Additive CHARMM force field for naturally occurring modified ribonucleotides
暂无分享,去创建一个
Alexander D. MacKerell | You Xu | Lennart Nilsson | Kenno Vanommeslaeghe | Alexey Aleksandrov | L. Nilsson | You Xu | K. Vanommeslaeghe | A. Aleksandrov
[1] Alexander D. MacKerell,et al. Robustness in the fitting of molecular mechanics parameters , 2015, J. Comput. Chem..
[2] L. Nilsson,et al. Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations. , 2014, Biopolymers.
[3] Richard Lavery,et al. Significance of Molecular Dynamics Simulations for Life Sciences , 2014 .
[4] D. Mathews,et al. Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics , 2014, Journal of chemical theory and computation.
[5] Lennart Nilsson,et al. Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields , 2014, J. Chem. Inf. Model..
[6] Mark Helm,et al. Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland. , 2014, Chemistry & biology.
[7] Benjamin D. Madej,et al. Lipid14: The Amber Lipid Force Field , 2014, Journal of chemical theory and computation.
[8] Douglas H. Turner,et al. The contribution of pseudouridine to stabilities and structure of RNAs , 2013, Nucleic acids research.
[9] Graham A. Hudson,et al. Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides , 2013, RNA.
[10] X. Xuan,et al. Molecular structure and vibrational spectra of N4-acetylcytosine. , 2013, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.
[11] Maria C. Nagan,et al. Backbone-base interactions critical to quantum stabilization of transfer RNA anticodon structure. , 2013, The journal of physical chemistry. B.
[12] J. Alfonzo,et al. Transfer RNA modifications: nature's combinatorial chemistry playground , 2013, Wiley interdisciplinary reviews. RNA.
[13] Alexander D. MacKerell,et al. Extension of the CHARMM general force field to sulfonyl‐containing compounds and its utility in biomolecular simulations , 2012, J. Comput. Chem..
[14] Alexander D. MacKerell,et al. Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing , 2012, J. Chem. Inf. Model..
[15] Alexander D. MacKerell,et al. Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges , 2012, J. Chem. Inf. Model..
[16] V. de Crécy-Lagard,et al. Biosynthesis and function of posttranscriptional modifications of transfer RNAs. , 2012, Annual review of genetics.
[17] T. Carell,et al. Structure and function of noncanonical nucleobases. , 2012, Angewandte Chemie.
[18] Alexander D. MacKerell,et al. Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity. , 2012, Journal of the American Chemical Society.
[19] Alexander D. MacKerell,et al. Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. , 2012, Journal of chemical theory and computation.
[20] Lennart Nilsson,et al. Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome. , 2011, RNA.
[21] Alexander D. MacKerell,et al. Impact of 2′‐hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all‐atom additive force field for RNA , 2011, J. Comput. Chem..
[22] V. Ramakrishnan,et al. How mutations in tRNA distant from the anticodon affect the fidelity of decoding , 2010, Nature Structural &Molecular Biology.
[23] Jef Rozenski,et al. The RNA modification database, RNAMDB: 2011 update , 2010, Nucleic Acids Res..
[24] Alexander D. MacKerell,et al. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. , 2010, The journal of physical chemistry. B.
[25] C. A. Theimer,et al. Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA , 2010, Nucleic acids research.
[26] Harry A. Stern,et al. Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine , 2010, Journal of chemical theory and computation.
[27] Alexander D. MacKerell,et al. CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields , 2009, J. Comput. Chem..
[28] Jianpeng Ma,et al. CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..
[29] Lennart Nilsson,et al. Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations , 2009, J. Comput. Chem..
[30] Alexander D. MacKerell,et al. Additive empirical force field for hexopyranose monosaccharides , 2008, J. Comput. Chem..
[31] Paul F Agris,et al. Bringing order to translation: the contributions of transfer RNA anticodon‐domain modifications , 2008, EMBO reports.
[32] Yu-Cheng Chang,et al. Synthesis and solution conformation studies of 3-substituted uridine and pseudouridine derivatives. , 2008, Bioorganic & medicinal chemistry.
[33] Effect of a water molecule on the sugar puckering of uridine, 2'-deoxyuridine, and 2'-O-methyl uridine inserted in duplexes. , 2008, The journal of physical chemistry. A.
[34] Karl Nicholas Kirschner,et al. GLYCAM06: A generalizable biomolecular force field. Carbohydrates , 2008, J. Comput. Chem..
[35] John SantaLucia,et al. AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA. , 2007, Journal of chemical theory and computation.
[36] J. Šponer,et al. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers , 2007 .
[37] Paul F Agris,et al. tRNA's wobble decoding of the genome: 40 years of modification. , 2007, Journal of molecular biology.
[38] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[39] Maria C. Nagan,et al. Molecular dynamics simulations of human tRNAUUULys,3: the role of modified bases in mRNA recognition , 2006, Nucleic acids research.
[40] Mark Helm,et al. Post-transcriptional nucleotide modification and alternative folding of RNA , 2006, Nucleic acids research.
[41] C. Chow,et al. Solution conformations of two naturally occurring RNA nucleosides: 3-methyluridine and 3-methylpseudouridine. , 2005, Bioorganic & medicinal chemistry.
[42] Nicolas Foloppe,et al. Toward a full characterization of nucleic acid components in aqueous solution: simulations of nucleosides. , 2005, The journal of physical chemistry. B.
[43] Chris Oostenbrink,et al. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..
[44] Alexander D. MacKerell. Empirical force fields for biological macromolecules: Overview and issues , 2004, J. Comput. Chem..
[45] Alexander D. MacKerell,et al. Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations , 2004, J. Comput. Chem..
[46] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[47] P. Agris,et al. Highly conserved modified nucleosides influence Mg2+-dependent tRNA folding. , 2002, Nucleic acids research.
[48] N. L. Greenbaum,et al. Investigation of Overhauser effects between pseudouridine and water protons in RNA helices , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[49] Alexander D. MacKerell,et al. Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. , 2002, Biophysical journal.
[50] Alexander D. MacKerell,et al. Combined ab initio/empirical approach for optimization of Lennard‐Jones parameters for polar‐neutral compounds , 2002, J. Comput. Chem..
[51] E. Westhof,et al. Hydrophobic Groups Stabilize the Hydration Shell of 2'-O-Methylated RNA Duplexes. , 2001, Angewandte Chemie.
[52] G. Fox,et al. NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop. , 2001, Nucleic acids research.
[53] R. Micura,et al. Methylation of the nucleobases in RNA oligonucleotides mediates duplex-hairpin conversion. , 2001, Nucleic acids research.
[54] Wilfred F. van Gunsteren,et al. An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase , 2001, J. Comput. Chem..
[55] Vadim V. Demidov,et al. Nucleic Acids: Structures, Properties and Functions , 2001 .
[56] Alexander D. MacKerell,et al. Ab initio conformational analysis of nucleic acid components: Intrinsic energetic contributions to nucleic acid structure and dynamics , 2001, Biopolymers.
[57] P. Moore,et al. The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited. , 2000, RNA.
[58] M. W. Gray,et al. Pseudouridine in RNA: What, Where, How, and Why , 2000, IUBMB life.
[59] S. Yokoyama,et al. Effects of anticodon 2'-O-methylations on tRNA codon recognition in an Escherichia coli cell-free translation. , 2000, RNA.
[60] D. Crothers,et al. Nucleic Acids: Structures, Properties, and Functions , 2000 .
[61] Alexander D. MacKerell,et al. All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000 .
[62] Alexander D. MacKerell,et al. Contribution of the Phosphodiester Backbone and Glycosyl Linkage Intrinsic Torsional Energetics to DNA Structure and Dynamics , 1999 .
[63] P. Agris,et al. Structural and functional roles of the N1- and N3-protons of psi at tRNA's position 39. , 1999, Nucleic acids research.
[64] Alexander D. MacKerell,et al. Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA. , 1999, Biophysical journal.
[65] A. Warshel,et al. Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution: Ab Initio/Langevin Dipoles Study , 1999 .
[66] D. Davis,et al. Stabilization of the anticodon stem-loop of tRNALys,3 by an A+-C base-pair and by pseudouridine. , 1999, Journal of molecular biology.
[67] C. Veltri,et al. An RNA model system for investigation of pseudouridine stabilization of the codon-anticodon interaction in tRNALys, tRNAHis and tRNATyr. , 1998, Journal of biomolecular structure & dynamics.
[68] Wilfred F. van Gunsteren,et al. Parametrization of aliphatic CHn united atoms of GROMOS96 force field , 1998, J. Comput. Chem..
[69] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[70] Alexander D. MacKerell,et al. Combined ab initio/empirical approach for optimization of Lennard–Jones parameters , 1998 .
[71] William L. Jorgensen,et al. OPLS all‐atom force field for carbohydrates , 1997 .
[72] C. Sich,et al. Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry. , 1997, Biochemistry.
[73] R. Adamiak,et al. Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions. , 1997, Nucleic acids research.
[74] R. Y. Morita,et al. Posttranscriptional modification of tRNA in psychrophilic bacteria , 1997, Journal of bacteriology.
[75] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[76] Leo Radom,et al. Harmonic Vibrational Frequencies: An Evaluation of Hartree−Fock, Møller−Plesset, Quadratic Configuration Interaction, Density Functional Theory, and Semiempirical Scale Factors , 1996 .
[77] J. McCloskey,et al. Conformational flexibility in RNA: the role of dihydrouridine. , 1996, Nucleic acids research.
[78] J. Plavec,et al. How do the energetics of the stereoelectronic gauche and anomeric effects modulate the conformation of nucleos(t)ides? , 1996 .
[79] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197 , 1996 .
[80] Lennart Nilsson,et al. Stacking Free Energy Profiles for All 16 Natural Ribodinucleoside Monophosphates in Aqueous Solution , 1995 .
[81] Lennart Nilsson,et al. Temperature dependence of the stacking propensity of adenylyl-3',5'-adenosine , 1995 .
[82] D. Davis. Stabilization of RNA stacking by pseudouridine. , 1995, Nucleic acids research.
[83] M. Egli,et al. Stabilizing effects of the RNA 2'-substituent: crystal structure of an oligodeoxynucleotide duplex containing 2'-O-methylated adenosines. , 1994, Chemistry & biology.
[84] L. Nilsson,et al. Stacking-unstacking of the dinucleoside monophosphate guanylyl-3',5'-uridine studied with molecular dynamics. , 1994, Biophysical journal.
[85] Bernard R. Brooks,et al. New spherical‐cutoff methods for long‐range forces in macromolecular simulation , 1994, J. Comput. Chem..
[86] T. Steitz,et al. Crystal structure of unmodified tRNA(Gln) complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure. , 1994, Biochemistry.
[87] The crystal structure of N 4-methylcytosine-guanosine base-pairs in the synthetic hexanucleotide d ( CGCGm 4 CG ) , 2004 .
[88] D. Turner,et al. Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics. , 1993, Biochemistry.
[89] M. Sekine,et al. Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group. , 1992, Biochemistry.
[90] S. Yokoyama,et al. Conformational Rigidity of N4-Acetyl-2′-O-methylcytidine Found in tRNA of Extremely Thermophilic Archaebacteria (Archaea) , 1992 .
[91] Alexander D. MacKerell,et al. Importance of attractive van der Waals contribution in empirical energy function models for the heat of vaporization of polar liquids , 1991 .
[92] P. Sigler,et al. The 3 A crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination. , 1991, The EMBO journal.
[93] William H. Press,et al. Numerical recipes , 1990 .
[94] E. Darżynkiewicz,et al. Base stacking of simple mRNA cap analogues. Association of 7,9-dimethylguanine, 7-methylguanosine and 7-methylguanosine 5'-monophosphate with indole and purine derivatives in aqueous solution. , 1989, Biophysical chemistry.
[95] A. Matsuda,et al. A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli , 1989, The Journal of biological chemistry.
[96] W. L. Jorgensen,et al. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.
[97] R. Teoule,et al. NMR and CD studies on an oligonucleotide containing N4-methylcytosine. , 1987, Nucleic acids research.
[98] P. Agris,et al. Comparative structural analysis of 1-methyladenosine, 7-methylguanosine, ethenoadenosine and their protonated salts IV: 1H, 13C, and 15N NMR studies at natural isotope abundance. , 1986, Nucleic acids research.
[99] Y. Yamagata,et al. A novel guanine-guanine base pairing: crystal structure of a complex between 7-methylguanosine and its iodide. , 1983, Nucleic acids research.
[100] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[101] J. Reiner,et al. On the conformation of 5-substituted uridines as studied by proton magnetic resonance. , 1983, Nucleic acids research.
[102] B. Thole. Molecular polarizabilities calculated with a modified dipole interaction , 1981 .
[103] M. Guéron,et al. Comparative conformations of uridine and pseudouridine and their derivatives. , 1980, European journal of biochemistry.
[104] W. Hillen,et al. INFLUENCE OF SUBSTITUENTS AT THE 5 POSITION ON THE STRUCTURE OF URIDINE , 1980 .
[105] Peter Pulay,et al. Systematic AB Initio Gradient Calculation of Molecular Geometries, Force Constants, and Dipole Moment Derivatives , 1979 .
[106] L. H. Schulman,et al. The role of the minor base N4-acetylcytidine in the function of the Escherichia coli noninitiator methionine transfer RNA. , 1978, The Journal of biological chemistry.
[107] S. Ginell,et al. Conformation of N4-acetylcytidine, a modified nucleoside of tRNA, and stereochemistry of codon-anticodon interaction. , 1978, Biochemical and biophysical research communications.
[108] R. Sarma,et al. Nuclear magnetic resonance study of the impact of ribose 2′‐O‐methylation on the aqueous solution conformation of cytidylyl‐(3′ → 5′)‐cytidine , 1977 .
[109] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[110] C. H. Kim,et al. A relation between inhibition of protein synthesis and conformation of 5'-phosphorylated 7-methylguanosine derivatives. , 1977, Journal of molecular biology.
[111] D. J. Wood,et al. Effect of temperature and protonation upon the conformation of 2'-o-methyladenosine. Correlation of conformational parameters in purine nucleosides. , 1977, Biochimica et biophysica acta.
[112] A. Shatkin. Capping of eucaryotic mRNAs , 1976, Cell.
[113] R. Sarma,et al. Conformational features of 2′‐O‐methyl‐adenosylyl‐adenosine , 1976 .
[114] P. V. von Hippel,et al. Effects of methylation on the stability of nucleic acid conformations: studies at the monomer level. , 1974, Biochemistry.
[115] A. Drake,et al. Optical studies of the base-stacking properties of 2'-O-methylated dinucleoside monophosphates. , 1974, Journal of molecular biology.
[116] M. Sundaralingam,et al. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. , 1972, Journal of the American Chemical Society.
[117] D. Suck,et al. Molecular and crystal structure of the tRNA minor constituent dihydrouridine , 1972 .
[118] E. Becker,et al. Restricted rotation about the exocyclic carbon-nitrogen bond in cytosine derivatives. , 1972, The Journal of physical chemistry.
[119] M. Sundaralingam,et al. Stereochemistry of nucleic acids and their constituents. 23. Crystal and molecular structure of dihydrouridine "hemihydrate," a rare nucleoside with a saturated base occurring in the dihydrouridine loop of transfer ribonucleic acids. , 1971, Journal of the American Chemical Society.
[120] R. Deslauriers,et al. A proton magnetic resonance study of the molecular conformation of a modified nucleoside from transfer RNA. Dihydrouridine. , 1971, Canadian journal of biochemistry.
[121] D. Hirsh. Tryptophan transfer RNA as the UGA suppressor. , 1971, Journal of molecular biology.