Applying high-performance computing in drug discovery and molecular simulation
暂无分享,去创建一个
Cheng Luo | Weiliang Zhu | Hualiang Jiang | Ting-ting Liu | Dong Lu | Hao Zhang | Mingyue Zheng | Huaiyu Yang | Yechun Xu | Kunqian Yu | Weiliang Zhu | Kunqian Yu | Hualiang Jiang | Yechun Xu | M. Zheng | C. Luo | Hao Zhang | Huaiyu Yang | Dong Lu | Ting-ting Liu | Hao Zhang
[1] I. Eberini,et al. In-silico studies in Chinese herbal medicines’ research: Evaluation of in-silico methodologies and phytochemical data sources, and a review of research to date , 2012, Journal of Ethnopharmacology.
[2] Roderick MacKinnon,et al. Crystal Structure of the Mammalian GIRK2 K+ Channel and Gating Regulation by G Proteins, PIP2, and Sodium , 2011, Cell.
[3] K.-C. Chou,et al. Virtual screening for finding natural inhibitor against cathepsin-L for SARS therapy , 2006, Amino Acids.
[4] T. Iwatsubo,et al. Visualization of Aβ42(43) and Aβ40 in senile plaques with end-specific Aβ monoclonals: Evidence that an initially deposited species is Aβ42(43) , 1994, Neuron.
[5] Kai Huang,et al. PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach , 2010, Nucleic Acids Res..
[6] Holger Gohlke,et al. Target flexibility: an emerging consideration in drug discovery and design. , 2008, Journal of medicinal chemistry.
[7] Edward Lyman,et al. Predictions for cholesterol interaction sites on the A2A adenosine receptor. , 2012, Journal of the American Chemical Society.
[8] R. Tycko. Solid-state NMR studies of amyloid fibril structure. , 2011, Annual review of physical chemistry.
[9] Xian Liu,et al. TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds , 2015, Bioinform..
[10] Hualiang Jiang,et al. Identifying novel selective non-nucleoside DNA methyltransferase 1 inhibitors through docking-based virtual screening. , 2014, Journal of medicinal chemistry.
[11] Cheng Luo,et al. Regulation of Histone Acetylation in the Nucleus by Sphingosine-1-Phosphate , 2009, Science.
[12] Richard Bond,et al. Subtype-specific beta-adrenoceptor signaling pathways in the heart and their potential clinical implications. , 2004, Trends in pharmacological sciences.
[13] Cheng Luo,et al. Binding interaction of quercetin-3-β-galactoside and its synthetic derivatives with SARS-CoV 3CLpro: Structure–activity relationship studies reveal salient pharmacophore features , 2006, Bioorganic & Medicinal Chemistry.
[14] A. Harvey,et al. The re-emergence of natural products for drug discovery in the genomics era , 2015, Nature Reviews Drug Discovery.
[15] F. Bezanilla,et al. A proton pore in a potassium channel voltage sensor reveals a focused electric field , 2004, Nature.
[16] J. Mccammon,et al. Exploring the role of receptor flexibility in structure-based drug discovery. , 2014, Biophysical chemistry.
[17] Hualiang Jiang,et al. Pharmacophore-based virtual screening and biological evaluation of small molecule inhibitors for protein arginine methylation. , 2012, Journal of medicinal chemistry.
[18] Muhammad Saeed,et al. Anti-inflammatory activities of Sieboldogenin from Smilax china Linn.: experimental and computational studies. , 2009, Journal of ethnopharmacology.
[19] David Rogers,et al. Extended-Connectivity Fingerprints , 2010, J. Chem. Inf. Model..
[20] Meng Wu,et al. Isoform-specific Prolongation of Kv7 (KCNQ) Potassium Channel Opening Mediated by New Molecular Determinants for Drug-Channel Interactions* , 2010, The Journal of Biological Chemistry.
[21] Hesham H. Ali,et al. Applications of High Performance Computing in Bioinformatics, Computational Biology and Computational Chemistry , 2015, IWBBIO.
[22] Panagiotis Korantzopoulos,et al. Drug-induced prolongation of the QT interval. , 2004, The New England journal of medicine.
[23] Cheng Luo,et al. Structural optimization and biological evaluation of substituted bisphenol A derivatives as beta-amyloid peptide aggregation inhibitors. , 2010, Journal of medicinal chemistry.
[24] Fabrício F. Costa. Big data in biomedicine. , 2014, Drug discovery today.
[25] J. Hardy,et al. Alzheimer's disease: the amyloid cascade hypothesis. , 1992, Science.
[26] Ehud Y. Isacoff,et al. Transmembrane Movement of the Shaker K+ Channel S4 , 1996, Neuron.
[27] Weiliang Zhu,et al. Synthesis of C-4-modified zanamivir analogs as neuraminidase inhibitors and their anti-AIV activities. , 2012, European journal of medicinal chemistry.
[28] Nikolaus Grigorieff,et al. Recent progress in understanding Alzheimer's β-amyloid structures. , 2011, Trends in biochemical sciences.
[29] Cheng Luo,et al. Active, phosphorylated fingolimod inhibits histone deacetylases and facilitates fear extinction memory , 2014, Nature Neuroscience.
[30] Hong Liu,et al. QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR , 2006, J. Comput. Aided Mol. Des..
[31] Alan Grossfield,et al. A role for direct interactions in the modulation of rhodopsin by ω-3 polyunsaturated lipids , 2006 .
[32] Cheng Luo,et al. Computational methods for drug design and discovery: focus on China , 2013, Trends in Pharmacological Sciences.
[33] Zhuxi Chen,et al. The gating charge pathway of an epilepsy-associated potassium channel accommodates chemical ligands , 2013, Cell Research.
[34] Cheng Luo,et al. Cholesterol‐β1AR interaction versus cholesterol‐β2AR interaction , 2014, Proteins.
[35] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[36] George F. Gao,et al. Induced opening of influenza virus neuraminidase N2 150-loop suggests an important role in inhibitor binding , 2013, Scientific Reports.
[37] Yu Kun-qian. DDGrid:A Grid with Massive Drug Virtual-Screening Support , 2009 .
[38] Hualiang Jiang,et al. Dynamic PIP2 interactions with voltage sensor elements contribute to KCNQ2 channel gating , 2013, Proceedings of the National Academy of Sciences.
[39] M. Wolfe,et al. A Portrait of Alzheimer Secretases--New Features and Familiar Faces , 2001, Science.
[40] Jianpeng Ma,et al. Conformational transition of amyloid β-peptide , 2005 .
[41] Jianpeng Ma,et al. Inhibitor discovery targeting the intermediate structure of beta-amyloid peptide on the conformational transition pathway: implications in the aggregation mechanism of beta-amyloid peptide. , 2006, Biochemistry.
[42] Yi Shi,et al. Enabling the 'host jump': structural determinants of receptor-binding specificity in influenza A viruses , 2014, Nature Reviews Microbiology.
[43] Li Du,et al. Severe Acute Respiratory Syndrome Coronavirus 3C-like Proteinase N Terminus Is Indispensable for Proteolytic Activity but Not for Enzyme Dimerization , 2005, Journal of Biological Chemistry.
[44] Jiye Shi,et al. A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions , 2015, Journal of Molecular Modeling.
[45] L. Hood,et al. Predictive, personalized, preventive, participatory (P4) cancer medicine , 2011, Nature Reviews Clinical Oncology.
[46] Weiliang Zhu,et al. mD3DOCKxb: A Deep Parallel Optimized Software for Molecular Docking with Intel Xeon Phi Coprocessors , 2015, 2015 15th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing.
[47] Xiao Tao,et al. Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2 , 2011, Nature.
[48] Durba Sengupta,et al. Identification of cholesterol binding sites in the serotonin1A receptor. , 2012, The journal of physical chemistry. B.
[49] N. Buchete,et al. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. , 2015, Chemical reviews.
[50] Christopher J. Woods,et al. Computational Assay of H7N9 Influenza Neuraminidase Reveals R292K Mutation Reduces Drug Binding Affinity , 2013, Scientific Reports.
[51] R. Nussinov,et al. Polymorphism in Alzheimer Aβ Amyloid Organization Reflects Conformational Selection in a Rugged Energy Landscape , 2010, Chemical reviews.
[52] Cheng Luo,et al. A 3D model of SARS_CoV 3CL proteinase and its inhibitors design by virtual screening. , 2003, Acta pharmacologica Sinica.
[53] Heping Cheng,et al. Subtype-specific β-adrenoceptor signaling pathways in the heart and their potential clinical implications , 2004 .
[54] Xu Shen,et al. Techniques used for the discovery of therapeutic compounds: The case of SARS , 2006, Drug Discovery Today: Technologies.
[55] Gareth Jones,et al. The cloud and other new computational methods to improve molecular modelling , 2014, Expert opinion on drug discovery.
[56] T. Iwatsubo,et al. Visualization of A beta 42(43) and A beta 40 in senile plaques with end-specific A beta monoclonals: evidence that an initially deposited species is A beta 42(43). , 1994, Neuron.
[57] Lin He,et al. DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical–protein interactome , 2011, Nucleic Acids Res..
[58] Michael J. Keiser,et al. Relating protein pharmacology by ligand chemistry , 2007, Nature Biotechnology.
[59] S. Younkin,et al. An increased percentage of long amyloid beta protein secreted by familial amyloid beta protein precursor (beta APP717) mutants. , 1994, Science.
[60] Haibo Yu,et al. Phosphatidylinositol 4,5-bisphosphate alters pharmacological selectivity for epilepsy-causing KCNQ potassium channels , 2013, Proceedings of the National Academy of Sciences.
[61] Michelle Y Cheng,et al. Differential effects of dietary supplements on metabolomic profile of smokers versus non-smokers , 2011, Genome Medicine.
[62] D. Sawyer,et al. Opposing effects of beta(1)- and beta(2)-adrenergic receptors on cardiac myocyte apoptosis : role of a pertussis toxin-sensitive G protein. , 1999, Circulation.
[63] Cheng Luo,et al. K63-linked polyubiquitination of transcription factor IRF1 is essential for IL-1-induced production of chemokines CXCL10 and CCL5 , 2014, Nature Immunology.
[64] Jiye Shi,et al. Mapping central α-helix linker mediated conformational transition pathway of calmodulin via simple computational approach. , 2014, The journal of physical chemistry. B.
[65] Cheng Luo,et al. Nucleocapsid protein of SARS coronavirus tightly binds to human cyclophilin A , 2004, Biochemical and Biophysical Research Communications - BBRC.
[66] Catherine Communal,et al. Opposing Effects of β1- and β2-Adrenergic Receptors on Cardiac Myocyte Apoptosis Role of a Pertussis Toxin–Sensitive G Protein , 1999 .
[67] Jianpeng Ma,et al. Conformational transition of amyloid beta-peptide. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[68] Paul Krause,et al. Feature combination networks for the interpretation of statistical machine learning models: application to Ames mutagenicity , 2014, Journal of Cheminformatics.
[69] Weiliang Zhu,et al. Structure-based design and synthesis of C-1- and C-4-modified analogs of zanamivir as neuraminidase inhibitors. , 2013, Journal of medicinal chemistry.
[70] T. Kieffer,et al. Targeting the glucagon receptor family for diabetes and obesity therapy. , 2012, Pharmacology & therapeutics.
[71] Cheng Luo,et al. Putative hAPN receptor binding sites in SARS_CoV spike protein. , 2003, Acta pharmacologica Sinica.
[72] Jiye Shi,et al. Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics. , 2014, The journal of physical chemistry. B.
[73] Mark S. Shapiro,et al. Regulation of ion transport proteins by membrane phosphoinositides , 2007, Nature Reviews Neuroscience.
[74] G.E. Moore,et al. Cramming More Components Onto Integrated Circuits , 1998, Proceedings of the IEEE.
[75] D. Roden. Drug-induced prolongation of the QT interval. , 2004, The New England journal of medicine.
[76] Kyu-Ho Park,et al. Impaired KCNQ1–KCNE1 and Phosphatidylinositol-4,5-Bisphosphate Interaction Underlies the Long QT Syndrome , 2005, Circulation research.
[77] Darren R. Flower,et al. On the Properties of Bit String-Based Measures of Chemical Similarity , 1998, J. Chem. Inf. Comput. Sci..
[78] Ruibo Wu,et al. Molecular Dynamics-Based Virtual Screening: Accelerating the Drug Discovery Process by High-Performance Computing , 2013, J. Chem. Inf. Model..
[79] Fei Zhao,et al. Recent Advances in Neuraminidase Inhibitor Development as Anti‐influenza Drugs , 2012, ChemMedChem.
[80] George Khelashvili,et al. Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations , 2009, Proteins.
[81] Wanling Song,et al. Varied Probability of Staying Collapsed/Extended at the Conformational Equilibrium of Monomeric Aβ40 and Aβ42 , 2015, Scientific Reports.
[82] Meng Cui,et al. PIP2 controls voltage-sensor movement and pore opening of Kv channels through the S4–S5 linker , 2012, Proceedings of the National Academy of Sciences.
[83] Diomedes E Logothetis,et al. PIP2 Activates KCNQ Channels, and Its Hydrolysis Underlies Receptor-Mediated Inhibition of M Currents , 2003, Neuron.
[84] Xiaomin Luo,et al. TarFisDock: a web server for identifying drug targets with docking approach , 2006, Nucleic Acids Res..
[85] Rui Chen,et al. Promise of personalized omics to precision medicine , 2013, Wiley interdisciplinary reviews. Systems biology and medicine.
[86] Alan Grossfield,et al. A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[87] J. Hardy,et al. The Amyloid Hypothesis of Alzheimer ’ s Disease : Progress and Problems on the Road to Therapeutics , 2009 .
[88] Cheng Luo,et al. SPHINGOSINE-1-PHOSPHATE: A MISSING COFACTOR FOR THE E3 UBIQUITIN LIGASE TRAF2 , 2010, Nature.
[89] Chris de Graaf,et al. Structure of the human glucagon class B G-protein-coupled receptor , 2013, Nature.
[90] Francisco Bezanilla,et al. Histidine Scanning Mutagenesis of Basic Residues of the S4 Segment of the Shaker K+ Channel , 2001, The Journal of general physiology.
[91] Xian Liu,et al. In Silico target fishing: addressing a “Big Data” problem by ligand-based similarity rankings with data fusion , 2014, Journal of Cheminformatics.
[92] Diomedes E. Logothetis,et al. Channelopathies linked to plasma membrane phosphoinositides , 2010, Pflügers Archiv - European Journal of Physiology.
[93] Fei Ye,et al. In vitro biochemical and thermodynamic characterization of nucleocapsid protein of SARS , 2004, Biophysical Chemistry.
[94] T. McDonald,et al. Molecular analysis of PIP2 regulation of HERG and IKr. , 2004, American journal of physiology. Heart and circulatory physiology.
[95] Weiliang Zhu,et al. Neuraminidase pharmacophore model derived from diverse classes of inhibitors. , 2006, Bioorganic & medicinal chemistry letters.
[96] Bertil Hille,et al. PIP2 is a necessary cofactor for ion channel function: how and why? , 2008, Annual review of biophysics.
[97] Cheng Luo,et al. Why are oseltamivir and zanamivir effective against the newly emerged influenza A virus (A/H1N1)? , 2009, Cell Research.
[98] Ehud Y Isacoff,et al. The Orientation and Molecular Movement of a K+ Channel Voltage-Sensing Domain , 2003, Neuron.
[99] Garrett M Morris,et al. The emerging role of cloud computing in molecular modelling. , 2013, Journal of molecular graphics & modelling.
[100] Cheng Luo,et al. Astemizole arrests the proliferation of cancer cells by disrupting the EZH2-EED interaction of polycomb repressive complex 2. , 2014, Journal of medicinal chemistry.
[101] Ron O. Dror,et al. Mechanism of Voltage Gating in Potassium Channels , 2012, Science.
[102] G. Ginsburg,et al. Personalized medicine: revolutionizing drug discovery and patient care. , 2001, Trends in biotechnology.
[103] Xia Wang,et al. iDrug: a web-accessible and interactive drug discovery and design platform , 2014, Journal of Cheminformatics.
[104] Steven J. M. Jones,et al. Drug repositioning for personalized medicine , 2012, Genome Medicine.