PortPred: Exploiting deep learning embeddings of amino acid sequences for the identification of transporter proteins and their substrates

ProteinBERT: a universal deep-learning model of protein sequence and function

(2022) Nadav Brandes et al.   BIOINFORMATICS

OrganelX web server for sub-peroxisomal and sub-mitochondrial protein localization and peroxisomal target signal detection

(2022) Marco Anteghini et al.   Computational and Structural Biotechnology Journal

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

(2021) Alexander Rives et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In-Pero: Exploiting Deep Learning Embeddings of Protein Sequences to Predict the Localisation of Peroxisomal Proteins

(2021) Marco Anteghini et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Lipid Transporters Beam Signals from Cell Membranes

(2021) Miliça Ristovski et al.   Membranes

TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information

(2020) Munira Alballa et al.   PLoS One

Corruption of the Pearson correlation coefficient by measurement error and its estimation, bias, and correction under different error models

(2020) Edoardo Saccenti et al.   Scientific Reports

TooT-T: discrimination of transport proteins from non-transport proteins

(2020) Munira Alballa et al.   BMC BIOINFORMATICS

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Using word embedding technique to efficiently represent protein sequences for identifying substrate specificities of transporters

(2019) Trinh-Trung-Duong Nguyen et al.   ANALYTICAL BIOCHEMISTRY

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

Modeling aspects of the language of life through transfer-learning protein sequences

(2019) Michael Heinzinger et al.   BMC BIOINFORMATICS

Optimal classifier for imbalanced data using Matthews Correlation Coefficient metric

(2017) Sabri Boughorbel et al.   PLoS One

Prediction the Substrate Specificities of Membrane Transport Proteins Based on Support Vector Machine and Hybrid Features

(2016) Liqi Li et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Logistic Regression

(2016) Juliana Tolles et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

SCMMTP: identifying and characterizing membrane transport proteins using propensity scores of dipeptides

(2015) Yi-Fan Liou et al.   BMC GENOMICS

The Organic Anion Transporter (OAT) Family: A Systems Biology Perspective

(2015) Sanjay K. Nigam et al.   PHYSIOLOGICAL REVIEWS

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction

(2014) Jia-Ming Chang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Prediction of Membrane Transport Proteins and Their Substrate Specificities Using Primary Sequence Information

(2014) Nitish K. Mishra et al.   PLoS One

Expansion of the APC superfamily of secondary carriers

(2014) Ake Vastermark et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease

(2014) Swagatika Sahoo et al.   Frontiers in Physiology

The ABCs of membrane transporters in health and disease (SLC series): Introduction

(2013) Matthias A. Hediger et al.   MOLECULAR ASPECTS OF MEDICINE

Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties

(2011) Shu-An Chen et al.   BIOINFORMATICS

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

(2011) P. Di Tommaso et al.   NUCLEIC ACIDS RESEARCH

Identification of Mannose Interacting Residues Using Local Composition

(2011) Sandhya Agarwal et al.   PLoS One

Coordination Chemistry of Bacterial Metal Transport and Sensing

(2009) Zhen Ma et al.   CHEMICAL REVIEWS