Published in PLoS One on July 06, 2012
ΔΔPT: a comprehensive toolbox for the analysis of protein motion. BMC Bioinformatics (2013) 0.85
Is it possible to stabilize a thermophilic protein further using sequences and structures of mesophilic proteins: a theoretical case study concerning DgAS. Theor Biol Med Model (2013) 0.75
Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model. J Chem Phys (2016) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis (1997) 57.27
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res (2008) 27.83
Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct (2000) 17.81
A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J (1991) 14.56
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des (1997) 11.73
Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. Phys Rev Lett (1996) 9.75
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74
Modeling of loops in protein structures. Protein Sci (2000) 9.68
Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J (2001) 9.04
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
Structural and sequence-based classification of glycoside hydrolases. Curr Opin Struct Biol (1997) 7.71
Conformational change of proteins arising from normal mode calculations. Protein Eng (2001) 6.59
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol (1994) 6.41
The FoldX web server: an online force field. Nucleic Acids Res (2005) 6.30
Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A (1983) 5.27
Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci (1994) 3.92
Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol (2005) 3.88
Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc Natl Acad Sci U S A (1987) 3.85
Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure (2005) 3.85
Global ribosome motions revealed with elastic network model. J Struct Biol (2004) 2.84
Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys J (2002) 2.71
Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales. Proteins (1994) 2.52
Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. J Mol Biol (1999) 2.32
Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci U S A (2005) 2.31
A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase. Biophys J (2002) 2.26
Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details. Protein Eng Des Sel (2009) 2.25
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol (1997) 2.20
Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition. J Mol Biol (2003) 2.14
How to describe protein motion without amino acid sequence and atomic coordinates. Proc Natl Acad Sci U S A (2002) 2.06
Identification of kinetically hot residues in proteins. Protein Sci (1998) 1.82
Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies. Phys Biol (2005) 1.64
Relating molecular flexibility to function: a case study of tubulin. Biophys J (2002) 1.62
Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models. Proteins (2004) 1.51
Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution. Curr Opin Biotechnol (2001) 1.36
A new taxon in the genus Neisseria. Ann Microbiol (Paris) (1984) 1.34
Local water bridges and protein conformational stability. Protein Sci (1999) 1.32
Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding. Curr HIV Res (2004) 1.26
Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase. Proteins (2002) 1.23
Functional motions of influenza virus hemagglutinin: a structure-based analytical approach. Biophys J (2002) 1.17
Amylosucrase, a glucan-synthesizing enzyme from the alpha-amylase family. J Biol Chem (2001) 1.08
ADPG synthetase and ADPG- -glucan 4-glucosyl transferase: enzymes involved in bacterial glycogen and plant starch synthesis. Ann N Y Acad Sci (1973) 1.04
Relationship between local structural entropy and protein thermostability. Proteins (2004) 1.04
Sequence analysis of the gene encoding amylosucrase from Neisseria polysaccharea and characterization of the recombinant enzyme. J Bacteriol (1999) 1.02
Crystal structure of the covalent intermediate of amylosucrase from Neisseria polysaccharea. Biochemistry (2004) 0.98
Conserved water molecules in a large family of microbial ribonucleases. Proteins (1999) 0.96
Bioinformatic method for protein thermal stabilization by structural entropy optimization. Proc Natl Acad Sci U S A (2008) 0.95
Geometric algorithms for the conformational analysis of long protein loops. J Comput Chem (2004) 0.94
Analysis of domain movements in glutamine-binding protein with simple models. Biophys J (2006) 0.93
Oligosaccharide and sucrose complexes of amylosucrase. Structural implications for the polymerase activity. J Biol Chem (2002) 0.93
Crystallization and preliminary X-ray studies of recombinant amylosucrase from Neisseria polysaccharea. Acta Crystallogr D Biol Crystallogr (2000) 0.90
Protein unfolding behavior studied by elastic network model. Biophys J (2008) 0.89
Amylosucrase from Neisseria polysaccharea: novel catalytic properties. FEBS Lett (2000) 0.88
Study on the inhibitory mechanism and binding mode of the hydroxycoumarin compound NSC158393 to HIV-1 integrase by molecular modeling. Biopolymers (2009) 0.83
Characterisation of a novel amylosucrase from Deinococcus radiodurans. FEBS Lett (2005) 0.83
Structural investigation of the thermostability and product specificity of amylosucrase from the bacterium Deinococcus geothermalis. J Biol Chem (2011) 0.83
Glycogen metabolism in the genus Neisseria: synthesis from sucrose by amylosucrase. Can J Microbiol (1978) 0.83
Molecular basis of the amylose-like polymer formation catalyzed by Neisseria polysaccharea amylosucrase. J Biol Chem (2003) 0.82
Study on the mechanism of the BtuF periplasmic-binding protein for vitamin B12. Biophys Chem (2008) 0.82
Thermal stability and unfolding pathways of Sso7d and its mutant F31A: insight from molecular dynamics simulation. J Biomol Struct Dyn (2011) 0.82
Synthesis of a polysaccharide of the starch-glycogen class from sucrose by a cell free, bacterial enzyme system. J Biol Chem (1949) 0.81
Characterisation of the activator effect of glycogen on amylosucrase from Neisseria polysaccharea. FEMS Microbiol Lett (2000) 0.81
Molecular dynamics simulations of the bacterial periplasmic heme binding proteins ShuT and PhuT. Biophys Chem (2008) 0.80
Increased amylosucrase activity and specificity, and identification of regions important for activity, specificity and stability through molecular evolution. FEBS J (2006) 0.80
Molecular cloning and functional expression of a new amylosucrase from Alteromonas macleodii. Biosci Biotechnol Biochem (2009) 0.79
Combinatorial engineering to enhance thermostability of amylosucrase. Protein Sci (2008) 0.78
Dynamics of endoglucanase catalytic domains: implications towards thermostability. J Biomol Struct Dyn (2011) 0.78
Cloning, purification and characterization of a thermostable amylosucrase from Deinococcus geothermalis. FEMS Microbiol Lett (2008) 0.77
Bacterial synthesis of an amylopectin-like polysaccharide from sucrose. J Biol Chem (1946) 0.76
An analysis of the influence of protein intrinsic dynamical properties on its thermal unfolding behavior. J Biomol Struct Dyn (2011) 0.76
Urinary neutrophil gelatinase-associated lipocalin and acute kidney injury after cardiac surgery. Am J Kidney Dis (2008) 3.95
Urinary biomarkers in the early detection of acute kidney injury after cardiac surgery. Clin J Am Soc Nephrol (2009) 2.57
Prenatal airborne polycyclic aromatic hydrocarbon exposure and child IQ at age 5 years. Pediatrics (2009) 2.43
High myopia and glaucoma susceptibility the Beijing Eye Study. Ophthalmology (2006) 2.40
Perioperative acute ischemic stroke in noncardiac and nonvascular surgery: incidence, risk factors, and outcomes. Anesthesiology (2009) 2.12
Subfoveal choroidal thickness: the Beijing Eye Study. Ophthalmology (2012) 2.04
Hybrid silicon nanocone-polymer solar cells. Nano Lett (2012) 2.00
A transparent electrode based on a metal nanotrough network. Nat Nanotechnol (2013) 1.88
CHRM2 gene predisposes to alcohol dependence, drug dependence and affective disorders: results from an extended case-control structured association study. Hum Mol Genet (2005) 1.85
Diplotype trend regression analysis of the ADH gene cluster and the ALDH2 gene: multiple significant associations with alcohol dependence. Am J Hum Genet (2006) 1.82
Genome-wide DNA methylation profiles in hepatocellular carcinoma. Hepatology (2012) 1.81
Prenatal polycyclic aromatic hydrocarbon (PAH) exposure and child behavior at age 6-7 years. Environ Health Perspect (2012) 1.63
Cannabis withdrawal in the United States: results from NESARC. J Clin Psychiatry (2008) 1.59
Transcriptional patterns, biomarkers and pathways characterizing nasopharyngeal carcinoma of Southern China. J Transl Med (2008) 1.57
Localized retinal nerve fiber layer defects and arterial hypertension. Am J Hypertens (2013) 1.51
Prenatal bisphenol a exposure and child behavior in an inner-city cohort. Environ Health Perspect (2012) 1.50
Radiation exposure of the anesthesiologist in the neurointerventional suite. Anesthesiology (2011) 1.47
Prevalence and progression of myopic retinopathy in Chinese adults: the Beijing Eye Study. Ophthalmology (2010) 1.46
Prospective study of wound infections in Mohs micrographic surgery using clean surgical technique in the absence of prophylactic antibiotics. J Am Acad Dermatol (2010) 1.45
Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches. PLoS One (2009) 1.44
Prenatal exposure to airborne polycyclic aromatic hydrocarbons and children's intelligence at 5 years of age in a prospective cohort study in Poland. Environ Health Perspect (2010) 1.44
Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips. Epigenetics (2012) 1.39
Anesthesia-Induced Neuronal Apoptosis in the Developing Retina: A Window of Opportunity. Anesth Analg (2015) 1.39
A community assessment of privacy preserving techniques for human genomes. BMC Med Inform Decis Mak (2014) 1.37
alpha2-Adrenergic agonists protect against radiocontrast-induced nephropathy in mice. Am J Physiol Renal Physiol (2008) 1.36
Systematic review of Chinese studies of short-term exposure to air pollution and daily mortality. Environ Int (2013) 1.34
Prevalence of rectal carriage of extended-spectrum beta-lactamase-producing Escherichia coli among elderly people in community settings in China. Can J Microbiol (2008) 1.32
Promotion of colorectal cancer growth and metastasis by the LIM and SH3 domain protein 1. Gut (2010) 1.31
Vertical heterostructure of two-dimensional MoS₂ and WSe₂ with vertically aligned layers. Nano Lett (2015) 1.29
P2X7 blockade attenuates murine lupus nephritis by inhibiting activation of the NLRP3/ASC/caspase 1 pathway. Arthritis Rheum (2013) 1.28
Polycyclic aromatic hydrocarbons-aromatic DNA adducts in cord blood and behavior scores in New York city children. Environ Health Perspect (2011) 1.28
Characteristics of highly myopic eyes: the Beijing Eye Study. Ophthalmology (2006) 1.25
Cytotoxicity and mitochondrial damage caused by silica nanoparticles. Toxicol In Vitro (2011) 1.23
Three-dimensional culture and cAMP signaling promote the maturation of human pluripotent stem cell-derived hepatocytes. Development (2013) 1.23
Genetic polymorphisms in cytochrome P450 oxidoreductase influence microsomal P450-catalyzed drug metabolism. Pharmacogenet Genomics (2008) 1.22
Impact of non-pharmaceutical interventions on URIs and influenza in crowded, urban households. Public Health Rep (2010) 1.21
Performance enhancement of metal nanowire transparent conducting electrodes by mesoscale metal wires. Nat Commun (2013) 1.21
Interacting genetic loci on chromosomes 20 and 10 influence extreme human obesity. Am J Hum Genet (2002) 1.21
Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure. BMC Genet (2005) 1.20
Quantitative trait loci in Anopheles gambiae controlling the encapsulation response against Plasmodium cynomolgi Ceylon. BMC Genet (2003) 1.19
Differentially private genome data dissemination through top-down specialization. BMC Med Inform Decis Mak (2014) 1.18
Size-dependent cytotoxicity of amorphous silica nanoparticles in human hepatoma HepG2 cells. Toxicol In Vitro (2011) 1.17
An upstream activation sequence controls the expression of AOX1 gene in Pichia pastoris. FEMS Yeast Res (2009) 1.14
Reactogenicity of live-attenuated Vibrio cholerae vaccines is dependent on flagellins. Proc Natl Acad Sci U S A (2010) 1.14
Multiple ADH genes modulate risk for drug dependence in both African- and European-Americans. Hum Mol Genet (2006) 1.14
Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. Proc Natl Acad Sci U S A (2012) 1.13
Bottom-up synthesis of porous coordination frameworks: apical substitution of a pentanuclear tetrahedral precursor. Angew Chem Int Ed Engl (2009) 1.13
Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms. PLoS One (2012) 1.13
Hypoxic retinal Muller cells promote vascular permeability by HIF-1-dependent up-regulation of angiopoietin-like 4. Proc Natl Acad Sci U S A (2013) 1.12
Racial and insurance disparities in the receipt of transplant among patients with hepatocellular carcinoma. Cancer (2010) 1.12
Hidden in plain sight: bias towards sick patients when sampling patients with sufficient electronic health record data for research. BMC Med Inform Decis Mak (2014) 1.12
Cardiovascular toxicity evaluation of silica nanoparticles in endothelial cells and zebrafish model. Biomaterials (2013) 1.11
Bacitracin-resistant clone of Streptococcus pyogenes isolated from pharyngitis patients in Belgium. J Clin Microbiol (2003) 1.10
The signatures of autozygosity among patients with colorectal cancer. Cancer Res (2008) 1.10
Childhood exposure to fine particulate matter and black carbon and the development of new wheeze between ages 5 and 7 in an urban prospective cohort. Environ Int (2012) 1.08
Overexpression of Tiam1 in hepatocellular carcinomas predicts poor prognosis of HCC patients. Int J Cancer (2009) 1.08
Retinal vascular abnormalities and prevalence of age-related macular degeneration in adult Chinese: the Beijing Eye Study. Am J Ophthalmol (2006) 1.07
NK cells induce apoptosis in tubular epithelial cells and contribute to renal ischemia-reperfusion injury. J Immunol (2008) 1.07
Toxic effect of silica nanoparticles on endothelial cells through DNA damage response via Chk1-dependent G2/M checkpoint. PLoS One (2013) 1.06
Bay11-7082 attenuates murine lupus nephritis via inhibiting NLRP3 inflammasome and NF-κB activation. Int Immunopharmacol (2013) 1.06
Prevalence and risk factors for diabetic retinopathy: the Beijing Communities Diabetes Study 6. Retina (2012) 1.06
Increased incidence of acute kidney injury with aprotinin use during cardiac surgery detected with urinary NGAL. Am J Nephrol (2008) 1.05
Recent trends in biomedical informatics: a study based on JAMIA articles. J Am Med Inform Assoc (2013) 1.05
Clustering and principal-components approach based on heritability for mapping multiple gene expressions. BMC Proc (2007) 1.04
A fast and noise-resilient approach to detect rare-variant associations with deep sequencing data for complex disorders. Genet Epidemiol (2012) 1.04
Single endemic genotype of measles virus continuously circulating in China for at least 16 years. PLoS One (2012) 1.03
Diabetes, body mass index, and outcomes in hepatocellular carcinoma patients undergoing liver transplantation. Transplantation (2012) 1.03
Comparative proteomic analysis of seedling leaves of different salt tolerant soybean genotypes. J Proteomics (2011) 1.03
Edwardsiella tarda T6SS component evpP is regulated by esrB and iron, and plays essential roles in the invasion of fish. Fish Shellfish Immunol (2009) 1.02
Genome-wide aberrant DNA methylation of microRNA host genes in hepatocellular carcinoma. Epigenetics (2012) 1.02
Acute toxicity of amorphous silica nanoparticles in intravenously exposed ICR mice. PLoS One (2013) 1.01
Lentivirus-mediated silencing of Tiam1 gene influences multiple functions of a human colorectal cancer cell line. Neoplasia (2006) 1.01
WebGLORE: a web service for Grid LOgistic REgression. Bioinformatics (2013) 1.01
Emergence and continuous evolution of genotype 1E rubella viruses in China. J Clin Microbiol (2011) 1.01
Reproducibility of subfoveal choroidal thickness measurements with enhanced depth imaging by spectral-domain optical coherence tomography. Invest Ophthalmol Vis Sci (2013) 1.00
Pharmacokinetics of single-dose and multiple-dose memantine in healthy chinese volunteers using an analytic method of liquid chromatography-tandem mass spectrometry. Clin Ther (2008) 1.00
The recombinant Hc subunit of Clostridium botulinum neurotoxin serotype A is an effective botulism vaccine candidate. Vaccine (2009) 1.00
Identification of potential genes/proteins regulated by Tiam1 in colorectal cancer by microarray analysis and proteome analysis. Cell Biol Int (2008) 1.00
Field and long-term demonstration of a wide area quantum key distribution network. Opt Express (2014) 0.99
Combining identity by descent and association in genetic case-control studies. BMC Genet (2008) 0.99
The 10-year incidence and risk factors of retinal vein occlusion: the Beijing eye study. Ophthalmology (2013) 0.99
QseBC controls flagellar motility, fimbrial hemagglutination and intracellular virulence in fish pathogen Edwardsiella tarda. Fish Shellfish Immunol (2011) 0.98
Linkage and linkage disequilibrium mapping of genes influencing human obesity in chromosome region 7q22.1-7q35. Diabetes (2003) 0.98
Biomaterial selection for tooth regeneration. Tissue Eng Part B Rev (2011) 0.98
CO-releasing molecules (CORM-2)-liberated CO attenuates leukocytes infiltration in the renal tissue of thermally injured mice. Int J Biol Sci (2008) 0.98
GAB2 amplifications refine molecular classification of melanoma. Clin Cancer Res (2009) 0.97
Protective effects of repetitive transcranial magnetic stimulation in a rat model of transient cerebral ischaemia: a microPET study. Eur J Nucl Med Mol Imaging (2010) 0.97
Indoleamine 2,3-dioxygenase expression promotes renal ischemia-reperfusion injury. Am J Physiol Renal Physiol (2008) 0.97
Optimal DNA pooling-based two-stage designs in case-control association studies. Hum Hered (2008) 0.97
Effects of a novel tylophorine analog on collagen-induced arthritis through inhibition of the innate immune response. Arthritis Rheum (2006) 0.97
RNA-seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish. BMC Genomics (2012) 0.96
Penalized logistic regression for high-dimensional DNA methylation data with case-control studies. Bioinformatics (2012) 0.96
Whole-genome association studies on alcoholism comparing different phenotypes using single-nucleotide polymorphisms and microsatellites. BMC Genet (2005) 0.96
Differential proteomic analysis of human colorectal carcinoma cell lines metastasis-associated proteins. J Cancer Res Clin Oncol (2007) 0.95
ADH7 variation modulates extraversion and conscientiousness in substance-dependent subjects. Am J Med Genet B Neuropsychiatr Genet (2008) 0.95
Cardiovascular toxicity of different sizes amorphous silica nanoparticles in rats after intratracheal instillation. Cardiovasc Toxicol (2013) 0.95
Structural requirements for the BARD1 tumor suppressor in chromosomal stability and homology-directed DNA repair. J Biol Chem (2007) 0.95
Predictors and consequences of global DNA methylation in cord blood and at three years. PLoS One (2013) 0.94
Trends in the hospitalization of ischemic stroke in the United States, 1998-2007. Int J Stroke (2011) 0.94
Time course of cortisol loss in hair segments under immersion in hot water. Clin Chim Acta (2011) 0.94