Pfam: the protein families database

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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Accelerated Profile HMM Searches

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Profile hidden Markov models

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The Pfam protein families database

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The Pfam protein families database

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Multiple Sequence Alignment Using ClustalW and ClustalX

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GeneWise and GenomewisePreprint

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The Pfam protein families database

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A Combined Transmembrane Topology and Signal Peptide Prediction Method

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Pfam: clans, web tools and services

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Hidden Markov Models in Computational Biology

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A NEW GENERATION OF HOMOLOGY SEARCH TOOLS BASED ON PROBABILISTIC INFERENCE

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The Pfam Protein Families Database

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Reorganizing the protein space at the Universal Protein Resource (UniProt)

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A transposase strategy for creating libraries of circularly permuted proteins

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The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins

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Database resources of the National Center for Biotechnology Information

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Intrinsically disordered proteins: regulation and disease

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The RCSB Protein Data Bank: new resources for research and education

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An analysis of protein domain linkers: their classification and role in protein folding

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Linkers in the structural biology of protein–protein interactions

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PDBe: Protein Data Bank in Europe

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SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

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New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures

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Control of protein functional dynamics by peptide linkers

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Role of linkers in communication between protein modules

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Alternative splicing of intrinsically disordered regions and rewiring of protein interactions

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Pfam 10 years on: 10 000 families and still growing

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Intrinsic disorder in cell signaling and gene transcription

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Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation

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PDBe: Protein Data Bank in Europe

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Unfoldomics of Human Genetic Diseases: Illustrative Examples of Ordered and Intrinsically Disordered Members of the Human Diseasome

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Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB

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AntiFam: a tool to help identify spurious ORFs in protein annotation

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Determination of Structural Principles Underlying Three Different Modes of Lymphocytic Choriomeningitis Virus Escape from CTL Recognition

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Functional evaluation of domain–domain interactions and human protein interaction networks

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The challenge of increasing Pfam coverage of the human proteome

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Enhanced protein domain discovery using taxonomy

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CheckM: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes

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The Pfam protein families database: towards a more sustainable future

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CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

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

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Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

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A survey of best practices for RNA-seq data analysis

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GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

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The BioPlex network: a systematic exploration of the human interactome

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MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins

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Strains, functions and dynamics in the expanded Human Microbiome Project

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Large language models generate functional protein sequences across diverse families

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

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Rare coding variants in ten genes confer substantial risk for schizophrenia

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EAACI Molecular Allergology User's Guide

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Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

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A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

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CAMP _R3 : a database on sequences, structures and signatures of antimicrobial peptides: Table 1.

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MMseqs2 desktop and local web server app for fast, interactive sequence searches

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Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

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Current challenges and best-practice protocols for microbiome analysis

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Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

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Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

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Impact of regulatory variation from RNA to protein

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Gene regulation in the immediate-early response process

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Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

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Defining the consequences of genetic variation on a proteome-wide scale

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

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Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors

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Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

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SIRT4 is a lysine deacylase that controls leucine metabolism and insulin secretion

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Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

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Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome

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A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

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Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen <i>Candida auris</i>

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Biosynthesis of a broad-spectrum nicotianamine-like metallophore in <i>Staphylococcus aureus</i>

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Deeply conserved synteny and the evolution of metazoan chromosomes

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Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements

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Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination

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Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation

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Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents.

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High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids

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Association between gut microbiota and bone health: Potential mechanisms and prospective

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A clinician's guide to microbiome analysis

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Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system

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