Leveraging transformers‐based language models in proteome bioinformatics

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

(2023) Haiwei Zhou et al.   BRIEFINGS IN BIOINFORMATICS

Transformer-based deep learning for predicting protein properties in the life sciences

(2023) Abel Chandra et al.   eLife

Improving drug-target affinity prediction via feature fusion and knowledge distillation

(2023) Ruiqiang Lu et al.   BRIEFINGS IN BIOINFORMATICS

STMHCpan, an accurate Star-Transformer-based extensible framework for predicting MHC I allele binding peptides

(2023) Zheng Ye et al.   BRIEFINGS IN BIOINFORMATICS

UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity

(2023) Zhenjiao Du et al.   BRIEFINGS IN BIOINFORMATICS

Designing antimicrobial peptides using deep learning and molecular dynamic simulations

(2023) Qiushi Cao et al.   BRIEFINGS IN BIOINFORMATICS

Auto-Kla: a novel web server to discriminate lysine lactylation sites using automated machine learning

(2023) Fei-Liao Lai et al.   BRIEFINGS IN BIOINFORMATICS

Predicting gene and protein expression levels from DNA and protein sequences with Perceiver

(2023) Matteo Stefanini et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

NeuroPpred-SVM: A New Model for Predicting Neuropeptides Based on Embeddings of BERT

(2023) Yufeng Liu et al.   Journal of Proteome Research

Using ATCLSTM-Kcr to predict and generate the human lysine crotonylation database

(2023) Ye-Hong Yang et al.   Journal of Proteomics

A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics

(2023) Thang V. Pham et al.   PROTEOMICS

ADOPT: intrinsic protein disorder prediction through deep bidirectional transformers

(2023) Istvan Redl et al.   NAR Genomics and Bioinformatics

DeepGene Transformer: Transformer for the gene expression-based classification of cancer subtypes

(2023) Anwar Khan et al.   EXPERT SYSTEMS WITH APPLICATIONS

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

(2022) Nadav Brandes et al.   BIOINFORMATICS

Protein–DNA/RNA interactions: Machine intelligence tools and approaches in the era of artificial intelligence and big data

(2022) Feifei Cui et al.   PROTEOMICS

TransDTI: Transformer-Based Language Models for Estimating DTIs and Building a Drug Recommendation Workflow

(2022) Yogesh Kalakoti et al.   ACS Omega

Prior Knowledge Facilitates Low Homologous Protein Secondary Structure Prediction with DSM Distillation

(2022) Qin Wang et al.   BIOINFORMATICS

MHCRoBERTa: pan-specific peptide–MHC class I binding prediction through transfer learning with label-agnostic protein sequences

(2022) Fuxu Wang et al.   BRIEFINGS IN BIOINFORMATICS

HLAB: learning the BiLSTM features from the ProtBert-encoded proteins for the class I HLA-peptide binding prediction

(2022) Yaqi Zhang et al.   BRIEFINGS IN BIOINFORMATICS

An analysis of protein language model embeddings for fold prediction

(2022) Amelia Villegas-Morcillo et al.   BRIEFINGS IN BIOINFORMATICS

Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities

(2022) Markus Ekvall et al.   JOURNAL OF PROTEOME RESEARCH

Attention-wise masked graph contrastive learning for predicting molecular property

(2022) Hui Liu et al.   BRIEFINGS IN BIOINFORMATICS

Targeted proteomics on its way to discovery

(2022) Marta L. Mendes et al.   PROTEOMICS

DistilProtBert: a distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts

(2022) Yaron Geffen et al.   BIOINFORMATICS

NeuroPred-CLQ: incorporating deep temporal convolutional networks and multi-head attention mechanism to predict neuropeptides

(2022) Shouzhi Chen et al.   BRIEFINGS IN BIOINFORMATICS

Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning

(2022) Qianmu Yuan et al.   BRIEFINGS IN BIOINFORMATICS

SPRoBERTa: protein embedding learning with local fragment modeling

(2022) Lijun Wu et al.   BRIEFINGS IN BIOINFORMATICS

CoaDTI: multi-modal co-attention based framework for drug–target interaction annotation

(2022) Lei Huang et al.   BRIEFINGS IN BIOINFORMATICS

Improved Prediction Model of Protein and Peptide Toxicity by Integrating Channel Attention into a Convolutional Neural Network and Gated Recurrent Units

(2022) Zhengyun Zhao et al.   ACS Omega

Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities

(2022) Yuxuan Pang et al.   BIOINFORMATICS

PhaTYP: predicting the lifestyle for bacteriophages using BERT

(2022) Jiayu Shang et al.   BRIEFINGS IN BIOINFORMATICS

Deepro-Glu: combination of convolutional neural network and Bi-LSTM models using ProtBert and handcrafted features to identify lysine glutarylation sites

(2022) Xiao Wang et al.   BRIEFINGS IN BIOINFORMATICS

Generative multiscale analysis of de novo proteome-inspired molecular structures and nanomechanical optimization using a VoxelPerceiver transformer model

(2022) Zhenze Yang et al.   JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS

BERT-GT: Cross-sentence n-ary relation extraction with BERT and graph transformer

(2021) Po-Ting Lai et al.   BIOINFORMATICS

BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides

(2021) Phasit Charoenkwan et al.   BIOINFORMATICS

PepFormer: End-to-End Transformer-Based Siamese Network to Predict and Enhance Peptide Detectability Based on Sequence Only

(2021) Hao Cheng et al.   ANALYTICAL CHEMISTRY

TALE: Transformer-based protein function Annotation with joint sequence–Label Embedding

(2021) Yue Cao et al.   BIOINFORMATICS

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

BERTMHC: improved MHC–peptide class II interaction prediction with transformer and multiple instance learning

(2021) Jun Cheng et al.   BIOINFORMATICS

Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins

(2021) Hideki Yamaguchi et al.   BRIEFINGS IN BIOINFORMATICS

DeepR2cov: deep representation learning on heterogeneous drug networks to discover anti-inflammatory agents for COVID-19

(2021) Xiaoqi Wang et al.   BRIEFINGS IN BIOINFORMATICS

A novel antibacterial peptide recognition algorithm based on BERT

(2021) Yue Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

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

(2021) Yanhua Qiao et al.   BIOINFORMATICS

EGRET: edge aggregated graph attention networks and transfer learning improve protein–protein interaction site prediction

(2021) Sazan Mahbub et al.   BRIEFINGS IN BIOINFORMATICS

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

(2021) Qianmu Yuan et al.   BRIEFINGS IN BIOINFORMATICS

T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model

(2021) Yumeng Zhang et al.   BRIEFINGS IN BIOINFORMATICS

MolGPT: Molecular Generation Using a Transformer-Decoder Model

(2021) Viraj Bagal et al.   Journal of Chemical Information and Modeling

prPred‐DRLF: Plant R protein predictor using deep representation learning features

(2021) Yansu Wang et al.   PROTEOMICS

Potential of deep representative learning features to interpret the sequence information in proteomics

(2021) Nguyen Quoc Khanh Le   PROTEOMICS

Mul-SNO: A Novel Prediction Tool for S-Nitrosylation Sites Based on Deep Learning Methods

(2021) Qian Zhao et al.   IEEE Journal of Biomedical and Health Informatics

MolTrans: Molecular interaction transformer for drug target interaction prediction

(2020) Kexin Huang et al.   BIOINFORMATICS

Next-Generation Sequencing Strategies

(2018) Shawn E. Levy et al.   Cold Spring Harbor Perspectives in Medicine

Protein post-translational modifications: In silico prediction tools and molecular modeling

(2017) Martina Audagnotto et al.   Computational and Structural Biotechnology Journal

Multidimensional proteomics for cell biology

(2015) Mark Larance et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Target profiling of small molecules by chemical proteomics

(2009) Uwe Rix et al.   Nature Chemical Biology