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

No abstract is available for this paper.

• Publication year

  2014

• Venue

  Proteins: Structure, Function, and Bioinformatics

• Publication date

  2014-01-25

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1002/prot.24489PMID 24318984PMCID PMC4072496
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Definition and classification of evaluation units for CASP10

  2014cited by this paper
• Assessment of template‐free modeling in CASP10 and ROLL

  2014cited by this paper
• Critical assessment of methods of protein structure prediction (CASP) — round x

  2014cited by this paper
• Assessment of template‐based protein structure predictions in CASP10

  2014cited by this paper
• Assessment of ligand binding site predictions in CASP10

  2014cited by this paper
• CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL

  2014cited by this paper
• Evaluation of predictions in the CASP10 model refinement category

  2013cited by this paper
• Mechanisms of molecular transport through the urea channel of Helicobacter pylori

  2013cited by this paper
• The Bacteriophage T7 Virion Undergoes Extensive Structural Remodeling During Infection

  2013cited by this paper
• lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

  2013cited by this paper
• CAD‐score: A new contact area difference‐based function for evaluation of protein structural models

  2013influential reference
• Artificial Neural Networks Trained to Detect Viral and Phage Structural Proteins

  2012cited by this paper
• Exploring ORFan Domains in Giant Viruses: Structure of Mimivirus Sulfhydryl Oxidase R596

  2012cited by this paper
• Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori

  2012cited by this paper
• Crystallization of the C-terminal domain of the bacteriophage T7 fibre protein gp17.

  2012cited by this paper
• Extracellular assembly and activation principles of oncogenic class III receptor tyrosine kinases

  2012cited by this paper
• Bacteriophages and their implications on future biotechnology: a review

  2012cited by this paper
• A suggested new bacteriophage genus: “Viunalikevirus”

  2012cited by this paper
• Related Giant Viruses in Distant Locations and Different Habitats: Acanthamoeba polyphaga moumouvirus Represents a Third Lineage of the Mimiviridae That Is Close to the Megavirus Lineage

  2012cited by this paper
• Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers

  2012cited by this paper
• The mechanism of shared but distinct CSF-1R signaling by the non-homologous cytokines IL-34 and CSF-1.

  2012influential reference
• Short noncontractile tail machines: adsorption and DNA delivery by podoviruses.

  2012cited by this paper
• Phage pierces the host cell membrane with the iron-loaded spike.

  2012cited by this paper
• Structural basis for the dual recognition of helical cytokines IL-34 and CSF-1 by CSF-1R.

  2012influential reference
• Natural and engineered cystine knot miniproteins for diagnostic and therapeutic applications.

  2011cited by this paper
• Characterization of a ViI-like Phage Specific to Escherichia coli O157:H7

  2011cited by this paper
• SAD phasing using iodide ions in a high-throughput structural genomics environment

  2011influential reference
• Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids

  2011cited by this paper
• Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction

  2011cited by this paper
• Atomic Structure of Bacteriophage Sf6 Tail Needle Knob*

  2011cited by this paper
• Four Small Puzzles That Rosetta Doesn't Solve

  2011cited by this paper
• Dali server: conservation mapping in 3D

  2010cited by this paper
• Fast and accurate automatic structure prediction with HHpred

  2009cited by this paper
• Engineered cystine knot peptides that bind αvβ3, αvβ5, and α5β1 integrins with low‐nanomolar affinity

  2009cited by this paper
• Engineered knottin peptides: a new class of agents for imaging integrin expression in living subjects.

  2009cited by this paper
• Outcome of a workshop on applications of protein models in biomedical research.

  2009cited by this paper
• Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike.

  2009cited by this paper
• The conserved baculovirus protein p33 (Ac92) is a flavin adenine dinucleotide-linked sulfhydryl oxidase.

  2009cited by this paper
• Tailed Bacteriophages: The Order Caudovirales

  2008cited by this paper
• An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6.

  2008cited by this paper
• A novel trehalose synthesizing pathway in the hyperthermophilic Crenarchaeon Thermoproteus tenax: the unidirectional TreT pathway

  2008cited by this paper
• The Erv family of sulfhydryl oxidases.

  2008cited by this paper
• Structure of macrophage colony stimulating factor bound to FMS: Diverse signaling assemblies of class III receptor tyrosine kinases

  2008cited by this paper
• Crystal structure of Escherichia coli phage HK620 tailspike: podoviral tailspike endoglycosidase modules are evolutionarily related

  2008cited by this paper
• Discovery of a Cytokine and Its Receptor by Functional Screening of the Extracellular Proteome

  2008cited by this paper
• Optimal Foraging by Bacteriophages through Host Avoidance

  2008cited by this paper
• Unique genes in giant viruses: regular substitution pattern and anomalously short size.

  2007cited by this paper
• Structure of the Receptor-Binding Protein of Bacteriophage Det7: a Podoviral Tail Spike in a Myovirus

  2007cited by this paper
• Marine viruses — major players in the global ecosystem

  2007cited by this paper
• Genomewide screens for Escherichia coli genes affecting growth of T7 bacteriophage

  2006cited by this paper
• African Swine Fever Virus pB119L Protein Is a Flavin Adenine Dinucleotide-Linked Sulfhydryl Oxidase

  2006cited by this paper
• HHrep: de novo protein repeat detection and the origin of TIM barrels

  2006cited by this paper
• Using Dali for structural comparison of proteins.

  2006cited by this paper
• THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

  2006cited by this paper
• Viruses in the sea

  2005cited by this paper
• Structure of Ecballium elaterium trypsin inhibitor II (EETI-II): a rigid molecular scaffold.

  2005cited by this paper
• Effects of the cowpea chlorotic mottle bromovirus beta-hexamer structure on virion assembly.

  2003cited by this paper
• LGA: a method for finding 3D similarities in protein structures

  2003cited by this paper
• The Genome Sequence of Yersinia pestis Bacteriophage φA1122 Reveals an Intimate History with the Coliphage T3 and T7 Genomes

  2003cited by this paper
• Helicobacter pylori and gastrointestinal tract adenocarcinomas

  2002cited by this paper
• A viral member of the ERV1/ALR protein family participates in a cytoplasmic pathway of disulfide bond formation.

  2000cited by this paper
• A H+-gated urea channel: the link between Helicobacter pylori urease and gastric colonization.

  2000cited by this paper
• Protein secondary structure prediction based on position-specific scoring matrices.

  1999cited by this paper
• Crystal structure of phage P22 tailspike protein complexed with Salmonella sp. O-antigen receptors.

  1996cited by this paper
• Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy.

  1995cited by this paper
• The prevalence of Helicobacter pylori infection in different countries.

  1995cited by this paper
• Structural comparisons among the short-chain helical cytokines.

  1994cited by this paper
• Genetic and structural homology of stem cell factor and macrophage colony-stimulating factor.

  1991influential reference
• Haemopoietic receptors and helical cytokines.

  1990cited by this paper
• Icosahedral RNA virus structure.

  1989cited by this paper
• Molecular substructure of a viral receptor-recognition protein. The gp17 tail-fiber of bacteriophage T7.

  1988cited by this paper
• Proteins

  1987cited by this paper
• Metabolism of RNA phosphorus in Escherichia coli infected with bacteriophage T7.

  1958cited by this paper
• Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions

  year unknowninfluential reference

• Protein Target Highlights in CASP16: Insights From the Structure Providers

  2025cites this paper
• Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge

  2024cites this paper
• Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

  2024cites this paper
• Interleukin 34 in Disease Progressions: A Comprehensive Review.

  2023cites this paper
• Protein target highlights in CASP15: Analysis of models by structure providers

  2023cites this paper
• RNA target highlights in CASP15: Evaluation of predicted models by structure providers

  2023cites this paper
• Evolution of Artificial Intelligence-Powered Technologies in Biomedical Research and Healthcare.

  2022cites this paper
• Prediction of Protein Secondary Structure Based on WS-BiLSTM Model

  2022cites this paper
• Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction

  2022cites this paper
• Patterns in Protein Flexibility: A Comparison of NMR “Ensembles”, MD Trajectories, and Crystallographic B-Factors

  2021cites this paper
• IL-34 and coronary heart disease complicated with diabetes mellitus.

  2021cites this paper
• IL-34, the rationale of its expression in physiological and pathological condition.

  2021cites this paper
• Target highlights in CASP14: Analysis of models by structure providers

  2021cites this paper
• Effect of Dietary Incorporation of Curcuma longa Powder on Haematology and Serological Properties of Guinea Pigs (Cavia porcellus)

  2020cites this paper
• Protocol for Protein Structure Modelling

  2019cites this paper
• Structural basis of the differential binding of engineered knottins to integrins αVβ3 and α5β1

  2019cites this paper
• Interleukin‐34, a comprehensive review

  2018cites this paper
• Xenoprotein engineering via synthetic libraries

  2018cites this paper
• A Genetic Algorithm Based on Restricted Tournament Selection for the 3D-PSP Problem

  2018influential citation
• A Constant Proportion in Protein Structure

  2018cites this paper
• Target highlights from the first post‐PSI CASP experiment (CASP12, May–August 2016)

  2018cites this paper
• Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes

  2018cites this paper
• A tangled tale of convergence and divergence: archaeal chromosomal proteins and Chromo-like domains in bacteria and eukaryotes

  2017cites this paper
• Patterns in protein flexibility: a comparison of NMR “ensembles”, MD trajectories and crystallographic B-factors

  2017cites this paper
• Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure

  2017cites this paper
• FliD , the flagellar cap protein from Pseudomonas aeruginosa PAO 1 ( CASP : T 0886 , Ts 886 , PDB : 5 FHY ) : Provided by

  2017cites this paper
• Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures

  2017cites this paper
• Biological and functional relevance of CASP predictions

  2017influential citation
• SURPASS Low-Resolution Coarse-Grained Protein Modeling.

  2017cites this paper
• Coarse-grained modeling of RNA 3D structure.

  2016cites this paper
• Structural difficulty index: a reliable measure for modelability of protein tertiary structures.

  2016cites this paper
• Protein structure prediction (RMSD ≤ 5 Å) using machine learning models

  2016cites this paper
• Crowdsourcing biomedical research: leveraging communities as innovation engines

  2016cites this paper
• Modelling and Analysis of TLR3 Signalling Pathway and Protein-Protein Interaction Studies to Understand the Mechanism of Dengue Virus Mediated Interferon Inhibition.

  2016cites this paper
• Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations

  2016cites this paper
• Evaluation of a combined energy fitness function for a distributed memetic algorithm to tackle the 3D protein structure prediction problem

  2016cites this paper
• Blind testing cross-linking/mass spectrometry under the auspices of the 11 th critical assessment of methods of protein structure prediction (CASP11)

  2016cites this paper
• In silico structural characterization of protein targets for drug development against Trypanosoma cruzi

  2016cites this paper
• Some of the most interesting CASP11 targets through the eyes of their authors

  2015cites this paper
• Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest

  2015cites this paper
• LoopIng: a template-based tool for predicting the structure of protein loops

  2015cites this paper
• Protein design: Past, present, and future

  2015cites this paper
• Refinement by shifting secondary structure elements improves sequence alignments

  2015cites this paper
• APL: An angle probability list to improve knowledge-based metaheuristics for the three-dimensional protein structure prediction

  2015cites this paper
• Protein Structure and Function: Looking through the Network of Side-Chain Interactions.

  2015cites this paper
• Quality assessment of modeled protein structure using physicochemical properties

  2015cites this paper
• Structural modeling and analysis of dengue-mediated inhibition of interferon signaling pathway.

  2015cites this paper
• Using homology relations within a database markedly boosts protein sequence similarity search

  2015cites this paper
• Crystal Structure of ORF210 from E. coli O157:H1 Phage CBA120 (TSP1), a Putative Tailspike Protein

  2014cites this paper
• Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges.

  2014cites this paper
• Cystine-knot peptides: emerging tools for cancer imaging and therapy

  2014cites this paper
• Assessment of ligand binding site predictions in CASP10

  2014cites this paper
• Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17)

  2014cites this paper
• Structural evaluation of BTK and PKCδ mediated phosphorylation of MAL at positions Tyr86 and Tyr106

  2014cites this paper
• CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL

  2014cites this paper
• Evaluation of residue–residue contact prediction in CASP10

  2014cites this paper
• A hybrid method for identification of structural domains

  2014cites this paper
• CASP10 results compared to those of previous CASP experiments

  2014cites this paper
• Critical assessment of methods of protein structure prediction (CASP) — round x

  2014cites this paper