Published in J Chem Theory Comput on November 17, 2016
Human cytomegalovirus activates inflammatory cytokine responses via CD14 and Toll-like receptor 2. J Virol (2003) 3.97
Sculpting the proteome with AAA(+) proteases and disassembly machines. Cell (2004) 3.83
Herpes simplex virus 1 interaction with Toll-like receptor 2 contributes to lethal encephalitis. Proc Natl Acad Sci U S A (2004) 3.74
Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J Virol (2003) 2.98
Negative regulation of Toll-like receptor 4 signaling by the Toll-like receptor homolog RP105. Nat Immunol (2005) 2.85
Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. Structure (2002) 2.69
DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol (2011) 2.63
Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor. J Med Chem (2005) 2.58
Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor. J Virol (2004) 2.47
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Asymmetric interactions of ATP with the AAA+ ClpX6 unfoldase: allosteric control of a protein machine. Cell (2005) 2.33
Dephosphorylation of the RNA sensors RIG-I and MDA5 by the phosphatase PP1 is essential for innate immune signaling. Immunity (2013) 2.33
Ion motions in molecular dynamics simulations on DNA. Proc Natl Acad Sci U S A (2004) 2.19
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophys J (2004) 2.17
Hepatitis C core and nonstructural 3 proteins trigger toll-like receptor 2-mediated pathways and inflammatory activation. Gastroenterology (2004) 2.16
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys J (2005) 2.09
Cooperative extraction of membrane nanotubes by molecular motors. Proc Natl Acad Sci U S A (2004) 2.08
Role of toll-like receptor 2 (TLR2) in neutrophil activation: GM-CSF enhances TLR2 expression and TLR2-mediated interleukin 8 responses in neutrophils. Blood (2002) 1.94
Identification and characterization of broadly neutralizing human monoclonal antibodies directed against the E2 envelope glycoprotein of hepatitis C virus. J Virol (2009) 1.92
MyD88 is critical for the development of innate and adaptive immunity during acute lymphocytic choriomeningitis virus infection. Eur J Immunol (2005) 1.85
Respiratory syncytial virus activates innate immunity through Toll-like receptor 2. J Virol (2008) 1.80
Replacement of the P1 amino acid of human immunodeficiency virus type 1 Gag processing sites can inhibit or enhance the rate of cleavage by the viral protease. J Virol (2002) 1.71
Covariation of amino acid positions in HIV-1 protease. Virology (2003) 1.65
Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces. Structure (2010) 1.65
Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease. J Virol (2004) 1.65
Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding. Proc Natl Acad Sci U S A (2010) 1.65
Complement receptor 1 is a sialic acid-independent erythrocyte receptor of Plasmodium falciparum. PLoS Pathog (2010) 1.65
The folding mechanics of a knotted protein. J Mol Biol (2007) 1.64
Uveitis and Systemic Inflammatory Markers in Convalescent Phase of Ebola Virus Disease. Emerg Infect Dis (2016) 1.62
Flavivirus activation of plasmacytoid dendritic cells delineates key elements of TLR7 signaling beyond endosomal recognition. J Immunol (2006) 1.61
Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA+ ClpXP protease. Mol Cell (2003) 1.61
Analyses of the effects of all ubiquitin point mutants on yeast growth rate. J Mol Biol (2013) 1.59
Apoptosis associated with deregulated E2F activity is dependent on E2F1 and Atm/Nbs1/Chk2. Mol Cell Biol (2004) 1.57
Human cytomegalovirus immediate early proteins and cell growth control. Gene (2002) 1.54
Induction and inhibition of type I interferon responses by distinct components of lymphocytic choriomeningitis virus. J Virol (2010) 1.52
Human erythrocytes bind and inactivate type 5 adenovirus by presenting Coxsackie virus-adenovirus receptor and complement receptor 1. Blood (2009) 1.51
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Lack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease. Protein Sci (2002) 1.49
Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants. PLoS Pathog (2011) 1.45
Development and characterization of a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody that provides effective immunoprophylaxis in mice. J Infect Dis (2005) 1.44
HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc (2008) 1.43
The challenge of developing robust drugs to overcome resistance. Drug Discov Today (2011) 1.43
A nonredundant role for plasmacytoid dendritic cells in host defense against the human fungal pathogen Aspergillus fumigatus. Cell Host Microbe (2011) 1.41
Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J Virol (2010) 1.39
Methylcytosine and normal cytosine deamination by the foreign DNA restriction enzyme APOBEC3A. J Biol Chem (2012) 1.38
The cell adhesion molecule "CAR" and sialic acid on human erythrocytes influence adenovirus in vivo biodistribution. PLoS Pathog (2009) 1.37
Compensation of BRG-1 function by Brm: insight into the role of the core SWI-SNF subunits in retinoblastoma tumor suppressor signaling. J Biol Chem (2001) 1.37
Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy. J Virol (2003) 1.37
Role for TLR2 in NK cell-mediated control of murine cytomegalovirus in vivo. J Virol (2006) 1.35
Human monoclonal antibody HCV1 effectively prevents and treats HCV infection in chimpanzees. PLoS Pathog (2012) 1.35
Inhibition of the ATM/p53 signal transduction pathway by Kaposi's sarcoma-associated herpesvirus interferon regulatory factor 1. J Virol (2006) 1.33
Importance of extra- and intracellular domains of TLR1 and TLR2 in NFkappa B signaling. J Cell Biol (2003) 1.32
The role of toll-like receptors in herpes simplex infection in neonates. J Infect Dis (2005) 1.32
Viral Bcl-2-mediated evasion of autophagy aids chronic infection of gammaherpesvirus 68. PLoS Pathog (2009) 1.31
E2F1 induces phosphorylation of p53 that is coincident with p53 accumulation and apoptosis. Mol Cell Biol (2002) 1.30
The molecular basis of drug resistance against hepatitis C virus NS3/4A protease inhibitors. PLoS Pathog (2012) 1.30
Toll-like receptor 9-dependent immune activation by unmethylated CpG motifs in Aspergillus fumigatus DNA. Infect Immun (2008) 1.30
Distinct patterns of dendritic cell cytokine release stimulated by fungal beta-glucans and toll-like receptor agonists. Infect Immun (2009) 1.29
First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G. ACS Chem Biol (2012) 1.28
MDA5 and MAVS mediate type I interferon responses to coxsackie B virus. J Virol (2010) 1.28
PTEN enters the nucleus by diffusion. J Cell Biochem (2005) 1.28
Newcastle disease virus-like particles containing respiratory syncytial virus G protein induced protection in BALB/c mice, with no evidence of immunopathology. J Virol (2009) 1.28
Cutting Edge: Antibody-mediated TLR7-dependent recognition of viral RNA. J Immunol (2007) 1.28
Resilience to resistance of HIV-1 protease inhibitors: profile of darunavir. AIDS Rev (2008) 1.26
Use of murine embryonic fibroblasts to define Toll-like receptor activation and specificity. J Endotoxin Res (2004) 1.25
Toll-like receptor-mediated activation of neutrophils by influenza A virus. Blood (2008) 1.24
Lymphocytic choriomeningitis virus (LCMV) infection of CNS glial cells results in TLR2-MyD88/Mal-dependent inflammatory responses. J Neuroimmunol (2008) 1.24
Herpes simplex virus immediate-early ICP0 protein inhibits Toll-like receptor 2-dependent inflammatory responses and NF-kappaB signaling. J Virol (2010) 1.23
Co-evolution of nelfinavir-resistant HIV-1 protease and the p1-p6 substrate. Virology (2006) 1.22
Dimerization of Hsp90 is required for in vivo function. Design and analysis of monomers and dimers. J Biol Chem (2007) 1.21
C21orf91 genotypes correlate with herpes simplex labialis (cold sore) frequency: description of a cold sore susceptibility gene. J Infect Dis (2011) 1.21
Hydrophobic sliding: a possible mechanism for drug resistance in human immunodeficiency virus type 1 protease. Structure (2007) 1.20
Molecular Basis for Drug Resistance in HIV-1 Protease. Viruses (2010) 1.20
Genetic analysis of cytomegalovirus in malignant gliomas. J Virol (2012) 1.19
Varicella-zoster virus activates inflammatory cytokines in human monocytes and macrophages via Toll-like receptor 2. J Virol (2005) 1.19
Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5. Nat Struct Mol Biol (2008) 1.17
Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands. J Med Chem (2006) 1.17
Molecular dynamics simulations of DNA curvature and flexibility: helix phasing and premelting. Biopolymers (2004) 1.17
Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate. J Virol (2006) 1.15
Toll like receptors and viruses. Rev Med Virol (2006) 1.14
Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope. J Mol Biol (2011) 1.14
Crystal structure of the DNA cytosine deaminase APOBEC3F: the catalytically active and HIV-1 Vif-binding domain. Structure (2013) 1.13
Activated checkpoint kinase 2 provides a survival signal for tumor cells. Cancer Res (2006) 1.12
Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations. Proteins (2003) 1.12
Therapeutic targeting of C-terminal binding protein in human cancer. Cell Cycle (2010) 1.12
Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des (2007) 1.12
MyD88 intrinsically regulates CD4 T-cell responses. J Virol (2008) 1.11
Design of HIV-1 protease inhibitors active on multidrug-resistant virus. J Med Chem (2005) 1.10
Role of invariant Thr80 in human immunodeficiency virus type 1 protease structure, function, and viral infectivity. J Virol (2006) 1.10
Assembly and immunological properties of Newcastle disease virus-like particles containing the respiratory syncytial virus F and G proteins. J Virol (2010) 1.10
Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection. PLoS Genet (2013) 1.09
Role of specific innate immune responses in herpes simplex virus infection of the central nervous system. J Virol (2011) 1.09
Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH. Appl Environ Microbiol (2008) 1.09
A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments. Genetics (2014) 1.07
Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance. J Virol (2009) 1.07
Latent effects of Hsp90 mutants revealed at reduced expression levels. PLoS Genet (2013) 1.07
Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease. J Virol (2007) 1.06
Coxsackievirus and adenovirus receptor is essential for cardiomyocyte development. Genesis (2005) 1.06