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 …

[HTML][HTML] Molecular basis for specificity of nuclear import and prediction of nuclear localization

M Marfori, A Mynott, JJ Ellis, AM Mehdi… - … et Biophysica Acta (BBA …, 2011 - Elsevier
Although proteins are translated on cytoplasmic ribosomes, many of these proteins play
essential roles in the nucleus, mediating key cellular processes including but not limited to …

Identifying SNARE proteins using an alignment-free method based on multiscan convolutional neural network and PSSM profiles

QH Kha, QT Ho, NQK Le - Journal of Chemical Information and …, 2022 - ACS Publications
Background: SNARE proteins play a vital role in membrane fusion and cellular physiology
and pathological processes. Many potential therapeutics for mental diseases or even cancer …

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 …

AlgPred: prediction of allergenic proteins and mapping of IgE epitopes

S Saha, GPS Raghava - Nucleic acids research, 2006 - academic.oup.com
In this study a systematic attempt has been made to integrate various approaches in order to
predict allergenic proteins with high accuracy. The dataset used for testing and training …

iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition

SH Guo, EZ Deng, LQ Xu, H Ding, H Lin, W Chen… - …, 2014 - academic.oup.com
Motivation: Nucleosome positioning participates in many cellular activities and plays
significant roles in regulating cellular processes. With the avalanche of genome sequences …

Pseudo amino acid composition and its applications in bioinformatics, proteomics and system biology

KC Chou - Current Proteomics, 2009 - ingentaconnect.com
With the avalanche of protein sequences generated in the post-genomic age, it is highly
desired to develop automated methods for efficiently identifying various attributes of …

Nuclear outsourcing of RNA interference components to human mitochondria

S Bandiera, S Rüberg, M Girard, N Cagnard, S Hanein… - PloS one, 2011 - journals.plos.org
MicroRNAs (miRNAs) are small non-coding RNAs that associate with Argonaute proteins to
regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent …

MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction

T Blum, S Briesemeister, O Kohlbacher - BMC bioinformatics, 2009 - Springer
Background Knowledge of subcellular localization of proteins is crucial to proteomics, drug
target discovery and systems biology since localization and biological function are highly …

Classification of nuclear receptors based on amino acid composition and dipeptide composition

M Bhasin, GPS Raghava - Journal of Biological Chemistry, 2004 - ASBMB
Nuclear receptors are key transcription factors that regulate crucial gene networks
responsible for cell growth, differentiation, and homeostasis. Nuclear receptors form a …