Published in J Mol Graph Model on February 03, 2006
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Oroxylin A inhibits hemolysis via hindering the self-assembly of α-hemolysin heptameric transmembrane pore. PLoS Comput Biol (2013) 1.02
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Surveying implicit solvent models for estimating small molecule absolute hydration free energies. J Comput Chem (2011) 1.00
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Disruption of ionic interactions between the nucleotide binding domain 1 (NBD1) and middle (M) domain in Hsp100 disaggregase unleashes toxic hyperactivity and partial independence from Hsp70. J Biol Chem (2012) 0.90
Stabilization of the GluCl ligand-gated ion channel in the presence and absence of ivermectin. Biophys J (2013) 0.90
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. J Comput Aided Mol Des (2014) 0.89
Novel ligands that target the mitochondrial membrane protein mitoNEET. J Mol Graph Model (2011) 0.89
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Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations. MAbs (2013) 0.89
Discovery of Staphylococcus aureus sortase A inhibitors using virtual screening and the relaxed complex scheme. Chem Biol Drug Des (2013) 0.89
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Structure-based mechanism of CMP-2-keto-3-deoxymanno-octulonic acid synthetase: convergent evolution of a sugar-activating enzyme with DNA/RNA polymerases. J Biol Chem (2009) 0.88
Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir. J Comput Aided Mol Des (2012) 0.88
Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies. J Chem Theory Comput (2014) 0.88
Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design. J Chem Theory Comput (2009) 0.88
On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations. J Chem Theory Comput (2012) 0.88
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. J Comput Aided Mol Des (2013) 0.87
Structure of the 1,N2-ethenodeoxyguanosine adduct opposite cytosine in duplex DNA: Hoogsteen base pairing at pH 5.2. Chem Res Toxicol (2008) 0.87
Exploring the mechanism of zanamivir resistance in a neuraminidase mutant: a molecular dynamics study. PLoS One (2012) 0.87
An internal reaction chamber in dimethylglycine oxidase provides efficient protection from exposure to toxic formaldehyde. J Biol Chem (2009) 0.87
Crystal structure of the human sterol transporter ABCG5/ABCG8. Nature (2016) 0.87
A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2. J Am Chem Soc (2014) 0.86
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Towards automated binding affinity prediction using an iterative linear interaction energy approach. Int J Mol Sci (2014) 0.86
Bringing Clarity to the Prediction of Protein-Ligand Binding Free Energies via "Blurring" J Chem Theory Comput (2014) 0.86
CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Adv Protein Chem Struct Biol (2014) 0.86
CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application. J Chem Inf Model (2012) 0.86
Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. J Chem Theory Comput (2011) 0.86
Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications. J Chem Theory Comput (2013) 0.86
Revealing origin of decrease in potency of darunavir and amprenavir against HIV-2 relative to HIV-1 protease by molecular dynamics simulations. Sci Rep (2014) 0.86
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
Development and testing of a general amber force field. J Comput Chem (2004) 23.29
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet (2008) 12.51
piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature (2009) 11.27
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins (2004) 9.15
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74
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A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell (2004) 8.06
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol (2009) 7.59
Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism. Cell (2012) 7.36
Acute renal failure and sepsis. N Engl J Med (2004) 7.18
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
High-performance neuroprosthetic control by an individual with tetraplegia. Lancet (2012) 6.66
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
New loci associated with kidney function and chronic kidney disease. Nat Genet (2010) 5.58
Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med (2008) 5.54
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Predictive value for the Chinese population of the Framingham CHD risk assessment tool compared with the Chinese Multi-Provincial Cohort Study. JAMA (2004) 5.34
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De novo mutations in histone-modifying genes in congenital heart disease. Nature (2013) 5.15
Evidence for HIV-associated B cell exhaustion in a dysfunctional memory B cell compartment in HIV-infected viremic individuals. J Exp Med (2008) 5.14
MicroRNA-34b and MicroRNA-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth. Cancer Res (2007) 4.95
Hepatocyte growth factor induces gefitinib resistance of lung adenocarcinoma with epidermal growth factor receptor-activating mutations. Cancer Res (2008) 4.30
Probable limited person-to-person transmission of highly pathogenic avian influenza A (H5N1) virus in China. Lancet (2008) 4.17
EpCAM and alpha-fetoprotein expression defines novel prognostic subtypes of hepatocellular carcinoma. Cancer Res (2008) 4.17
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J Mol Biol (2003) 3.89
Pelvic Organ Support Study (POSST): the distribution, clinical definition, and epidemiologic condition of pelvic organ support defects. Am J Obstet Gynecol (2005) 3.85
Association between adverse clinical outcome in human disease caused by novel influenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance. Lancet (2013) 3.83
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem (2004) 3.83
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell (2013) 3.81
Epidemiological transition of stroke in China: twenty-one-year observational study from the Sino-MONICA-Beijing Project. Stroke (2008) 3.81
Natural selection on EPAS1 (HIF2alpha) associated with low hemoglobin concentration in Tibetan highlanders. Proc Natl Acad Sci U S A (2010) 3.78
Acute renal failure: definitions, diagnosis, pathogenesis, and therapy. J Clin Invest (2004) 3.75
Discovery and annotation of functional chromatin signatures in the human genome. PLoS Comput Biol (2009) 3.61
Residential proximity to naturally occurring asbestos and mesothelioma risk in California. Am J Respir Crit Care Med (2005) 3.55
Clinical application of massively parallel sequencing-based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11,105 pregnancies with mixed risk factors. Prenat Diagn (2012) 3.54
Surgical treatment of giant coronary artery aneurysm. J Thorac Cardiovasc Surg (2005) 3.53
ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol (2008) 3.46
A proprotein convertase subtilisin/kexin type 9 neutralizing antibody reduces serum cholesterol in mice and nonhuman primates. Proc Natl Acad Sci U S A (2009) 3.39
Characteristics associated with differences in survival among black and white women with breast cancer. JAMA (2013) 3.35
Effects of acupuncture on pregnancy rates in women undergoing in vitro fertilization: a systematic review and meta-analysis. Fertil Steril (2012) 3.33
Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res (2011) 3.25
Effects of a universal classroom behavior management program in first and second grades on young adult behavioral, psychiatric, and social outcomes. Drug Alcohol Depend (2008) 3.22
Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res (2010) 3.17
Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state. Stem Cells (2005) 3.16
A recalibrated molecular clock and independent origins for the cholera pandemic clones. PLoS One (2008) 3.16
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Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J Comput Chem (2004) 3.12
Methods for testing theory and evaluating impact in randomized field trials: intent-to-treat analyses for integrating the perspectives of person, place, and time. Drug Alcohol Depend (2008) 3.09
Quantum-sized carbon dots for bright and colorful photoluminescence. J Am Chem Soc (2006) 3.08
Adverse metabolic consequences in humans of prolonged sleep restriction combined with circadian disruption. Sci Transl Med (2012) 3.08
Oxidative damage targets complexes containing DNA methyltransferases, SIRT1, and polycomb members to promoter CpG Islands. Cancer Cell (2011) 3.07
Effective Born radii in the generalized Born approximation: the importance of being perfect. J Comput Chem (2002) 3.06
Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model (2010) 3.04
Epidemiology of Alzheimer's disease and other forms of dementia in China, 1990-2010: a systematic review and analysis. Lancet (2013) 3.02
Long non-coding RNA H19 increases bladder cancer metastasis by associating with EZH2 and inhibiting E-cadherin expression. Cancer Lett (2013) 2.99
The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics. Mamm Genome (2007) 2.82
Sleep restriction for 1 week reduces insulin sensitivity in healthy men. Diabetes (2010) 2.81
NPR3 and NPR4 are receptors for the immune signal salicylic acid in plants. Nature (2012) 2.76
DOCK 6: combining techniques to model RNA-small molecule complexes. RNA (2009) 2.75
Autophosphorylation of the catalytic subunit of the DNA-dependent protein kinase is required for efficient end processing during DNA double-strand break repair. Mol Cell Biol (2003) 2.74
U-Pb ages from the neoproterozoic Doushantuo Formation, China. Science (2005) 2.71
Plk1-dependent phosphorylation of FoxM1 regulates a transcriptional programme required for mitotic progression. Nat Cell Biol (2008) 2.68
Phase II randomized study of vaccine treatment of advanced prostate cancer (E7897): a trial of the Eastern Cooperative Oncology Group. J Clin Oncol (2004) 2.65
Enhanced sarcoplasmic reticulum Ca2+ leak and increased Na+-Ca2+ exchanger function underlie delayed afterdepolarizations in patients with chronic atrial fibrillation. Circulation (2012) 2.58
1-(2-Benzoyl-1-phenyl-eth-yl)-4-[(2-hy-droxy-1-naphth-yl)methyl-idene-amino]-3-methyl-1H-1,2,4-triazole-5(4H)-thione. Acta Crystallogr Sect E Struct Rep Online (2011) 2.58
Appearance of immature/transitional B cells in HIV-infected individuals with advanced disease: correlation with increased IL-7. Proc Natl Acad Sci U S A (2006) 2.54
Molecular classification of human cancers using a 92-gene real-time quantitative polymerase chain reaction assay. Arch Pathol Lab Med (2006) 2.53
Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet (2012) 2.51
Reduced H3K27me3 and DNA hypomethylation are major drivers of gene expression in K27M mutant pediatric high-grade gliomas. Cancer Cell (2013) 2.50
Clinical, experimental, and genomic differences between intermediately pathogenic, highly pathogenic, and epidemic Streptococcus suis. J Infect Dis (2009) 2.49
Mesp1 coordinately regulates cardiovascular fate restriction and epithelial-mesenchymal transition in differentiating ESCs. Cell Stem Cell (2008) 2.46
Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem (2004) 2.43
FGF23 neutralization improves chronic kidney disease-associated hyperparathyroidism yet increases mortality. J Clin Invest (2012) 2.41
Calibrating the end-Permian mass extinction. Science (2011) 2.41
MicroRNA-133a protects against myocardial fibrosis and modulates electrical repolarization without affecting hypertrophy in pressure-overloaded adult hearts. Circ Res (2009) 2.40
Regulated ATP release from astrocytes through lysosome exocytosis. Nat Cell Biol (2007) 2.38
Scavenger receptor class B type I-mediated protection against atherosclerosis in LDL receptor-negative mice involves its expression in bone marrow-derived cells. Arterioscler Thromb Vasc Biol (2003) 2.38
Replanning during intensity modulated radiation therapy improved quality of life in patients with nasopharyngeal carcinoma. Int J Radiat Oncol Biol Phys (2012) 2.34
PiggyBac transposon mutagenesis: a tool for cancer gene discovery in mice. Science (2010) 2.31
Investigation of dry eye disease and analysis of the pathogenic factors in patients after cataract surgery. Cornea (2007) 2.30
Mismatch repair genes identified using genetic screens in Blm-deficient embryonic stem cells. Nature (2004) 2.29
SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Res (2011) 2.27
Two key residues in ephrinB3 are critical for its use as an alternative receptor for Nipah virus. PLoS Pathog (2006) 2.26
Caseation of human tuberculosis granulomas correlates with elevated host lipid metabolism. EMBO Mol Med (2010) 2.26
Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models. J Am Chem Soc (2004) 2.26
Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing. Nat Protoc (2010) 2.24
Carbohydrate-binding molecules inhibit viral fusion and entry by crosslinking membrane glycoproteins. Nat Immunol (2005) 2.24
Angiotensin II-accelerated atherosclerosis and aneurysm formation is attenuated in osteopontin-deficient mice. J Clin Invest (2003) 2.23
Synergy of p53 and Rb deficiency in a conditional mouse model for metastatic prostate cancer. Cancer Res (2006) 2.23
Disrupted junctional membrane complexes and hyperactive ryanodine receptors after acute junctophilin knockdown in mice. Circulation (2011) 2.21
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res (2009) 2.20
Comprehensive genomic access to vector integration in clinical gene therapy. Nat Med (2009) 2.19