular localization
(SCL) predictor since it was first made available in 2003. However, the recall needs to be …

A protocol for generating a high-quality genome-scale metabolic reconstruction

I Thiele, BØ Palsson - Nature protocols, 2010 - nature.com
Network reconstructions are a common denominator in systems biology. Bottom–up
metabolic network reconstructions have been developed over the last 10 years. These …

Locating proteins in the cell using TargetP, SignalP and related tools

O Emanuelsson, S Brunak, G Von Heijne, H Nielsen - Nature protocols, 2007 - nature.com
Determining the subcellular localization of a protein is an important first step toward
understanding its function. Here, we describe the properties of three well-known N-terminal …

Prediction of protein subcellular localization

CS Yu, YC Chen, CH Lu… - … : Structure, Function, and …, 2006 - Wiley Online Library
Because the protein's function is usually related to its subcellular localization, the ability to
predict subcellular localization directly from protein sequences will be useful for inferring …

[HTML][HTML] pLoc-mEuk: Predict subcellular localization of multi-label eukaryotic proteins by extracting the key GO information into general PseAAC

X Cheng, X Xiao, KC Chou - Genomics, 2018 - Elsevier
Many efforts have been made in predicting the subcellular localization of eukaryotic
proteins, but most of the existing methods have the following two limitations:(1) their …

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

GL Winsor, DKW Lam, L Fleming, R Lo… - Nucleic acids …, 2010 - academic.oup.com
Pseudomonas is a metabolically-diverse genus of bacteria known for its flexibility and
leading free living to pathogenic lifestyles in a wide range of hosts. The Pseudomonas …

Some remarks on predicting multi-label attributes in molecular biosystems

KC Chou - Molecular Biosystems, 2013 - pubs.rsc.org
Many molecular biosystems and biomedical systems belong to the multi-label systems in
which each of their constituent molecules possesses one or more than one function or …

NetB, a new toxin that is associated with avian necrotic enteritis caused by Clostridium perfringens

AL Keyburn, JD Boyce, P Vaz, TL Bannam… - PLoS …, 2008 - journals.plos.org
For over 30 years a phospholipase C enzyme called alpha-toxin was thought to be the key
virulence factor in necrotic enteritis caused by Clostridium perfringens. However, using a …