Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space

Using AlphaFold to predict the impact of single mutations on protein stability and function

(2023) Marina A. Pak et al.   PLoS One

Evolutionary-scale prediction of atomic-level protein structure with a language model

(2023) Zeming Lin et al.   SCIENCE

Structural Bases of Prion Variation in Yeast

(2022) Vitaly V. Kushnirov et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Exploring the glycosylation of mucins by use of O-glycodomain reporters recombinantly expressed in glycoengineered HEK293 cells

(2022) Andriana Konstantinidi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Search and sequence analysis tools services from EMBL-EBI in 2022

(2022) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Dali server: structural unification of protein families

(2022) Liisa Holm   NUCLEIC ACIDS RESEARCH

Characterizing the mucin-degrading capacity of the human gut microbiota

(2022) Janiece S. Glover et al.   Scientific Reports

Functional Bacterial Amyloids: Understanding Fibrillation, Regulating Biofilm Fibril Formation and Organizing Surface Assemblies

(2022) Thorbjørn Vincent Sønderby et al.   MOLECULES

Unique SMYD5 Structure Revealed by AlphaFold Correlates with Its Functional Divergence

(2022) Yingxue Zhang et al.   Biomolecules

FapA is an Intrinsically Disordered Chaperone for Pseudomonas Functional Amyloid FapC

(2022) Helena Ø. Rasmussen et al.   JOURNAL OF MOLECULAR BIOLOGY

A structural biology community assessment of AlphaFold2 applications

(2022) Mehmet Akdel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

(2022) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

Conformational change of α-synuclein fibrils in cerebrospinal fluid from different clinical phases of Parkinson’s disease

(2022) Yun Fan et al.   STRUCTURE

Suprabasin—A Review

(2021) Miroslav Pribyl et al.   Genes

Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families

(2021) Claudio Bassot et al.   PLoS Computational Biology

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

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

(2021) Minkyung Baek et al.   SCIENCE

Chlamydia trachomatis Polymorphic Membrane Proteins (Pmps) Form Functional Homomeric and Heteromeric Oligomers

(2021) Alison Favaroni et al.   Frontiers in Microbiology

New Family Members of FG Repeat Proteins and Their Unexplored Roles During Phase Separation

(2021) Yoichi Shinkai et al.   Frontiers in Cell and Developmental Biology

The AlphaFold Database of Protein Structures: A Biologist’s Guide

(2021) Alessia David et al.   JOURNAL OF MOLECULAR BIOLOGY

Suprabasin: Role in human cancers and other diseases

(2021) Hao Tan et al.   MOLECULAR BIOLOGY REPORTS

Structure-based classification of tauopathies

(2021) Yang Shi et al.   NATURE

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Gut microbiome in Parkinson's disease: New insights from meta-analysis

(2021) Tzi Shin Toh et al.   PARKINSONISM & RELATED DISORDERS

Presence and structure‐activity relationship of intrinsically disordered regions across mucins

(2020) Joseph Carmicheal et al.   FASEB JOURNAL

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A gut bacterial amyloid promotes α-synuclein aggregation and motor impairment in mice

(2020) Timothy R Sampson et al.   eLife

Carrot “antifreeze” protein has an irregular ice-binding site that confers weak freezing point depression but strong inhibition of ice recrystallization.

(2020) Yannan Wang et al.   BIOCHEMICAL JOURNAL

Gut Microbiome, Intestinal Permeability, and Tissue Bacteria in Metabolic Disease: Perpetrators or Bystanders?

(2020) Rima M. Chakaroun et al.   Nutrients

Evolutionary Remodelling of the Cell Envelope in Bacteria of the Planctomycetes Phylum

(2020) Mayank Mahajan et al.   Genome Biology and Evolution

Accelerated Amyloid Beta Pathogenesis by Bacterial Amyloid FapC

(2020) Ibrahim Javed et al.   Advanced Science

RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures

(2020) Lisanna Paladin et al.   NUCLEIC ACIDS RESEARCH

Brain-Gut-Microbiota Axis in Alzheimer’s Disease

(2019) Karol Kowalski et al.   Journal of Neurogastroenterology and Motility

Structural Insights into Curli CsgA Cross-β Fibril Architecture Inspire Repurposing of Anti-amyloid Compounds as Anti-biofilm Agents

(2019) Sergei Perov et al.   PLoS Pathogens

The structure of bactofilin filaments reveals their mode of membrane binding and lack of polarity

(2019) Xian Deng et al.   Nature Microbiology

Mucins and Pathogenic Mucin-Like Molecules Are Immunomodulators During Infection and Targets for Diagnostics and Vaccines

(2019) Sandra Pinzón Martín et al.   Frontiers in Chemistry

A bacterial surface layer protein exploits multistep crystallization for rapid self-assembly

(2019) Jonathan Herrmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mucins: Structural diversity, biosynthesis, its role in pathogenesis and as possible therapeutic targets

(2018) Suresh Sulekha Dhanisha et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

Structural and functional characterization of the Curli adaptor protein CsgF

(2018) Tobias Schubeis et al.   FEBS LETTERS

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Structure and application of antifreeze proteins from Antarctic bacteria

(2017) Patricio A. Muñoz et al.   Microbial Cell Factories

A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis

(2017) Sarah L. Rouse et al.   Nature Communications

Mucin 2 silencing promotes colon cancer metastasis through interleukin-6 signaling

(2017) Hui-Ping Hsu et al.   Scientific Reports

Gut instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration

(2016) Timothy G. Dinan et al.   JOURNAL OF PHYSIOLOGY-LONDON

Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein–Polysaccharide Interactions

(2016) Yu Kang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dali server update

(2016) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

(2016) Haim Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension

(2016) James T. MacDonald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of a Non-Pentapeptide Region Associated with Rapid Mycobacterial Evolution

(2016) Per Warholm et al.   PLoS One

Engineering Amyloid Fibrils from β-Solenoid Proteins for Biomaterials Applications

(2015) Maria D.R. Peralta et al.   ACS Nano

Mucins: A biologically relevant glycan barrier in mucosal protection

(2015) Anthony P. Corfield   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Functional Dynamics Revealed by the Structure of the SufBCD Complex, a Novel ATP-binding Cassette (ABC) Protein That Serves as a Scaffold for Iron-Sulfur Cluster Biogenesis

(2015) Kei Hirabayashi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Bacterial Curli System Possesses a Potent and Selective Inhibitor of Amyloid Formation

(2015) Margery L. Evans et al.   MOLECULAR CELL

Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation

(2014) Pengfei Tian et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Planctomycetes and macroalgae, a striking association

(2014) Olga M. Lage et al.   Frontiers in Microbiology

RepeatsDB: a database of tandem repeat protein structures

(2013) Tomás Di Domenico et al.   NUCLEIC ACIDS RESEARCH

Chlamydial Intracellular Survival Strategies

(2013) R. J. Bastidas et al.   Cold Spring Harbor Perspectives in Medicine

Expression of Fap amyloids inPseudomonas aeruginosa,P. fluorescens,andP. putidaresults in aggregation and increased biofilm formation

(2013) Morten S. Dueholm et al.   MicrobiologyOpen

Expression of Underglycosylated MUC1 Antigen in Cancerous and Adjacent Normal Breast Tissues

(2012) Subrata K. Ghosh et al.   Clinical Breast Cancer

A method for probing the mutational landscape of amyloid structure

(2011) Charles W. O'Donnell et al.   BIOINFORMATICS

Trophinin-mediated cell adhesion induces apoptosis of human endometrial epithelial cells through PKC-δ

(2011) Naoaki Tamura et al.   CELL CYCLE

Calcium-induced Folding and Stabilization of thePseudomonas aeruginosaAlkaline Protease

(2011) Liang Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Tandem repeats in proteins: From sequence to structure

(2011) Andrey V. Kajava   JOURNAL OF STRUCTURAL BIOLOGY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Anchored clathrate waters bind antifreeze proteins to ice

(2011) C. P. Garnham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interdomain Ca2+ effects in Escherichia coli α-haemolysin: Ca2+ binding to the C-terminal domain stabilizes both C- and N-terminal domains

(2010) Lissete Sánchez-Magraner et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Identification of protein binding surfaces using surface triplet propensities

(2010) Wissam Mehio et al.   BIOINFORMATICS

Molecular cloning of two novel mucin-like genes in the disease-susceptibility locus for diffuse panbronchiolitis

(2010) Minako Hijikata et al.   HUMAN GENETICS

Members of the Pmp protein family of Chlamydia pneumoniae mediate adhesion to human cells via short repetitive peptide motifs

(2010) Katja Mölleken et al.   MOLECULAR MICROBIOLOGY

New insights intoChlamydiaintracellular survival mechanisms

(2009) Jordan L. Cocchiaro et al.   CELLULAR MICROBIOLOGY

Mucin-type O-glycosylation - putting the pieces together

(2009) Pia H. Jensen et al.   FEBS Journal

Crystallographic Insights into the Autocatalytic Assembly Mechanism of a Bacteriophage Tail Spike

(2009) Ye Xiang et al.   MOLECULAR CELL

QMEAN server for protein model quality estimation

(2009) Pascal Benkert et al.   NUCLEIC ACIDS RESEARCH

Localized and efficient curli nucleation requires the chaperone-like amyloid assembly protein CsgF

(2009) Ashley A. Nenninger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and Biochemistry of Cadherins and Catenins

(2009) L. Shapiro et al.   Cold Spring Harbor Perspectives in Biology

Repeat-protein folding: New insights into origins of cooperativity, stability, and topology

(2007) Ellen Kloss et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS