Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). (Q41928117)

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31 March 2020

title

Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016) (English)

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1

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Pedro Bule

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Johan C Hill

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object named as

Arnaud Baslé

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author name string

Reinhard Albrecht

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language of work or name

English

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publication date

16 October 2017

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31 March 2020

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31 March 2020

volume

86 Suppl 1

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31 March 2020

page(s)

27-50

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Assessment of protein assembly prediction in CASP12.

31 March 2020

cites work

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Structural Basis for Receptor Selectivity by the Whitewater Arroyo Mammarenavirus

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CdiA Effectors Use Modular Receptor-Binding Domains To Recognize Target Bacteria

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Gene polymorphism linked to increased asthma and IBD risk alters gasdermin-B structure, a sulfatide and phosphoinositide binding protein.

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Single Binding Mode Integration of Hemicellulose-degrading Enzymes via Adaptor Scaffoldins in Ruminococcus flavefaciens Cellulosome

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Cryo-protective effect of an ice-binding protein derived from Antarctic bacteria.

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The True Story and Advantages of RNA Phage Capsids as Nanotools

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Structural characterization of the thermostable Bradyrhizobium japonicumD-sorbitol dehydrogenase.

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Bacterial flagellar capping proteins adopt diverse oligomeric states

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Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages

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Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ

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Gasdermin B expression predicts poor clinical outcome in HER2-positive breast cancer

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Pore-forming activity and structural autoinhibition of the gasdermin family

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Properties and biotechnological applications of ice-binding proteins in bacteria.

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Ice-Binding Proteins and Their Function

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Some of the most interesting CASP11 targets through the eyes of their authors

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Contact-Dependent Growth Inhibition (CDI) and CdiB/CdiA Two-Partner Secretion Proteins

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Genetic Basis of Common Human Disease: Insight into the Role of Missense SNPs from Genome-Wide Association Studies

28 August 2018

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A new family of secreted toxins in pathogenic Neisseria species

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Crystal structure of the fibre head domain of the Atadenovirus Snake Adenovirus 1

28 August 2018

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Structural insight into substrate recognition by the endoplasmic reticulum folding-sensor enzyme: crystal structure of third thioredoxin-like domain of UDP-glucose:glycoprotein glucosyltransferase

28 August 2018

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Thalidomide mimics uridine binding to an aromatic cage in cereblon

28 August 2018

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Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains.

28 August 2018

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Hyperactive antifreeze protein from an Antarctic sea ice bacterium Colwellia sp. has a compound ice-binding site without repetitive sequences

28 August 2018

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28 August 2018

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Gasdermin-B promotes invasion and metastasis in breast cancer cells

28 August 2018

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28 August 2018

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Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

28 August 2018

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28 August 2018

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Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions

28 August 2018

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An L-glucitol oxidizing dehydrogenase from Bradyrhizobium japonicum USDA 110 for production of D-sorbose with enzymatic or electrochemical cofactor regeneration.

28 August 2018

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CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL.

28 August 2018

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lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.

28 August 2018

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Receptor polymorphism restricts contact-dependent growth inhibition to members of the same species

28 August 2018

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PRR1 coat protein binding to its RNA translational operator

28 August 2018

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28 August 2018

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Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems

28 August 2018

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Exploring ORFan domains in giant viruses: structure of mimivirus sulfhydryl oxidase R596

28 August 2018

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Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease

28 August 2018

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An integrated map of genetic variation from 1,092 human genomes

28 August 2018

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CAD-score: a new contact area difference-based function for evaluation of protein structural models.

28 August 2018

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Latest insights on adenovirus structure and assembly.

28 August 2018

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Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics

28 August 2018

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Linking Crystallographic Model and Data Quality

28 August 2018

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Optimal simultaneous superpositioning of multiple structures with missing data

28 August 2018

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The toxin/immunity network of Burkholderia pseudomallei contact-dependent growth inhibition (CDI) systems

28 August 2018

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Flagella and bacterial pathogenicity

28 August 2018

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Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts

28 August 2018

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Genetic association analyses of atopic illness and proinflammatory cytokine genes with type 1 diabetes

28 August 2018

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Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction

28 August 2018

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Novel dimeric β-helical model of an ice nucleation protein with bridged active sites

28 August 2018

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A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems

28 August 2018

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A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria.

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Ice restructuring inhibition activities in antifreeze proteins with distinct differences in thermal hysteresis.

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

A structural overview of the PDI family of proteins

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Dali server: conservation mapping in 3D

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Versatile virus-like particle carrier for epitope based vaccines

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Structural basis for receptor recognition by New World hemorrhagic fever arenaviruses

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Physiological truncation and domain organization of a novel uracil-DNA-degrading factor

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The structure of bacteriophage phiCb5 reveals a role of the RNA genome and metal ions in particle stability and assembly

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

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

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Contact-dependent growth inhibition causes reversible metabolic downregulation in Escherichia coli

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The coming of age of virus-like particle vaccines

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Contact-dependent growth inhibition requires the essential outer membrane protein BamA (YaeT) as the receptor and the inner membrane transport protein AcrB.

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Cryoelectron microscopy map of Atadenovirus reveals cross-genus structural differences from human adenovirus

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Evolution of a new enzyme activity from the same motif fold

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Divergence of quaternary structures among bacterial flagellar filaments

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Differential expression and localisation of gasdermin-like (GSDML), a novel member of the cancer-associated GSDMDC protein family, in neoplastic and non-neoplastic gastric, hepatic, and colon tissues

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Members of a novel gene family, Gsdm, are expressed exclusively in the epithelium of the skin and gastrointestinal tract in a highly tissue-specific manner

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

A novel fruitfly protein under developmental control degrades uracil-DNA.

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Clavulanic acid dehydrogenase: structural and biochemical analysis of the final step in the biosynthesis of the beta-lactamase inhibitor clavulanic acid

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

LH3, a "homologue" of the mastadenoviral E1B 55-kDa protein is a structural protein of atadenoviruses

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 A resolution

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Rhamnogalacturonan II: structure and function of a borate cross-linked cell wall pectic polysaccharide

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Structure, function and evolution of multidomain proteins

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Domain movements of HAP2 in the cap-filament complex formation and growth process of the bacterial flagellum

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Occurrence of the primary cell wall polysaccharide rhamnogalacturonan II in pteridophytes, lycophytes, and bryophytes. Implications for the evolution of vascular plants

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The noncatalytic portion of human UDP-glucose: glycoprotein glucosyltransferase I confers UDP-glucose binding and transferase function to the catalytic domain

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The UDP-glucose:glycoprotein glucosyltransferase is organized in at least two tightly bound domains from yeast to mammals.

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The rotary motor of bacterial flagella

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The modes of action of colicins E5 and D, and related cytotoxic tRNases

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

ParE toxin encoded by the broad-host-range plasmid RK2 is an inhibitor of Escherichia coli gyrase

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The bacterial flagellar cap as the rotary promoter of flagellin self-assembly.

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Inhibition of a ribosome-inactivating ribonuclease: the crystal structure of the cytotoxic domain of colicin E3 in complex with its immunity protein

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

T-Coffee: A novel method for fast and accurate multiple sequence alignment

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Calreticulin: one protein, one gene, many functions.

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Molecular cloning and characterization of the Helicobacter pylori fliD gene, an essential factor in flagellar structure and motility

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The protein disulphide-isomerase family: unravelling a string of folds

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The Pseudomonas aeruginosa flagellar cap protein, FliD, is responsible for mucin adhesion

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of Escherichia coli leviviruses

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Phage P22 tailspike protein: crystal structure of the head-binding domain at 2.3 A, fully refined structure of the endorhamnosidase at 1.56 A resolution, and the molecular basis of O-antigen recognition and cleavage

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Isolation and characterization of Whitewater Arroyo virus, a novel North American arenavirus

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The crystal structure of bacteriophage Q beta at 3.5 A resolution

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Comparison of super-secondary structures in proteins

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The three-dimensional structure of the bacterial virus MS2.

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

Adsorption inhibition as a mechanism of freezing resistance in polar fishes

28 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5820184

The Three-Dimensional Structure of Bacteriophage PP7 from Pseudomonas aeruginosa at 3.7-Å Resolution

28 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.25392

The influence of antigen organization on B cell responsiveness

21 January 2018

1 reference

12 December 2020

Durable cofactor immobilization in sol-gel bio-composite thin films for reagentless biosensors and bioreactors using dehydrogenases

1 reference

12 December 2020

Hepatitis B vaccines: WHO position paper--recommendations

1 reference

12 December 2020

The Bacterial Toxin RelE Displays Codon-Specific Cleavage of mRNAs in the Ribosomal A Site

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.25392

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28960539%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28960539%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference