Using deep learning to annotate the protein universe

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Fast and sensitive protein alignment using DIAMOND

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Multi-scale context aggregation by dilated convolutions

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UniProt: the Universal Protein knowledgebase

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Pfam: The protein families database in 2021

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Accelerated Profile HMM Searches

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Amino acid substitution matrices from protein blocks.

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HMMER web server: interactive sequence similarity searching

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UniProt: a hub for protein information

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MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

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The Pfam protein families database in 2019

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In-Datacenter Performance Analysis of a Tensor Processing Unit

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UniProt: the universal protein knowledgebase

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On the difficulty of training recurrent neural networks

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Axiomatic attribution for deep networks

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

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

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Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

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Protein homology detection by HMM–HMM comparison

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Pfam: clans, web tools and services

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UniProt: the universal protein knowledgebase

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Hidden Markov model speed heuristic and iterative HMM search procedure

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Unified rational protein engineering with sequence-based deep representation learning

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A Helix Propensity Scale Based on Experimental Studies of Peptides and Proteins

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Clustering huge protein sequence sets in linear time

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Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

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Google Vizier

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Mutant phenotypes for thousands of bacterial genes of unknown function

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DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier

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TOP-IDP-Scale: A New Amino Acid Scale Measuring Propensity for Intrinsic Disorder

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RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

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End-to-end Continuous Speech Recognition using Attention-based Recurrent NN: First ResultsPreprint

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DEEPre: sequence-based enzyme EC number prediction by deep learning

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A deep learning framework for modeling structural features of RNA-binding protein targets

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GPU-BLAST: using graphics processors to accelerate protein sequence alignment

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ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network

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DeepSF: deep convolutional neural network for mapping protein sequences to folds

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Embeddings from deep learning transfer GO annotations beyond homology

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Sequence context-specific profiles for homology searching

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mlDEEPre: Multi-Functional Enzyme Function Prediction With Hierarchical Multi-Label Deep Learning

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Deep Recurrent Neural Network for Protein Function Prediction from SequencePreprint

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Hydrophobic patches on protein subunit interfaces: Characteristics and prediction

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COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps

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Compressive genomics for protein databases

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Unified rational protein engineering with sequence-only deep representation learningPreprint

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Variational auto-encoding of protein sequencesPreprint

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Near perfect protein multi-label classification with deep neural networks

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CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets

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The bacterial copper resistance protein CopG contains a cysteine-bridged tetranuclear copper cluster

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SECLAF: a webserver and deep neural network design tool for hierarchical biological sequence classification

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What made you do this? Understanding black-box decisions with sufficient input subsetsPreprint

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Deep Semantic Protein Representation for Annotation, Discovery, and EngineeringPreprint

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ProLanGO: Protein Function Prediction Using Neural~Machine Translation Based on a Recurrent Neural NetworkPreprint

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Protein Family Classification with Multi-Layer Graph Convolutional Networks

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Deep Recurrent Neural Network for Protein Function Prediction from SequencePreprint

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Critiquing Protein Family Classification Models Using Sufficient Input Subsets

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DeepSF: deep convolutional neural network for mapping protein sequences to foldsPreprint

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Critiquing Protein Family Classification Models Using Sufficient Input SubsetsPreprint

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Evaluating Optimization Strategies for HMMer Acceleration on GPU

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InterPro in 2022

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Scientific discovery in the age of artificial intelligence.

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InterPro: the protein sequence classification resource in 2025

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Machine-learning-guided directed evolution for protein engineering

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Artificial intelligence and illusions of understanding in scientific research

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Efficient evolution of human antibodies from general protein language models

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MGnify: the microbiome sequence data analysis resource in 2023

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Expanding functional protein sequence spaces using generative adversarial networks

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The Pfam protein families database: embracing AI/ML

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The language of proteins: NLP, machine learning & protein sequences

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Opportunities and Challenges for Machine Learning-Assisted Enzyme Engineering

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SaProt: Protein Language Modeling with Structure-aware VocabularyPreprint

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Machine Learning-Guided Protein Engineering

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Learning functional properties of proteins with language models

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Controllable protein design with language models

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ProteInfer, deep neural networks for protein functional inference

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A general model to predict small molecule substrates of enzymes based on machine and deep learning

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UDSMProt: universal deep sequence models for protein classification

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

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ECNet is an evolutionary context-integrated deep learning framework for protein engineering

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Unifying the known and unknown microbial coding sequence space

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Diffusion models in bioinformatics and computational biology

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Machine learning for perturbational single-cell omics

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Artificial Intelligence in Molecular Medicine

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Functional annotation of enzyme-encoding genes using deep learning with transformer layers

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Next-Generation TB Vaccines: Progress, Challenges, and Prospects

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Antimicrobial resistance crisis: could artificial intelligence be the solution?

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CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters

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Convolutions are competitive with transformers for protein sequence pretraining

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AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

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PLMSearch: Protein language model powers accurate and fast sequence search for remote homology

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Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms

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Characteristics of seismic activity of the Upper Silesian Coal Basin in Poland

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Genomic language model predicts protein co-regulation and function

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Review of AlphaFold 3: Transformative Advances in Drug Design and Therapeutics

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Toward an Integrated Machine Learning Model of a Proteomics Experiment

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FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs

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GotEnzymes: an extensive database of enzyme parameter predictions

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