Protein function
View article
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability Open
Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based approaches for asse…
View article
Uniclust databases of clustered and deeply annotated protein sequences and alignments Open
We present three clustered protein sequence databases, Uniclust90, Uniclust50, Uniclust30 and three databases of multiple sequence alignments (MSAs), Uniboost10, Uniboost20 and Uniboost30, as a resource for protein sequence analysis, funct…
View article
Structure-based protein function prediction using graph convolutional networks Open
The rapid increase in the number of proteins in sequence databases and the diversity of their functions challenge computational approaches for automated function prediction. Here, we introduce DeepFRI, a Graph Convolutional Network for pre…
View article
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models Open
The prediction of protein subcellular localization is of great relevance for proteomics research. Here, we propose an update to the popular tool DeepLoc with multi-localization prediction and improvements in both performance and interpreta…
View article
COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information Open
The COFACTOR web server is a unified platform for structure-based multiple-level protein function predictions. By structurally threading low-resolution structural models through the BioLiP library, the COFACTOR server infers three categori…
View article
Progress in Top-Down Proteomics and the Analysis of Proteoforms Open
From a molecular perspective, enactors of function in biology are intact proteins that can be variably modified at the genetic, transcriptional, or post-translational level. Over the past 30 years, mass spectrometry (MS) has become a power…
View article
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier Open
Motivation A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and…
View article
DeepGOPlus: improved protein function prediction from sequence Open
Motivation Protein function prediction is one of the major tasks of bioinformatics that can help in wide range of biological problems such as understanding disease mechanisms or finding drug targets. Many methods are available for predicti…
View article
PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database Open
The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for al…
View article
Before and after AlphaFold2: An overview of protein structure prediction Open
Three-dimensional protein structure is directly correlated with its function and its determination is critical to understanding biological processes and addressing human health and life science problems in general. Although new protein str…
View article
State-of-the-Art Estimation of Protein Model Accuracy Using AlphaFold Open
The problem of predicting a protein's 3D structure from its primary amino acid sequence is a longstanding challenge in structural biology. Recently, approaches like alphafold have achieved remarkable performance on this task by combining d…
View article
Exploring the computational methods for protein-ligand binding site prediction Open
Proteins participate in various essential processes in vivo via interactions with other molecules. Identifying the residues participating in these interactions not only provides biological insights for protein function studies but also has…
View article
deepNF: deep network fusion for protein function prediction Open
Motivation The prevalence of high-throughput experimental methods has resulted in an abundance of large-scale molecular and functional interaction networks. The connectivity of these networks provides a rich source of information for infer…
View article
The Scope, Functions, and Dynamics of Posttranslational Protein Modifications Open
Assessing posttranslational modification (PTM) patterns within protein molecules and reading their functional implications present grand challenges for plant biology. We combine four perspectives on PTMs and their roles by considering five…
View article
DeepGOPlus: improved protein function prediction from sequence Open
Motivation: Protein function prediction is one of the major tasks of bioinformatics that can help in wide range of biological problems such as understanding disease mechanisms or finding drug targets.Many methods are available for predicti…
View article
Conformational dynamics and enzyme evolution Open
Enzymes are dynamic entities, and their dynamic properties are clearly linked to their biological function. It follows that dynamics ought to play an essential role in enzyme evolution. Indeed, a link between conformational diversity and t…
View article
Dissecting the role of protein phosphorylation: a chemical biology toolbox Open
Phosphorylation is a key regulator of protein and cellular function. In this review, we describe tools that enable access to homogeneously phosphorylated protein and discuss examples that demonstrate how they can be applied in functional s…
View article
ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network Open
With the development of next generation sequencing techniques, it is fast and cheap to determine protein sequences but relatively slow and expensive to extract useful information from protein sequences because of limitations of traditional…
View article
Nanobody Technology: A Versatile Toolkit for Microscopic Imaging, Protein–Protein Interaction Analysis, and Protein Function Exploration Open
Over the last two decades, nanobodies or single-domain antibodies have found their way in research, diagnostics, and therapy. These antigen-binding fragments, derived from Camelid heavy chain only antibodies, possess remarkable characteris…
View article
Computational prediction of protein–protein binding affinities Open
Protein–protein interactions form central elements of almost all cellular processes. Knowledge of the structure of protein–protein complexes but also of the binding affinity is of major importance to understand the biological function of p…
View article
Optical Control of Small Molecule-Induced Protein Degradation Open
As an emerging approach to protein perturbation, small molecule-induced protein degradation has gained significant attention as both a chemical tool and a potential therapeutic. To enable discrete control over its function, we have develop…
View article
Systematic approaches to identify E3 ligase substrates Open
Protein ubiquitylation is a widespread post-translational modification, regulating cellular signalling with many outcomes, such as protein degradation, endocytosis, cell cycle progression, DNA repair and transcription. E3 ligases are a cri…
View article
Power to the protein: enhancing and combining activities using the Spy toolbox Open
A peptide with simple and selective reactivity expands the function of proteins, from single molecule analysis to potential clinical application.
View article
Protein dynamics and function from solution state NMR spectroscopy Open
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Now…
View article
DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks Open
Automated protein function prediction is critical for the annotation of uncharacterized protein sequences, where accurate prediction methods are still required. Recently, deep learning based methods have outperformed conventional algorithm…
View article
Protein–protein interaction prediction with deep learning: A comprehensive review Open
Most proteins perform their biological function by interacting with themselves or other molecules. Thus, one may obtain biological insights into protein functions, disease prevalence, and therapy development by identifying protein-protein …
View article
Neural networks to learn protein sequence–function relationships from deep mutational scanning data Open
Significance Understanding the relationship between protein sequence and function is necessary to design new and useful proteins with applications in bioenergy, medicine, and agriculture. The mapping from sequence to function is tremendous…
View article
NetGO: improving large-scale protein function prediction with massive network information Open
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can be regarded as a problem of the large-scale multi-label classification where a protein can be associated with multiple gene ontology terms as its …
View article
Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy Open
The experiments demonstrate that our method could greatly improve the prediction accuracy and speed, thus allowing large-scale NGS data prediction to be practical. A web server is developed to facilitate the other researchers, which can be…
View article
Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs) Open
Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific proteins, including affinity chromat…