A Brief View of Molecular Modeling Approaches to P2 Receptors
暂无分享,去创建一个
L. A. Alves | A. P. Alberto | L. Santos | Anael V.P. Alberto | Lucianna H.S. Santos | R. Ferreira | Dinarte N.M. Ferreira | Luiz A. Alves | D. N. M. Ferreira
[1] S. Adelman. Quantum generalized Langevin equation approach to gas/solid collisions , 1976 .
[2] R. North,et al. A new class of ligand-gated ion channel defined by P2X receptor for extracellular ATP , 1994, Nature.
[3] D. Julius,et al. New structural motif for ligand-gated ion channels defined by an ionotropic ATP receptor , 1994, Nature.
[4] M. James,et al. A critical assessment of comparative molecular modeling of tertiary structures of proteins * , 1995, Proteins.
[5] R. North,et al. Pharmacological characterization of heterologously expressed ATP-gated cation channels (P2x purinoceptors). , 1995, Molecular pharmacology.
[6] J. T. Turner,et al. Site-directed Mutagenesis of P2U Purinoceptors , 1995, The Journal of Biological Chemistry.
[7] K. Jacobson,et al. Modelling the P2Y purinoceptor using rhodopsin as template. , 1995, Drug design and discovery.
[8] G. Burnstock,et al. A P2X purinoceptor expressed by a subset of sensory neurons , 1995, Nature.
[9] P Willett,et al. Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.
[10] R. Coutinho-Silva,et al. P2Z purinoceptor-associated pores induced by extracellular ATP in macrophages and J774 cells. , 1997, American journal of physiology. Cell physiology.
[11] S. Moro,et al. Human P2Y1 receptor: molecular modeling and site-directed mutagenesis as tools to identify agonist and antagonist recognition sites. , 1998, Journal of medicinal chemistry.
[12] Richard Bonneau,et al. Ab initio protein structure prediction of CASP III targets using ROSETTA , 1999, Proteins.
[13] S. Moro,et al. Synthesis, biological activity, and molecular modeling of ribose-modified deoxyadenosine bisphosphate analogues as P2Y(1) receptor ligands. , 2000, Journal of medicinal chemistry.
[14] K. Jacobson,et al. Acyclic and cyclopropyl analogues of adenosine bisphosphate antagonists of the P2Y1 receptor: structure-activity relationships and receptor docking. , 2001, Journal of medicinal chemistry.
[15] H. Jaap van den Herik,et al. Games solved: Now and in the future , 2002, Artif. Intell..
[16] P. Whittaker. What is the relevance of bioinformatics to pharmacology? , 2003, Trends in pharmacological sciences.
[17] Christian F. Schwenk,et al. Classical and QM/MM molecular dynamics simulations of Co2+ in water , 2003 .
[18] K. Jacobson,et al. Architecture of P2Y nucleotide receptors: structural comparison based on sequence analysis, mutagenesis, and homology modeling. , 2004, Journal of medicinal chemistry.
[19] Corinna Cortes,et al. Support-Vector Networks , 1995, Machine Learning.
[20] D. Major,et al. Molecular recognition in purinergic receptors. 2. Diastereoselectivity of the h-P2Y1-receptor. , 2004, Journal of medicinal chemistry.
[21] Hege S. Beard,et al. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. , 2004, Journal of medicinal chemistry.
[22] D. Major,et al. Molecular recognition in purinergic receptors. 1. A comprehensive computational study of the h-P2Y1-receptor. , 2004, Journal of medicinal chemistry.
[23] Matthew P. Repasky,et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.
[24] Sean Ekins,et al. Reengineering the pharmaceutical industry by crash-testing molecules. , 2005, Drug discovery today.
[25] K. Jacobson,et al. Human P2Y(6) receptor: molecular modeling leads to the rational design of a novel agonist based on a unique conformational preference. , 2005, Journal of medicinal chemistry.
[26] Weiliang Zhu,et al. New technologies in computer-aided drug design: Toward target identification and new chemical entity discovery , 2006, Drug Discovery Today: Technologies.
[27] K. Jacobson,et al. Structure activity and molecular modeling analyses of ribose- and base-modified uridine 5'-triphosphate analogues at the human P2Y2 and P2Y4 receptors. , 2006, Biochemical pharmacology.
[28] B. Honig,et al. On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. , 2006, Biophysical journal.
[29] R. Copeland,et al. Drug–target residence time and its implications for lead optimization , 2007, Nature Reviews Drug Discovery.
[30] Zonghe Yan,et al. Participation of the Lys313-Ile333 Sequence of the Purinergic P2X4 Receptor in Agonist Binding and Transduction of Signals to the Channel Gate* , 2006, Journal of Biological Chemistry.
[31] G. Reiser,et al. Structure and ligand-binding site characteristics of the human P2Y11 nucleotide receptor deduced from computational modelling and mutational analysis. , 2007, The Biochemical journal.
[32] Ben M. Webb,et al. Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.
[33] S. Ekins,et al. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling , 2007, British journal of pharmacology.
[34] K. Jacobson,et al. P2Y1 antagonists: combining receptor-based modeling and QSAR for a quantitative prediction of the biological activity based on consensus scoring. , 2007, Journal of medicinal chemistry.
[35] G. Morris,et al. Molecular docking. , 2008, Methods in molecular biology.
[36] Ross C. Walker,et al. The implementation of a fast and accurate QM/MM potential method in Amber , 2008, J. Comput. Chem..
[37] P. Biggin,et al. Molecular dynamics simulations of membrane proteins. , 2008, Methods in molecular biology.
[38] D. Spray,et al. P2X7 receptor-Pannexin1 complex: pharmacology and signaling. , 2008, American journal of physiology. Cell physiology.
[39] B. Testa,et al. The Biochemistry of Drug Metabolism – An Introduction , 2009, Chemistry & biodiversity.
[40] C. Müller,et al. Key determinants of nucleotide-activated G protein-coupled P2Y(2) receptor function revealed by chemical and pharmacological experiments, mutagenesis and homology modeling. , 2009, Journal of medicinal chemistry.
[41] E. Gouaux,et al. Crystal structure of the ATP-gated P2X4 ion channel in the closed state , 2009, Nature.
[42] David S. Goodsell,et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..
[43] R. Evans. Structural interpretation of P2X receptor mutagenesis studies on drug action , 2010, British journal of pharmacology.
[44] G. Schmalzing,et al. Amino acid residues constituting the agonist binding site of the human P2X3 receptor and subunit stoichiometry of heteromeric P2X2/3 and P2X2/6 receptors , 2012 .
[45] R. North,et al. New structure enlivens interest in P2X receptors , 2010, Trends in pharmacological sciences.
[46] Francesca Deflorian,et al. Comparison of three GPCR structural templates for modeling of the P2Y12 nucleotide receptor , 2011, J. Comput. Aided Mol. Des..
[47] S. Silberberg,et al. Ion access pathway to the transmembrane pore in P2X receptor channels , 2011, The Journal of general physiology.
[48] Weiliang Zhu,et al. Utilization of halogen bond in lead optimization: a case study of rational design of potent phosphodiesterase type 5 (PDE5) inhibitors. , 2011, Journal of medicinal chemistry.
[49] B. Khakh,et al. Preferential use of unobstructed lateral portals as the access route to the pore of human ATP-gated ion channels (P2X receptors) , 2011, Proceedings of the National Academy of Sciences.
[50] Jacobson,et al. Pyrimidine nucleotides with 4-alkyloxyimino and terminal tetraphosphate δ-ester modifications as selective agonists of the P2Y(4) receptor. , 2011, Journal of medicinal chemistry.
[51] J. Mccammon,et al. Molecular recognition in the case of flexible targets. , 2011, Current pharmaceutical design.
[52] S. Robinson,et al. CCT244747 Is a Novel Potent and Selective CHK1 Inhibitor with Oral Efficacy Alone and in Combination with Genotoxic Anticancer Drugs , 2012, Clinical Cancer Research.
[53] Pranita P. Kore,et al. Computer-Aided Drug Design: An Innovative Tool for Modeling , 2012 .
[54] Huan‐Xiang Zhou,et al. Gating mechanism of a P2X4 receptor developed from normal mode analysis and molecular dynamics simulations , 2012, Proceedings of the National Academy of Sciences.
[55] R. Schmid,et al. Agonist binding evokes extensive conformational changes in the extracellular domain of the ATP-gated human P2X1 receptor ion channel , 2012, Proceedings of the National Academy of Sciences.
[56] A. Taly,et al. Tightening of the ATP‐binding sites induces the opening of P2X receptor channels , 2012, The EMBO journal.
[57] K. Jacobson,et al. Virtual screening leads to the discovery of novel non-nucleotide P2Y₁ receptor antagonists. , 2012, Bioorganic & medicinal chemistry.
[58] M. Hattori,et al. Molecular mechanism of ATP binding and ion channel activation in P2X receptors , 2012, Nature.
[59] K. Jacobson,et al. Molecular Structure of P2Y Receptors: Mutagenesis, Modeling, and Chemical Probes. , 2012, Wiley interdisciplinary reviews. Membrane transport and signaling.
[60] G. Bahrenberg,et al. Salt Bridge Switching from Arg290/Glu167 to Arg290/ATP Promotes the Closed-to-Open Transition of the P2X2 Receptor , 2013, Molecular Pharmacology.
[61] S. Silberberg,et al. Inter- and intrasubunit interactions between transmembrane helices in the open state of P2X receptor channels , 2013, Proceedings of the National Academy of Sciences.
[62] R. North,et al. P2X7 Receptor Channels Allow Direct Permeation of Nanometer-Sized Dyes , 2013, The Journal of Neuroscience.
[63] L. A. Alves,et al. Is pannexin the pore associated with the P2X7 receptor? , 2013, Naunyn-Schmiedeberg's Archives of Pharmacology.
[64] G. Vistoli,et al. Naturally occurring N(6)-substituted adenosines (cytokinin ribosides) are in vitro inhibitors of platelet aggregation: an in silico evaluation of their interaction with the P2Y(12) receptor. , 2014, Bioorganic & medicinal chemistry letters.
[65] Kyle A. Brown,et al. Exploring a 2-Naphthoic Acid Template for the Structure-Based Design of P2Y14 Receptor Antagonist Molecular Probes , 2014, ACS chemical biology.
[66] Yang Yang,et al. Relative motions between left flipper and dorsal fin domains favour P2X4 receptor activation , 2014, Nature Communications.
[67] Hualiang Jiang,et al. Agonist-bound structure of the human P2Y12 receptor , 2014, Nature.
[68] R. North,et al. Ectodomain Movements of an ATP-gated Ion Channel (P2X2 Receptor) Probed by Disulfide Locking* , 2014, The Journal of Biological Chemistry.
[69] Steven M. Moss,et al. Structure of the human P2Y12 receptor in complex with an antithrombotic drug , 2014, Nature.
[70] Qiang Zhao,et al. Modeling ligand recognition at the P2Y12 receptor in light of X-ray structural information , 2015, Journal of Computer-Aided Molecular Design.
[71] Hualiang Jiang,et al. Two disparate ligand-binding sites in the human P2Y1 receptor , 2015, Nature.
[72] Kyle A. Brown,et al. Design, synthesis, pharmacological characterization of a fluorescent agonist of the P2Y₁₄ receptor. , 2015, Bioorganic & medicinal chemistry letters.
[73] K. Jacobson,et al. Molecular modeling of the human P2Y14 receptor: A template for structure-based design of selective agonist ligands. , 2015, Bioorganic & medicinal chemistry.
[74] Yu-chian Chen. Beware of docking! , 2015, Trends in pharmacological sciences.
[75] G. Bifulco,et al. Molecular mechanism of tanshinone IIA and cryptotanshinone in platelet anti-aggregating effects: an integrated study of pharmacology and computational analysis. , 2015, Fitoterapia.
[76] William J. Allen,et al. DOCK 6: Impact of new features and current docking performance , 2015, J. Comput. Chem..
[77] Antonio Lavecchia,et al. Machine-learning approaches in drug discovery: methods and applications. , 2015, Drug discovery today.
[78] N. Heinrich,et al. Computational Chemistry in the Pharmaceutical Industry: From Childhood to Adolescence , 2015, ChemMedChem.
[79] Daniel B. Roche,et al. Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods , 2015, International journal of molecular sciences.
[80] G. Marucci,et al. Purinergic P2X receptors: structural models and analysis of ligand-target interaction. , 2015, European journal of medicinal chemistry.
[81] Rafael C. Bernardi,et al. Enhanced sampling techniques in molecular dynamics simulations of biological systems. , 2015, Biochimica et biophysica acta.
[82] U. Rothlisberger,et al. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. , 2015, Chemical reviews.
[83] M. Young,et al. Purinergic P2X receptors: structural and functional features depicted by X-ray and molecular modelling studies. , 2014, Current medicinal chemistry.
[84] Claudio N. Cavasotto,et al. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. , 2015, Archives of biochemistry and biophysics.
[85] Jeffrey J. Gray,et al. Computational modeling of membrane proteins , 2015, Proteins.
[86] Kyle A. Brown,et al. Structure-Based Design of 3-(4-Aryl-1H-1,2,3-triazol-1-yl)-Biphenyl Derivatives as P2Y14 Receptor Antagonists , 2016, Journal of medicinal chemistry.
[87] Ben M. Webb,et al. Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.
[88] E. Gouaux,et al. X-ray structures define human P2X3 receptor gating cycle and antagonist action , 2016, Nature.
[89] Christopher A. Voigt,et al. Synthetic biology to access and expand nature's chemical diversity , 2016, Nature Reviews Microbiology.
[90] T. Kawate,et al. Structural basis for subtype-specific inhibition of the P2X7 receptor , 2016, eLife.
[91] C. Fishwick,et al. Structure-based identification and characterisation of structurally novel human P2X7 receptor antagonists , 2016, Biochemical pharmacology.
[92] F. Metzger,et al. Specific Correction of Alternative Survival Motor Neuron 2 Splicing by Small Molecules: Discovery of a Potential Novel Medicine To Treat Spinal Muscular Atrophy. , 2016, Journal of medicinal chemistry.
[93] T. Grutter,et al. Molecular structure and function of P2X receptors , 2016, Neuropharmacology.
[94] Alexander S. Bayden,et al. The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery. , 2017, Journal of medicinal chemistry.
[95] O. Nureki,et al. Structural insights into the competitive inhibition of the ATP-gated P2X receptor channel , 2017, Nature Communications.
[96] Yang Yang,et al. Intersubunit physical couplings fostered by the left flipper domain facilitate channel opening of P2X4 receptors , 2017, The Journal of Biological Chemistry.
[97] Wenjuan Wu,et al. Investigating the binding mechanism of novel 6-aminonicotinate-based antagonists with P2Y12 by 3D-QSAR, docking and molecular dynamics simulations , 2017, Journal of biomolecular structure & dynamics.
[98] R. Schmid,et al. Unique residues in the ATP gated human P2X7 receptor define a novel allosteric binding pocket for the selective antagonist AZ10606120 , 2017, Scientific Reports.
[99] C. Müller,et al. Molecular Recognition of Agonists and Antagonists by the Nucleotide-Activated G Protein-Coupled P2Y2 Receptor. , 2017, Journal of medicinal chemistry.
[100] G. Schmalzing,et al. Localization of the gate and selectivity filter of the full-length P2X7 receptor , 2017, Proceedings of the National Academy of Sciences.
[101] P. Xiao,et al. In silico Approach for Anti-Thrombosis Drug Discovery: P2Y1R Structure-Based TCMs Screening , 2017, Front. Pharmacol..
[102] C. Müller,et al. Development of Potent and Selective Antagonists for the UTP-Activated P2Y4 Receptor. , 2017, Journal of medicinal chemistry.
[103] Hong Liu,et al. Design, synthesis, and biological evaluation of 2-(phenoxyaryl)-3-urea derivatives as novel P2Y1 receptor antagonists. , 2018, European journal of medicinal chemistry.
[104] Min Xu,et al. The Fourth Industrial Revolution: Opportunities and Challenges , 2018 .
[105] A. Brancale,et al. The Molecular Determinants of Small-Molecule Ligand Binding at P2X Receptors , 2018, Front. Pharmacol..
[106] Torsten Schwede,et al. SWISS-MODEL: homology modelling of protein structures and complexes , 2018, Nucleic Acids Res..
[107] R. Schmid,et al. Mapping the Allosteric Action of Antagonists A740003 and A438079 Reveals a Role for the Left Flipper in Ligand Sensitivity at P2X7 Receptors , 2018, Molecular Pharmacology.
[108] Yao-Yuan Liu,et al. A review of bioinformatic methods for forensic DNA analyses. , 2018, Forensic science international. Genetics.
[109] Xudong Huang,et al. Deep learning and virtual drug screening , 2018, Future medicinal chemistry.
[110] D. Major,et al. A promising drug candidate for the treatment of glaucoma based on a P2Y6-receptor agonist , 2018, Purinergic Signalling.
[111] M. Hattori,et al. Druggable negative allosteric site of P2X3 receptors , 2018, Proceedings of the National Academy of Sciences.
[112] Chen Cui,et al. Computational chemical biology and drug design: Facilitating protein structure, function, and modulation studies , 2018, Medicinal research reviews.
[113] Demis Hassabis,et al. A general reinforcement learning algorithm that masters chess, shogi, and Go through self-play , 2018, Science.
[114] Kathia Maria Honorio,et al. Advances with support vector machines for novel drug discovery , 2018, Expert opinion on drug discovery.
[115] J. Angulo,et al. Mapping a novel positive allosteric modulator binding site in the central vestibule region of human P2X7 , 2019, Scientific Reports.
[116] Volkan Atalay,et al. Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases , 2018, Briefings Bioinform..