Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment.

PubWeight™: 0.88‹?›

🔗 View Article (PMC 3667494)

Published in Sci Rep on January 01, 2013

Authors

Dong Xu1, Yang Zhang

Author Affiliations

1: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

Articles citing this

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep (2013) 0.97

ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. BMC Bioinformatics (2015) 0.86

Systems biology of the structural proteome. BMC Syst Biol (2016) 0.84

General overview on structure prediction of twilight-zone proteins. Theor Biol Med Model (2015) 0.78

Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes. Mycorrhiza (2017) 0.76

Molecular dynamics simulation reveals insights into the mechanism of unfolding by the A130T/V mutations within the MID1 zinc-binding Bbox1 domain. PLoS One (2015) 0.75

Alignment behaviors of short peptides provide a roadmap for functional profiling of metagenomic data. BMC Genomics (2015) 0.75

Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC. Front Microbiol (2015) 0.75

Computational modeling suggests dimerization of equine infectious anemia virus Rev is required for RNA binding. Retrovirology (2014) 0.75

A hybrid method for identification of structural domains. Sci Rep (2014) 0.75

Molecular Modeling of Cloned Bacillus subtilis Keratinase and Its Insinuation in Psoriasis Treatment Using Docking Studies. Indian J Microbiol (2017) 0.75

Purification, Biochemical Characterization, and Amino Acid Sequence of a Novel Type of Lectin from Aplysia dactylomela Eggs with Antibacterial/Antibiofilm Potential. Mar Biotechnol (NY) (2017) 0.75

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

The Protein Data Bank. Nucleic Acids Res (2000) 187.10

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69

SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol (2001) 66.87

Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61

I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66

TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15

A method to identify protein sequences that fold into a known three-dimensional structure. Science (1991) 14.08

Dynamics of folded proteins. Nature (1977) 7.82

PROMOTIF--a program to identify and analyze structural motifs in proteins. Protein Sci (1996) 6.76

A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry (1994) 6.64

Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics (2007) 5.68

Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A (2004) 5.44

Computer simulation of protein folding. Nature (1975) 5.34

LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res (2007) 5.30

SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem (2004) 4.87

Assessment of CASP7 predictions for template-based modeling targets. Proteins (2007) 3.50

Progress and challenges in protein structure prediction. Curr Opin Struct Biol (2008) 3.48

Automated server predictions in CASP7. Proteins (2007) 3.40

How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics (2010) 3.22

Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins (2002) 3.09

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins (2012) 2.94

Folding of polypeptide chains in proteins: a proposed mechanism for folding. Proc Natl Acad Sci U S A (1971) 2.68

Evaluation of template-based models in CASP8 with standard measures. Proteins (2009) 2.46

Do transmembrane protein superfolds exist? FEBS Lett (1998) 2.40

Evaluation of comparative protein structure modeling by MODELLER-3. Proteins (1997) 2.39

Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J (2011) 2.24

Assessment of template based protein structure predictions in CASP9. Proteins (2011) 2.14

CASP9 assessment of free modeling target predictions. Proteins (2011) 1.90

Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr Opin Chem Biol (2004) 1.86

Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci U S A (1997) 1.81

Generating triangulated macromolecular surfaces by Euclidean Distance Transform. PLoS One (2009) 1.54

Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol (2007) 1.53

Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance. J Mol Biol (2007) 1.38

Protein domain decomposition using a graph-theoretic approach. Bioinformatics (2000) 1.31

Toward optimal fragment generations for ab initio protein structure assembly. Proteins (2012) 1.13

Articles by these authors

(truncated to the top 100)

I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39

LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res (2007) 5.30

Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol (2007) 5.07

IL-21 regulates germinal center B cell differentiation and proliferation through a B cell-intrinsic mechanism. J Exp Med (2010) 4.04

Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers. Nat Genet (2010) 4.01

RET fusions define a unique molecular and clinicopathologic subtype of non-small-cell lung cancer. J Clin Oncol (2012) 3.72

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins (2008) 3.38

How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics (2010) 3.22

Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure (2011) 2.97

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins (2012) 2.94

Three-field or two-field resection for thoracic esophageal cancer: a meta-analysis. Ann Thorac Surg (2013) 2.92

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res (2012) 2.75

Long noncoding RNAs with snoRNA ends. Mol Cell (2012) 2.71

BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res (2012) 2.56

Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics (2013) 2.43

Chibby, a nuclear beta-catenin-associated antagonist of the Wnt/Wingless pathway. Nature (2003) 2.42

Functional mesenchymal stem cells derived from human induced pluripotent stem cells attenuate limb ischemia in mice. Circulation (2010) 2.39

Arsenic detoxification and evolution of trimethylarsine gas by a microbial arsenite S-adenosylmethionine methyltransferase. Proc Natl Acad Sci U S A (2006) 2.37

MicroRNA-101 inhibited postinfarct cardiac fibrosis and improved left ventricular compliance via the FBJ osteosarcoma oncogene/transforming growth factor-β1 pathway. Circulation (2012) 2.36

Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins (2004) 2.34

Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J (2011) 2.24

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics (2004) 2.17

HAb18G/CD147 promotes activation of hepatic stellate cells and is a target for antibody therapy of liver fibrosis. J Hepatol (2012) 2.15

Genome-wide association study identifies a susceptibility locus for schizophrenia in Han Chinese at 11p11.2. Nat Genet (2011) 2.13

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics (2008) 2.08

Pattern of lymphatic spread in thoracic esophageal squamous cell carcinoma: A single-institution experience. J Thorac Cardiovasc Surg (2012) 2.08

Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Nat Chem Biol (2008) 1.96

REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins (2009) 1.89

The role of concurrent chemoradiotherapy in the treatment of locoregionally advanced nasopharyngeal carcinoma among endemic population: a meta-analysis of the phase III randomized trials. BMC Cancer (2010) 1.68

Gram-scale synthesis of submicrometer-long polythiophene wires in mesoporous silica matrices. Angew Chem Int Ed Engl (2003) 1.64

Outcomes of the POG 9340/9341/9342 trials for children with high-risk neuroblastoma: a report from the Children's Oncology Group. Pediatr Blood Cancer (2008) 1.60

Control of autophagy maturation by acid sphingomyelinase in mouse coronary arterial smooth muscle cells: protective role in atherosclerosis. J Mol Med (Berl) (2014) 1.59

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins (2011) 1.58

A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PLoS One (2010) 1.56

FGF21 and the late adaptive response to starvation in humans. J Clin Invest (2015) 1.55

Palladium-catalyzed enantioselective addition of two distinct nucleophiles across alkenes capable of quinone methide formation. J Am Chem Soc (2009) 1.54

Generating triangulated macromolecular surfaces by Euclidean Distance Transform. PLoS One (2009) 1.54

Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell (2012) 1.52

TRAIL death receptor 4 signaling via lysosome fusion and membrane raft clustering in coronary arterial endothelial cells: evidence from ASM knockout mice. J Mol Med (Berl) (2012) 1.52

HAb18G/CD147 functions in invasion and metastasis of hepatocellular carcinoma. Mol Cancer Res (2007) 1.48

HAb18G (CD147), a cancer-associated biomarker and its role in cancer detection. Histopathology (2009) 1.45

Potential role of human visceral pleura in pleural fluid turnover. Chin Med J (Engl) (2006) 1.44

Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement. Structure (2012) 1.42

Infant speech perception activates Broca's area: a developmental magnetoencephalography study. Neuroreport (2006) 1.40

Toxicity and cellular responses of intestinal cells exposed to titanium dioxide. Cell Biol Toxicol (2009) 1.38

Protein-protein complex structure predictions by multimeric threading and template recombination. Structure (2011) 1.34

Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc Natl Acad Sci U S A (2002) 1.33

National survey of the medical treatment status for non-small cell lung cancer (NSCLC) in China. Lung Cancer (2012) 1.30

[Phase III randomized clinical trial of intratumoral injection of E1B gene-deleted adenovirus (H101) combined with cisplatin-based chemotherapy in treating squamous cell cancer of head and neck or esophagus]. Ai Zheng (2004) 1.29

Critical role of lipid raft redox signaling platforms in endostatin-induced coronary endothelial dysfunction. Arterioscler Thromb Vasc Biol (2007) 1.29

Application of sparse NMR restraints to large-scale protein structure prediction. Biophys J (2004) 1.28

Improving protein structure prediction using multiple sequence-based contact predictions. Structure (2011) 1.24

Identification of near-native structures by clustering protein docking conformations. Proteins (2007) 1.23

A protocol for computer-based protein structure and function prediction. J Vis Exp (2011) 1.23

Lipid raft redox signaling platforms in endothelial dysfunction. Antioxid Redox Signal (2007) 1.22

Deletion of the cyclic di-AMP phosphodiesterase gene (cnpB) in Mycobacterium tuberculosis leads to reduced virulence in a mouse model of infection. Mol Microbiol (2014) 1.22

The use of quantitative real-time reverse transcriptase PCR for 5' and 3' portions of ALK transcripts to detect ALK rearrangements in lung cancers. Clin Cancer Res (2012) 1.21

TOUCHSTONE: a unified approach to protein structure prediction. Proteins (2003) 1.20

A multicenter, randomized, double-blind, placebo-controlled study to evaluate the efficacy of paclitaxel-carboplatin alone or with endostar for advanced non-small cell lung cancer. J Thorac Oncol (2011) 1.19

Uncoupling protein-2 protects endothelial function in diet-induced obese mice. Circ Res (2012) 1.19

Significance of MYCN amplification in international neuroblastoma staging system stage 1 and 2 neuroblastoma: a report from the International Neuroblastoma Risk Group database. J Clin Oncol (2008) 1.18

Lung adenocarcinomas with HER2-activating mutations are associated with distinct clinical features and HER2/EGFR copy number gains. J Thorac Oncol (2012) 1.17

Lysin motif-containing proteins LYP4 and LYP6 play dual roles in peptidoglycan and chitin perception in rice innate immunity. Plant Cell (2012) 1.16

Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. J Proteome Res (2011) 1.16

Cyclic di-AMP impairs potassium uptake mediated by a cyclic di-AMP binding protein in Streptococcus pneumoniae. J Bacteriol (2013) 1.16

miR-1 exacerbates cardiac ischemia-reperfusion injury in mouse models. PLoS One (2012) 1.15

Comparison of exposure estimation methods for air pollutants: ambient monitoring data and regional air quality simulation. Environ Res (2012) 1.15

Mechanistic studies of Ce(IV)-mediated oxidation of beta-dicarbonyls: solvent-dependent behavior of radical cation intermediates. J Org Chem (2007) 1.14

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Res (2009) 1.14

Genetic variants in cyclooxygenase-2: Expression and risk of gastric cancer and its precursors in a Chinese population. Gastroenterology (2006) 1.14

Toward optimal fragment generations for ab initio protein structure assembly. Proteins (2012) 1.13

Frequency of well-identified oncogenic driver mutations in lung adenocarcinoma of smokers varies with histological subtypes and graduated smoking dose. Lung Cancer (2012) 1.12

iTRAQ-2DLC-ESI-MS/MS based identification of a new set of immunohistochemical biomarkers for classification of dysplastic nodules and small hepatocellular carcinoma. J Proteome Res (2011) 1.11

TOUCHSTONEX: protein structure prediction with sparse NMR data. Proteins (2003) 1.10

A genetic linkage map of Pacific white shrimp (Litopenaeus vannamei): sex-linked microsatellite markers and high recombination rates. Genetica (2006) 1.09

Corneal nerve structure and function in patients with non-sjogren dry eye: clinical correlations. Invest Ophthalmol Vis Sci (2013) 1.09

TASSER-based refinement of NMR structures. Proteins (2006) 1.09

Function of HAb18G/CD147 in invasion of host cells by severe acute respiratory syndrome coronavirus. J Infect Dis (2005) 1.09

BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures. Proteins (2011) 1.08

Enhancement of autophagy by simvastatin through inhibition of Rac1-mTOR signaling pathway in coronary arterial myocytes. Cell Physiol Biochem (2013) 1.08

Analysis of major known driver mutations and prognosis in resected adenosquamous lung carcinomas. J Thorac Oncol (2014) 1.08

Bridging small-gap peripheral nerve defects using acellular nerve allograft implanted with autologous bone marrow stromal cells in primates. Brain Res (2007) 1.08

Redox regulation of NLRP3 inflammasomes: ROS as trigger or effector? Antioxid Redox Signal (2015) 1.07

Abnormal junctions and permeability of myelin in PMP22-deficient nerves. Ann Neurol (2014) 1.06

Negative Differential Resistance in ZnO Nanowires Bridging Two Metallic Electrodes. Nanoscale Res Lett (2010) 1.06

Glucagon stimulates exocytosis in mouse and rat pancreatic alpha-cells by binding to glucagon receptors. Mol Endocrinol (2004) 1.06

A theory of germinal center B cell selection, division, and exit. Cell Rep (2012) 1.06

A novel probe for the non-invasive detection of tumor-associated inflammation. Oncoimmunology (2013) 1.05

Mechanism of human S-adenosylmethionine decarboxylase proenzyme processing as revealed by the structure of the S68A mutant. Biochemistry (2003) 1.05

[Chemical constituents of Ligularia duciformis]. Yao Xue Xue Bao (2007) 1.05

ThreaDom: extracting protein domain boundary information from multiple threading alignments. Bioinformatics (2013) 1.05

Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon. PLoS One (2012) 1.05

Differential response between the p53 ubiquitin-protein ligases Pirh2 and MdM2 following DNA damage in human cancer cells. Exp Cell Res (2006) 1.04

TASSER-Lite: an automated tool for protein comparative modeling. Biophys J (2006) 1.03

Controllable synthesis of silver nanoparticle-decorated reduced graphene oxide hybrids for ammonia detection. Analyst (2013) 1.03

Modulation of CD147-induced matrix metalloproteinase activity: role of CD147 N-glycosylation. Biochem J (2013) 1.02

A comparative study on screw loosening in osteoporotic lumbar spine fusion between expandable and conventional pedicle screws. Arch Orthop Trauma Surg (2011) 1.02

ANGLOR: a composite machine-learning algorithm for protein backbone torsion angle prediction. PLoS One (2008) 1.02

Expression of TRF1, TRF2, TIN2, TERT, KU70, and BRCA1 proteins is associated with telomere shortening and may contribute to multistage carcinogenesis of gastric cancer. J Cancer Res Clin Oncol (2010) 1.02