Published in J Mol Model on July 15, 2014
Development and testing of a general amber force field. J Comput Chem (2004) 23.29
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem (2003) 15.88
Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins (2004) 9.15
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
Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu Rev Biophys Biomol Struct (1998) 3.48
Flexibility and function in HIV-1 protease. Nat Struct Biol (1995) 2.49
Broadly neutralizing antibodies and the search for an HIV-1 vaccine: the end of the beginning. Nat Rev Immunol (2013) 2.22
Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies. Immunity (2013) 2.17
Highly active antiretroviral therapy: current state of the art, new agents and their pharmacological interactions useful for improving therapeutic outcome. Curr Pharm Des (2005) 1.43
Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase. J Med Chem (2005) 1.37
Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. J Am Chem Soc (2008) 1.33
Drug Resistance Mutations in HIV-1. Top HIV Med (2003) 1.13
Predicting drug resistance of the HIV-1 protease using molecular interaction energy components. Proteins (2009) 1.07
A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings. J Comput Aided Mol Des (2013) 0.95
Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study. Chemistry (2008) 0.93
A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method. Proteins (2006) 0.93
HIV protease inhibition: limited recent progress and advances in understanding current pitfalls. Curr Top Med Chem (2004) 0.93
Computational simulations of HIV-1 proteases--multi-drug resistance due to nonactive site mutation L90M. J Am Chem Soc (2006) 0.92
Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations. Eur J Med Chem (2009) 0.89
Origin of decrease in potency of darunavir and two related antiviral inhibitors against HIV-2 compared to HIV-1 protease. J Phys Chem B (2012) 0.86
Ligand selectivity of estrogen receptors by a molecular dynamics study. Eur J Med Chem (2013) 0.85
A computational analysis of the binding model of MDM2 with inhibitors. J Comput Aided Mol Des (2010) 0.85
Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation. J Mol Model (2010) 0.81
Importance of polar solvation for cross-reactivity of antibody and its variants with steroids. J Phys Chem B (2011) 0.81
A contribution to the drug resistance mechanism of darunavir, amprenavir, indinavir, and saquinavir complexes with HIV-1 protease due to flap mutation I50V: a systematic MM-PBSA and thermodynamic integration study. J Chem Inf Model (2013) 0.80
Determination of the structure form of the fourth ligand of zinc in Acutolysin A using combined quantum mechanical and molecular mechanical simulation. J Phys Chem B (2009) 0.77
Structure-guided design of C2-symmetric HIV-1 protease inhibitors based on a pyrrolidine scaffold. J Med Chem (2008) 0.77
Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations. J Mol Model (2013) 0.76
Some insights into the stereochemistry of inhibition of macrophage migration inhibitory factor with 2-fluoro-p-hydroxycinnamate and its analogues from molecular dynamics simulations. J Med Chem (2005) 0.75
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
Two discrete promoters regulate the alternatively spliced human interferon regulatory factor-5 isoforms. Multiple isoforms with distinct cell type-specific expression, localization, regulation, and function. J Biol Chem (2005) 1.79
Phosphorylation of caveolin-1 regulates oxidant-induced pulmonary vascular permeability via paracellular and transcellular pathways. Circ Res (2009) 1.57
Ectodomain shedding and autocleavage of the cardiac membrane protease corin. J Biol Chem (2011) 1.27
Two Chinese families with pulverulent congenital cataracts and deltaG91 CRYBA1 mutations. Mol Vis (2007) 1.23
A novel locus (RP33) for autosomal dominant retinitis pigmentosa mapping to chromosomal region 2cen-q12.1. Hum Genet (2006) 1.22
Multivariate and geostatistical analyses of the spatial distribution and origin of heavy metals in the agricultural soils in Shunyi, Beijing, China. Sci Total Environ (2012) 1.19
Targeted sequencing of 179 genes associated with hereditary retinal dystrophies and 10 candidate genes identifies novel and known mutations in patients with various retinal diseases. Invest Ophthalmol Vis Sci (2013) 1.19
Tissue-type plasminogen activator and the low-density lipoprotein receptor-related protein induce Akt phosphorylation in the ischemic brain. Blood (2008) 1.17
Regulatory polymorphisms in the promoter of CXCL10 gene and disease progression in male hepatitis B virus carriers. Gastroenterology (2008) 1.16
Analysis of the changes of vegetation coverage of western Beijing mountainous areas using remote sensing and GIS. Environ Monit Assess (2008) 1.12
Association between mannose-binding lectin gene polymorphisms and susceptibility to severe acute respiratory syndrome coronavirus infection. J Infect Dis (2005) 1.09
MDM2 promoter SNP309 is associated with risk of occurrence and advanced lymph node metastasis of nasopharyngeal carcinoma in Chinese population. Clin Cancer Res (2007) 1.08
NADPH oxidase-derived ROS contributes to upregulation of TRPC6 expression in puromycin aminonucleoside-induced podocyte injury. Cell Physiol Biochem (2009) 1.07
Estrogen receptor alpha polymorphisms associated with susceptibility to hepatocellular carcinoma in hepatitis B virus carriers. Gastroenterology (2006) 1.05
Diversified reassortant H9N2 avian influenza viruses in chicken flocks in northern and eastern China. Virus Res (2010) 1.05
Hydroxysafflor yellow A protects rat brains against ischemia-reperfusion injury by antioxidant action. Neurosci Lett (2005) 1.04
Flavonoids from Halostachys caspica and their antimicrobial and antioxidant activities. Molecules (2010) 1.03
Development and application of a loop-mediated isothermal amplification method on rapid detection Escherichia coli O157 strains from food samples. Mol Biol Rep (2009) 1.00
Functional polymorphisms and haplotypes in the promoter of the MMP2 gene are associated with risk of nasopharyngeal carcinoma. Hum Mutat (2007) 0.99
Plasmodium vivax aldolase-specific monoclonal antibodies and its application in clinical diagnosis of malaria infections in China. Malar J (2013) 0.95
The G-113A polymorphism in CYP1A2 affects the caffeine metabolic ratio in a Chinese population. Clin Pharmacol Ther (2005) 0.93
Effect of sialylated O-glycans in pro-brain natriuretic peptide stability. Clin Chem (2010) 0.93
NOX2 deficiency ameliorates cerebral injury through reduction of complexin II-mediated glutamate excitotoxicity in experimental stroke. Free Radic Biol Med (2013) 0.92
Oridonin nanosuspension enhances anti-tumor efficacy in SMMC-7721 cells and H22 tumor bearing mice. Colloids Surf B Biointerfaces (2011) 0.91
Toll-like receptor 9 is required for opioid-induced microglia apoptosis. PLoS One (2011) 0.90
High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation. PLoS One (2013) 0.90
In vitro and in vivo antitumor activity of oridonin nanosuspension. Int J Pharm (2009) 0.90
Haplotype structure and evidence for positive selection at the human IL13 locus. Mol Biol Evol (2003) 0.89
Critical role of toll-like receptor 9 in morphine and Mycobacterium tuberculosis-Induced apoptosis in mice. PLoS One (2010) 0.89
Escin attenuates cognitive deficits and hippocampal injury after transient global cerebral ischemia in mice via regulating certain inflammatory genes. Neurochem Int (2010) 0.89
Performance evaluation of inpatient service in Beijing: a horizontal comparison with risk adjustment based on Diagnosis Related Groups. BMC Health Serv Res (2009) 0.89
In vitro selection of salinity tolerant variants from triploid bermudagrass (Cynodon transvaalensis x C. dactylon) and their physiological responses to salt and drought stress. Plant Cell Rep (2007) 0.88
Synthetic resveratrol aliphatic acid inhibits TLR2-mediated apoptosis and an involvement of Akt/GSK3beta pathway. Bioorg Med Chem (2009) 0.88
Cilostazol protects diabetic rats from vascular inflammation via nuclear factor-kappa B-dependent down-regulation of vascular cell adhesion molecule-1 expression. J Pharmacol Exp Ther (2006) 0.87
Insights into the functional role of protonation states in the HIV-1 protease-BEA369 complex: molecular dynamics simulations and free energy calculations. J Mol Model (2009) 0.86
Osteogenic differentiation of human ligament fibroblasts induced by conditioned medium of osteoclast-like cells. Biosci Trends (2011) 0.86
The Akt/GSK-3β pathway mediates flurbiprofen-induced neuroprotection against focal cerebral ischemia/reperfusion injury in rats. Biochem Biophys Res Commun (2011) 0.86
Global gene expression changes in Candidatus Liberibacter asiaticus during the transmission in distinct hosts between plant and insect. Mol Plant Pathol (2013) 0.86
Intervention with cilostazol attenuates renal inflammation in streptozotocin-induced diabetic rats. Life Sci (2008) 0.86
Evaluation of a DNA vaccine candidate co-expressing GP3 and GP5 of porcine reproductive and respiratory syndrome virus (PRRSV) with interferon α/γ in immediate and long-lasting protection against HP-PRRSV challenge. Virus Genes (2012) 0.86
Hydroxysafflor Yellow A suppresses thrombin generation and inflammatory responses following focal cerebral ischemia-reperfusion in rats. Bioorg Med Chem Lett (2010) 0.85
Molecular population genetics of human CYP3A locus: signatures of positive selection and implications for evolutionary environmental medicine. Environ Health Perspect (2009) 0.85
Isoquinoline alkaloids from Macleaya cordata active against plant microbial pathogens. Nat Prod Commun (2009) 0.85
Lack of association between the functional polymorphisms in the estrogen-metabolizing genes and risk for hepatocellular carcinoma. Cancer Epidemiol Biomarkers Prev (2008) 0.84
Mechanisms underlying the synergistic effect of SU5416 and cisplatin on cytotoxicity in human ovarian tumor cells. Int J Oncol (2004) 0.84
Subtoxic product levels limit the epoxidation capacity of recombinant E. coli by increasing microbial energy demands. J Biotechnol (2012) 0.84
Danshensu ameliorates the cognitive decline in streptozotocin-induced diabetic mice by attenuating advanced glycation end product-mediated neuroinflammation. J Neuroimmunol (2012) 0.84
Association of CYP1A2 genetic polymorphisms with hepatocellular carcinoma susceptibility: a case-control study in a high-risk region of China. Pharmacogenet Genomics (2006) 0.83
Effects of escin on acute inflammation and the immune system in mice. Pharmacol Rep (2009) 0.83
Avian influenza virus and Newcastle disease virus (NDV) surveillance in commercial breeding farm in China and the characterization of Class I NDV isolates. Vet Microbiol (2010) 0.83
S-allyl cysteine activates the Nrf2-dependent antioxidant response and protects neurons against ischemic injury in vitro and in vivo. J Neurochem (2015) 0.83
Oxidative damage and antioxidant responses in Microcystis aeruginosa exposed to the allelochemical berberine isolated from golden thread. J Plant Physiol (2010) 0.82
Effects of pH and temperature on the structural and thermodynamic character of alpha-syn12 peptide in aqueous solution. J Biomol Struct Dyn (2010) 0.82
Inhibitory effects of golden thread (Coptis chinensis) and berberine on Microcystis aeruginosa. Water Sci Technol (2010) 0.82
Eriodictyol protects against H(2)O(2)-induced neuron-like PC12 cell death through activation of Nrf2/ARE signaling pathway. Neurochem Int (2012) 0.82
Structural and thermodynamics characters of isolated α-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution. Acta Biochim Biophys Sin (Shanghai) (2011) 0.82
Losartan, an angiotensin II type 1 receptor blocker, ameliorates cerebral ischemia-reperfusion injury via PI3K/Akt-mediated eNOS phosphorylation. Brain Res Bull (2012) 0.82
Effects of different force fields and temperatures on the structural character of Abeta (12-28) peptide in aqueous solution. Int J Mol Sci (2011) 0.82
Hydroxysafflor yellow A protects against cerebral ischemia-reperfusion injury by anti-apoptotic effect through PI3K/Akt/GSK3β pathway in rat. Neurochem Res (2013) 0.81
SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction. Methods Mol Biol (2014) 0.81
Tetramethylpyrazine analogue CXC195 protects against cerebral ischemia/reperfusion injury in the rat by an antioxidant action via inhibition of NADPH oxidase and iNOS expression. Pharmacology (2013) 0.80
Label-free quantification proteomics reveals novel calcium binding proteins in matrix vesicles isolated from mineralizing Saos-2 cells. Biosci Trends (2013) 0.80
Comparison of the structural characteristics of Cu(2+)-bound and unbound α-syn12 peptide obtained in simulations using different force fields. J Mol Model (2012) 0.79
Effects of oridonin nanosuspension on cell proliferation and apoptosis of human prostatic carcinoma PC-3 cell line. Int J Nanomedicine (2010) 0.79
Beauvericin from the endophytic fungus, Fusarium redolens, isolated from Dioscorea zingiberensis and its antibacterial activity. Nat Prod Commun (2010) 0.79
Separation and identification of norcantharidin metabolites in vivo by GC-MS method. J Chromatogr B Analyt Technol Biomed Life Sci (2011) 0.79
Study and evaluation of Wondfo rapid diagnostic kit based on nano-gold immunochromatography assay for diagnosis of Plasmodium falciparum. Parasitol Res (2011) 0.79
Comparative performance of aldolase and lactate dehydrogenase rapid diagnostic tests in Plasmodium vivax detection. Malar J (2014) 0.79
Evolution analysis of the matrix (M) protein genes of 17 H9N2 chicken influenza viruses isolated in northern China during 1998-2008. Virus Genes (2009) 0.79
No association of MMP-7, MMP-8, and MMP-21 polymorphisms with the risk of hepatocellular carcinoma in a Chinese population. Cancer Epidemiol Biomarkers Prev (2008) 0.79
Luteolin suppresses growth and migration of human lung cancer cells. Mol Biol Rep (2010) 0.79
Association of mineralization-related genes TNAP and ANKH polymorphisms with ankylosing spondylitis in the Chinese Han population. Biosci Trends (2013) 0.78
Why the OPLS-AA force field cannot produce the β-hairpin structure of H1 peptide in solution when comparing with the GROMOS 43A1 force field? J Biomol Struct Dyn (2011) 0.78
Evolutionary mechanisms shaping the genetic population structure of coastal fish: insight from populations of Coilia nasus in Northwestern Pacific. Mitochondrial DNA (2013) 0.78
A comparative study of two different force fields on structural and thermodynamics character of H1 peptide via molecular dynamics simulations. J Biomol Struct Dyn (2010) 0.78
Antifungal activity of the essential oil of Illicium verum fruit and its main component trans-anethole. Molecules (2010) 0.78
Deepening constantly understanding of protein folding problem. J Biomol Struct Dyn (2013) 0.78
Anti-inflammatory effect of acetylpuerarin on eicosanoid signaling pathway in primary rat astrocytes. J Mol Neurosci (2013) 0.78
Characterization of an avian influenza virus of subtype H4N6 isolated from ducks in the northern China. Virus Genes (2013) 0.77
A non-synonymous SNP in the NOS2 associated with septic shock in patients with sepsis in Chinese populations. Hum Genet (2012) 0.77
Association of DLC1 gene polymorphism with susceptibility to hepatocellular carcinoma in Chinese hepatitis B virus carriers. Cancer Epidemiol (2009) 0.77
Variants in TNFRSF5 locus and association analysis with Hepatitis B virus (HBV) infection. Hum Mutat (2004) 0.77
Studying the unfolding process of protein G and protein L under physical property space. BMC Bioinformatics (2009) 0.77
Eriodictyol-7-O-glucoside activates Nrf2 and protects against cerebral ischemic injury. Toxicol Appl Pharmacol (2013) 0.77
Antimicrobial phenolic compounds from Anabasis aphylla L. Nat Prod Commun (2009) 0.77
Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z. J Mol Model (2012) 0.77
Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Brief Bioinform (2016) 0.77
[Transportation processes and rates of heavy metals in an artificial rainstorm runoff under different land use types]. Ying Yong Sheng Tai Xue Bao (2003) 0.77
Tetramethylpyrazine analogue CXC195 ameliorates cerebral ischemia-reperfusion injury by regulating endothelial nitric oxide synthase phosphorylation via PI3K/Akt signaling. Neurochem Res (2014) 0.76
Intravenous thrombolysis in Sneddon's syndrome. J Clin Neurosci (2011) 0.76
Isolation and identification of a putative scent-related gene RhMYB1 from rose. Mol Biol Rep (2010) 0.76
Preformulation study of methazolamide for topical ophthalmic delivery: physicochemical properties and degradation kinetics in aqueous solutions. Int J Pharm (2013) 0.76
[Research advances in behavioral ecology of penaeid shrimp II. Effects of environmental factors on behavior of penaeid shrimps]. Ying Yong Sheng Tai Xue Bao (2006) 0.76
Two genotypes of H1N2 swine influenza viruses appeared among pigs in China. J Clin Virol (2009) 0.76
Inhibition of sPLA₂-IIA prevents LPS-induced neuroinflammation by suppressing ERK1/2-cPLA₂α pathway in mice cerebral cortex. PLoS One (2013) 0.76
Rapid Visual Detection of Aflatoxin B1 by Label-Free Aptasensor Using Unmodified Gold Nanoparticles. J Nanosci Nanotechnol (2015) 0.76
Choriogenin and vitellogenin in red lip mullet (Chelon haematocheilus): purification, characterization, and evaluation as potential biomarkers for detecting estrogenic activity. Comp Biochem Physiol C Toxicol Pharmacol (2008) 0.76
Optimization of methazolamide-loaded solid lipid nanoparticles for ophthalmic delivery using Box-Behnken design. J Liposome Res (2014) 0.75
The effect of C-terminal helix on the stability of FF domain studied by molecular dynamics simulation. Int J Mol Sci (2012) 0.75