DeepGpgs: a novel deep learning framework for predicting arginine methylation sites combined with Gaussian prior and gated self-attention mechanism

AI-Based Protein Structure Prediction in Drug Discovery: Impacts and Challenges

(2022) Michael Schauperl et al.   Journal of Chemical Information and Modeling

Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles

(2022) Quang-Hien Kha et al.   Journal of Chemical Information and Modeling

An interpretable deep learning model for classifying adaptor protein complexes from sequence information

(2022) Quang-Hien Kha et al.   METHODS

PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein–protein interaction information

(2021) Hangyuan Yang et al.   BIOINFORMATICS

Addressing data imbalance problems in ligand-binding site prediction using a variational autoencoder and a convolutional neural network

(2021) Trinh-Trung-Duong Nguyen et al.   BRIEFINGS IN BIOINFORMATICS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models

(2021) Yanhua Qiao et al.   BIOINFORMATICS

AlphaFold2-aware protein–DNA binding site prediction using graph transformer

(2021) Qianmu Yuan et al.   BRIEFINGS IN BIOINFORMATICS

Improved Prediction Model of Protein Lysine Crotonylation Sites Using Bidirectional Recurrent Neural Networks

(2021) Sian Soo Tng et al.   JOURNAL OF PROTEOME RESEARCH

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

(2020)   Nature Microbiology

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

(2020) David E. Gordon et al.   NATURE

MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization

(2020) Duolin Wang et al.   NUCLEIC ACIDS RESEARCH

DeepPSP: A Global–Local Information-Based Deep Neural Network for the Prediction of Protein Phosphorylation Sites

(2020) Lei Guo et al.   JOURNAL OF PROTEOME RESEARCH

PPI-Detect: A support vector machine model for sequence-based prediction of protein-protein interactions

(2019) Sandra Romero-Molina et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction of Protein Metal Binding Sites Using Deep Neural Networks

(2019) İsmail Haberal et al.   Molecular Informatics

New High-throughput Screen Identifies Compounds That Reduce Viability Specifically In Liver Cancer Cells That Express High Levels of SALL4 by Inhibiting Oxidative Phosphorylation

(2019) Justin L. Tan et al.   GASTROENTEROLOGY

Proteomic analysis and prediction of amino acid variations that influence protein posttranslational modifications

(2018) Shaoping Shi et al.   BRIEFINGS IN BIOINFORMATICS

Protein Language: Post-Translational Modifications Talking to Each Other

(2018) Lam Dai Vu et al.   TRENDS IN PLANT SCIENCE

DeepPhos: prediction of protein phosphorylation sites with deep learning

(2018) Fenglin Luo et al.   BIOINFORMATICS

Fast prediction of protein methylation sites using a sequence-based feature selection technique

(2017) Leyi Wei et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Arginine Methylation: The Coming of Age

(2017) Roméo S. Blanc et al.   MOLECULAR CELL

LSTM: A Search Space Odyssey

(2017) Klaus Greff et al.   IEEE Transactions on Neural Networks and Learning Systems

Ensemble Linear Neighborhood Propagation for Predicting Subchloroplast Localization of Multi-Location Proteins

(2016) Shibiao Wan et al.   JOURNAL OF PROTEOME RESEARCH

mPLR-Loc: An adaptive decision multi-label classifier based on penalized logistic regression for protein subcellular localization prediction

(2015) Shibiao Wan et al.   ANALYTICAL BIOCHEMISTRY

GOASVM: A subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou's pseudo-amino acid composition

(2013) Shibiao Wan et al.   JOURNAL OF THEORETICAL BIOLOGY

Computational prediction of eukaryotic phosphorylation sites

(2011) B. Trost et al.   BIOINFORMATICS

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Understanding protein phosphorylation on a systems level

(2010) J. Lin et al.   Briefings in Functional Genomics

Prediction of protein solubility inEscherichia coliusing logistic regression

(2009) Armando A. Diaz et al.   BIOTECHNOLOGY AND BIOENGINEERING

Introducing the acetylome

(2009) Karen T Smith et al.   NATURE BIOTECHNOLOGY