Published in J Chem Theory Comput on September 14, 2010
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Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylation. Genes Dev (2013) 1.30
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Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations. Proc Natl Acad Sci U S A (2012) 1.14
Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle. J Comput Chem (2011) 1.04
Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery. Biochemistry (2012) 0.97
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Structures and free energy landscapes of aqueous zinc(II)-bound amyloid-β(1-40) and zinc(II)-bound amyloid-β(1-42) with dynamics. J Biol Inorg Chem (2012) 0.83
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Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B (2014) 0.80
Structure and dynamics of the N-terminal domain of the Cu(I) binding protein CusB. Biochemistry (2013) 0.80
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Calculation of Heats of Formation for Zn Complexes: Comparison of Density Functional Theory, Second Order Perturbation Theory, Coupled-Cluster and Complete Active Space Methods. J Chem Theory Comput (2013) 0.79
Molecular dynamics simulation study of conformational changes of transcription factor TFIIS during RNA polymerase II transcriptional arrest and reactivation. PLoS One (2014) 0.78
Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water. J Phys Chem B (2014) 0.78
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Insight into the Mechanism of Intramolecular Inhibition of the Catalytic Activity of Sirtuin 2 (SIRT2). PLoS One (2015) 0.76
Exploring the RING-catalyzed ubiquitin transfer mechanism by MD and QM/MM calculations. PLoS One (2014) 0.76
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Metal binding mediated conformational change of XPA protein:a potential cytotoxic mechanism of nickel in the nucleotide excision repair. J Mol Model (2016) 0.75
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Mechanism of host substrate acetylation by a YopJ family effector. Nat Plants (2017) 0.75
Activity prediction of substrates in NADH-dependent carbonyl reductase by docking requires catalytic constraints and charge parameterization of catalytic zinc environment. J Comput Aided Mol Des (2015) 0.75
Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium. Acta Crystallogr D Biol Crystallogr (2002) 3.55
Geometry of metal-ligand interactions in proteins. Acta Crystallogr D Biol Crystallogr (2001) 3.20
Small revisions to predicted distances around metal sites in proteins. Acta Crystallogr D Biol Crystallogr (2006) 2.56
The architecture of metal coordination groups in proteins. Acta Crystallogr D Biol Crystallogr (2004) 2.33
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Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method. Proteins (2001) 1.28
Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach. Protein Sci (2000) 1.26
Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion. Proteins (1995) 1.21
Zn protein simulations including charge transfer and local polarization effects. J Am Chem Soc (2005) 1.17
Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations. J Comput Chem (2005) 1.10
Modeling enzymatic reactions involving transition metals. Acc Chem Res (2006) 1.06
Computer simulation of the initial proton transfer step in human carbonic anhydrase I. J Mol Biol (1992) 1.05
Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism. J Am Chem Soc (2001) 1.00
Molecular Mechanics (MM3) Parameters for Ruthenium(II)-Polypyridyl Complexes. Inorg Chem (1998) 0.99
Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems. J Chem Theory Comput (2010) 0.97
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The influence of axial ligands on the reduction potential of blue copper proteins. J Biol Inorg Chem (1999) 0.93
Computational studies of the farnesyltransferase ternary complex part I: substrate binding. Biochemistry (2005) 0.93
A new molecular mechanics force field for the oxidized form of blue copper proteins. J Comput Chem (2002) 0.92
Empirical force fields for biologically active divalent metal cations in water. J Phys Chem A (2006) 0.92
Insights into the structure and dynamics of the dinuclear zinc beta-lactamase site from Bacteroides fragilis. Biochemistry (2002) 0.91
Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from Bacteroides fragilis complexed with imipenem. J Comput Chem (2002) 0.89
Molecular dynamics simulations of the enzyme Cu, Zn superoxide dismutase. J Phys Chem B (2006) 0.87
Catalyzed decomposition of urea. Molecular dynamics simulations of the binding of urea to urease. Biochemistry (2006) 0.86
Protein strain in blue copper proteins studied by free energy perturbations. Proteins (1999) 0.86
Development, validation, and applications of anisotropic polarizable molecular mechanics to study ligand and drug-receptor interactions. Curr Pharm Des (2006) 0.85
Apo and nickel-bound forms of the Pyrococcus horikoshii species of the metalloregulatory protein: NikR characterized by molecular dynamics simulations. Biochemistry (2009) 0.85
Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching. J Comput Chem (2003) 0.85
Molecular dynamics simulations of the resting and hydrogen peroxide-bound states of cytochrome c peroxidase. Biochemistry (1992) 0.81
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
A conserved MST-FOXO signaling pathway mediates oxidative-stress responses and extends life span. Cell (2006) 5.36
Adeno-associated virus serotype 8 efficiently delivers genes to muscle and heart. Nat Biotechnol (2005) 5.27
The TEAD/TEF family of transcription factor Scalloped mediates Hippo signaling in organ size control. Dev Cell (2008) 4.90
Toxicity of cationic lipids and cationic polymers in gene delivery. J Control Release (2006) 3.85
The Drosophila Ste20 family kinase dMST functions as a tumor suppressor by restricting cell proliferation and promoting apoptosis. Genes Dev (2003) 3.53
Biological features of novel avian influenza A (H7N9) virus. Nature (2013) 3.24
Hedgehog-regulated Costal2-kinase complexes control phosphorylation and proteolytic processing of Cubitus interruptus. Dev Cell (2005) 2.50
Hedgehog signalling activity of Smoothened requires phosphorylation by protein kinase A and casein kinase I. Nature (2004) 2.39
Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. PLoS Genet (2011) 2.35
Shaggy/GSK3 antagonizes Hedgehog signalling by regulating Cubitus interruptus. Nature (2002) 2.26
Hippo signaling regulates Drosophila intestine stem cell proliferation through multiple pathways. Proc Natl Acad Sci U S A (2010) 2.16
A hedgehog-induced BTB protein modulates hedgehog signaling by degrading Ci/Gli transcription factor. Dev Cell (2006) 2.13
A novel Hsp90 inhibitor to disrupt Hsp90/Cdc37 complex against pancreatic cancer cells. Mol Cancer Ther (2008) 2.07
Phase 1 gene therapy for Duchenne muscular dystrophy using a translational optimized AAV vector. Mol Ther (2011) 2.04
Controlling the Kondo effect of an adsorbed magnetic ion through its chemical bonding. Science (2005) 1.98
Safety profile, pharmacokinetics, and biologic activity of MEDI-563, an anti-IL-5 receptor alpha antibody, in a phase I study of subjects with mild asthma. J Allergy Clin Immunol (2010) 1.86
Cationic lipids and polymers mediated vectors for delivery of siRNA. J Control Release (2007) 1.79
Bradykinin-induced microglial migration mediated by B1-bradykinin receptors depends on Ca2+ influx via reverse-mode activity of the Na+/Ca2+ exchanger. J Neurosci (2007) 1.74
Structural and biochemical studies identify tobacco SABP2 as a methyl salicylate esterase and implicate it in plant innate immunity. Proc Natl Acad Sci U S A (2005) 1.73
CD4+ T cells from elite controllers resist HIV-1 infection by selective upregulation of p21. J Clin Invest (2011) 1.71
The hOGG1 Ser326Cys polymorphism and breast cancer risk: a meta-analysis. Breast Cancer Res Treat (2010) 1.69
Myostatin propeptide gene delivery by adeno-associated virus serotype 8 vectors enhances muscle growth and ameliorates dystrophic phenotypes in mdx mice. Hum Gene Ther (2008) 1.65
Injection of AAV2-BMP2 and AAV2-TIMP1 into the nucleus pulposus slows the course of intervertebral disc degeneration in an in vivo rabbit model. Spine J (2011) 1.63
Phosphorylation by double-time/CKIepsilon and CKIalpha targets cubitus interruptus for Slimb/beta-TRCP-mediated proteolytic processing. Dev Cell (2005) 1.62
Inhibition of glucosylceramide accumulation results in effective blockade of polycystic kidney disease in mouse models. Nat Med (2010) 1.62
Microporous and photoluminescent chalcogenide zeolite analogs. Science (2002) 1.61
Structural basis for substrate recognition in the salicylic acid carboxyl methyltransferase family. Plant Cell (2003) 1.56
Adeno-associated virus vector-mediated minidystrophin gene therapy improves dystrophic muscle contractile function in mdx mice. Hum Gene Ther (2002) 1.56
Widespread muscle expression of an AAV9 human mini-dystrophin vector after intravenous injection in neonatal dystrophin-deficient dogs. Mol Ther (2010) 1.56
Acoustic environment determines phosphorylation state of the Kv3.1 potassium channel in auditory neurons. Nat Neurosci (2005) 1.55
An indole-3-acetic acid carboxyl methyltransferase regulates Arabidopsis leaf development. Plant Cell (2005) 1.53
Monoamine oxidase A gene polymorphism predicts adolescent outcome of attention-deficit/hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet (2007) 1.51
The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stages. PLoS One (2008) 1.48
Multiple Ser/Thr-rich degrons mediate the degradation of Ci/Gli by the Cul3-HIB/SPOP E3 ubiquitin ligase. Proc Natl Acad Sci U S A (2009) 1.47
BMN 673, a novel and highly potent PARP1/2 inhibitor for the treatment of human cancers with DNA repair deficiency. Clin Cancer Res (2013) 1.47
Fine-mapping gene-by-diet interactions on chromosome 13 in a LG/J x SM/J murine model of obesity. Diabetes (2005) 1.47
Traditional Chinese medicine in the Chinese health care system. Health Policy (2008) 1.47
Regulation of TopBP1 oligomerization by Akt/PKB for cell survival. EMBO J (2006) 1.45
Methylation of gibberellins by Arabidopsis GAMT1 and GAMT2. Plant Cell (2007) 1.43
Atomic structure, energetics, and dynamics of topological solitons in indium chains on Si(111) surfaces. Phys Rev Lett (2011) 1.42
Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J Med Chem (2005) 1.42
Retracted Investigation of the hub genes and related mechanism in ovarian cancer via bioinformatics analysis. J Ovarian Res (2013) 1.42
Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties. J Chem Theory Comput (2007) 1.42
Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science (2008) 1.41
Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes. J Chem Theory Comput (2011) 1.32
Cystatin C deficiency increases elastic lamina degradation and aortic dilatation in apolipoprotein E-null mice. Circ Res (2005) 1.32
Genomic imprinting effects on adult body composition in mice. Proc Natl Acad Sci U S A (2008) 1.31
MicroRNA let-7c inhibits migration and invasion of human non-small cell lung cancer by targeting ITGB3 and MAP4K3. Cancer Lett (2013) 1.31
SCD1 inhibition causes cancer cell death by depleting mono-unsaturated fatty acids. PLoS One (2012) 1.29
Poly(amidoamine) dendrimer-drug conjugates with disulfide linkages for intracellular drug delivery. Biomaterials (2009) 1.29
A method of calculating the second dimension retention index in comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. J Chromatogr A (2011) 1.28
Insights into the strength and origin of halogen bonding: the halobenzene-formaldehyde dimer. J Phys Chem A (2007) 1.28
Regulation of p53 by TopBP1: a potential mechanism for p53 inactivation in cancer. Mol Cell Biol (2009) 1.28
Pose scoring by NMR. J Am Chem Soc (2004) 1.27
A FOXO-Pak1 transcriptional pathway controls neuronal polarity. Genes Dev (2010) 1.27
Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis. BMC Bioinformatics (2013) 1.26
Identification of quantitative trait loci affecting murine long bone length in a two-generation intercross of LG/J and SM/J Mice. J Bone Miner Res (2008) 1.26
Macrophage migration inhibitory factor deficiency impairs atherosclerosis in low-density lipoprotein receptor-deficient mice. Circulation (2004) 1.25
The immediate environment during postnatal development has long-term impact on gut community structure in pigs. ISME J (2008) 1.25
Identification of likely orthologs of tobacco salicylic acid-binding protein 2 and their role in systemic acquired resistance in Arabidopsis thaliana. Plant J (2008) 1.25
Mineralization of the metre-long biosilica structures of glass sponges is templated on hydroxylated collagen. Nat Chem (2010) 1.22
An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure. Bioinformatics (2011) 1.22
The mutational spectrum of brachydactyly type C. Am J Med Genet (2002) 1.22
X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation. Proc Natl Acad Sci U S A (2006) 1.21
Genetic architecture of adiposity and organ weight using combined generation QTL analysis. Obesity (Silver Spring) (2008) 1.20
MetSign: a computational platform for high-resolution mass spectrometry-based metabolomics. Anal Chem (2011) 1.19
Synergistic antipancreatic tumor effect by simultaneously targeting hypoxic cancer cells with HSP90 inhibitor and glycolysis inhibitor. Clin Cancer Res (2008) 1.19
Comparative study of pulmonary responses to nano- and submicron-sized ferric oxide in rats. Toxicology (2008) 1.19
PIASx is a MEF2 SUMO E3 ligase that promotes postsynaptic dendritic morphogenesis. J Neurosci (2007) 1.19
Dietary anthocyanin-rich tart cherry extract inhibits intestinal tumorigenesis in APC(Min) mice fed suboptimal levels of sulindac. J Agric Food Chem (2006) 1.18
Pleiotropic patterns of quantitative trait loci for 70 murine skeletal traits. Genetics (2008) 1.18
Monitoring nitrogen deposition in typical forest ecosystems along a large transect in China. Environ Monit Assess (2012) 1.18
Efficacy and safety of mavrilimumab in subjects with rheumatoid arthritis. Ann Rheum Dis (2012) 1.17
G protein-coupled receptor kinase 2 promotes high-level Hedgehog signaling by regulating the active state of Smo through kinase-dependent and kinase-independent mechanisms in Drosophila. Genes Dev (2010) 1.17
Salmonella enterica serovar Senftenberg human clinical isolates lacking SPI-1. J Clin Microbiol (2008) 1.17
Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J Chem Theory Comput (2013) 1.16
Correlates of methadone client retention: a prospective cohort study in Guizhou province, China. Int J Drug Policy (2008) 1.16
PARC6, a novel chloroplast division factor, influences FtsZ assembly and is required for recruitment of PDV1 during chloroplast division in Arabidopsis. Plant J (2009) 1.16
A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding. J Am Chem Soc (2004) 1.15
Interface-confined ferrous centers for catalytic oxidation. Science (2010) 1.15
Dendrimer-drug conjugates for tailored intracellular drug release based on glutathione levels. Bioconjug Chem (2008) 1.13
Hybrid QM/MM and DFT investigations of the catalytic mechanism and inhibition of the dinuclear zinc metallo-beta-lactamase CcrA from Bacteroides fragilis. J Am Chem Soc (2005) 1.12
Hepatoprotective and antioxidant effects of licorice extract against CCl₄-induced oxidative damage in rats. Int J Mol Sci (2011) 1.12
Association analysis of IL-17A and IL-17F polymorphisms in Chinese Han women with breast cancer. PLoS One (2012) 1.11
iMatch: a retention index tool for analysis of gas chromatography-mass spectrometry data. J Chromatogr A (2011) 1.11
Anterior debridement and reconstruction via thoracoscopy-assisted mini-open approach for the treatment of thoracic spinal tuberculosis: minimum 5-year follow-up. Eur Spine J (2011) 1.11
Cationic compounds used in lipoplexes and polyplexes for gene delivery. J Control Release (2004) 1.10
Surgical treatment of cervical kyphosis. Eur Spine J (2010) 1.10
The energy computation paradox and ab initio protein folding. PLoS One (2011) 1.10
A novel mouse model of Niemann-Pick type C disease carrying a D1005G-Npc1 mutation comparable to commonly observed human mutations. Hum Mol Genet (2011) 1.10
Hedgehog-regulated ubiquitination controls smoothened trafficking and cell surface expression in Drosophila. PLoS Biol (2012) 1.09
Fish MITA serves as a mediator for distinct fish IFN gene activation dependent on IRF3 or IRF7. J Immunol (2011) 1.09
The role of quantum mechanics in structure-based drug design. Drug Discov Today (2007) 1.09