Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.
暂无分享,去创建一个
Yuto Komeiji | Kaori Fukuzawa | Yuji Mochizuki | Shigenori Tanaka | Yoshio Okiyama | Kaori Fukuzawa | Y. Komeiji | Shigenori Tanaka | Y. Mochizuki | Yoshio Okiyama | S. Tanaka
[1] Takeshi Ishikawa,et al. Ab initio fragment molecular orbital study of molecular interactions in liganded retinoid X receptor: specification of residues associated with ligand inducible information transmission. , 2008, The journal of physical chemistry. B.
[2] Svein Saebo,et al. Avoiding the integral storage bottleneck in LCAO calculations of electron correlation , 1989 .
[3] Kazuo Kitaura,et al. Fully analytic energy gradient in the fragment molecular orbital method. , 2011, The Journal of chemical physics.
[4] T. Nakano,et al. Fragment interaction analysis based on local MP2 , 2007 .
[5] Masami Uebayasi,et al. Pair interaction molecular orbital method: an approximate computational method for molecular interactions , 1999 .
[6] B. Dijkstra,et al. Structure and mechanism of bacterial dehalogenases: different ways to cleave a carbon-halogen bond. , 2003, Current opinion in structural biology.
[7] A. Vallée,et al. Peptide interactions with metal and oxide surfaces. , 2010, Accounts of chemical research.
[8] Masato Kobayashi,et al. Alternative linear-scaling methodology for the second-order Møller-Plesset perturbation calculation based on the divide-and-conquer method. , 2007, The Journal of chemical physics.
[9] Kazuo Kitaura,et al. Theoretical analysis of the intermolecular interaction effects on the excitation energy of organic pigments: solid state quinacridone. , 2008, The journal of physical chemistry. A.
[10] U. Nagashima,et al. Development of an ab initio MO-MD program based on fragment MO method – an attempt to analyze the fluctuation of protein , 2004 .
[11] Analysis of solute-solvent interactions in the fragment molecular orbital method interfaced with effective fragment potentials: theory and application to a solvated griffithsin-carbohydrate complex. , 2012, The journal of physical chemistry. A.
[12] Masato Kobayashi,et al. Linear-scaling divide-and-conquer second-order Møller–Plesset perturbation calculation for open-shell systems: implementation and application , 2011 .
[13] Masato Kobayashi,et al. Second-order Møller-Plesset perturbation energy obtained from divide-and-conquer Hartree-Fock density matrix. , 2006, The Journal of chemical physics.
[14] G. Forbes. Molecular Dynamics , 1885, Nature.
[15] K. Kitaura,et al. Fragment molecular orbital method: an approximate computational method for large molecules , 1999 .
[16] Takeshi Ishikawa,et al. Theoretical study of the prion protein based on the fragment molecular orbital method , 2009, J. Comput. Chem..
[17] Shigenori Tanaka,et al. Excitation energy transfer modulated by oscillating electronic coupling of a dimeric system embedded in a molecular environment. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.
[18] Yuto Komeiji,et al. Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD)☆ , 2010 .
[19] Yuri Alexeev,et al. Geometry Optimization of the Active Site of a Large System with the Fragment Molecular Orbital Method , 2011 .
[20] Kaori Fukuzawa,et al. Fragment molecular orbital method: use of approximate electrostatic potential , 2002 .
[21] Mark S Gordon,et al. Structure and dynamics of the 1-hydroxyethyl-4-amino-1,2,4-triazolium nitrate high-energy ionic liquid system. , 2012, The journal of physical chemistry. B.
[22] Yuichi Inadomi,et al. PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules. , 2004, Computational biology and chemistry.
[23] E. Starikov,et al. Analysis of electron-transfer rate constant in condensed media with inclusion of inelastic tunneling and nuclear quantum effects. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.
[24] Yuichi Inadomi,et al. Multi-physics Extension of OpenFMO Framework , 2007, ArXiv.
[25] Makoto Taiji,et al. Fast and accurate molecular dynamics simulation of a protein using a special‐purpose computer , 1997 .
[26] H. Nakai,et al. How does it become possible to treat delocalized and/or open-shell systems in fragmentation-based linear-scaling electronic structure calculations? The case of the divide-and-conquer method. , 2012, Physical chemistry chemical physics : PCCP.
[27] Y. Mochizuki. Application of Dyson-corrected second-order perturbation theories , 2009 .
[28] R. Mata,et al. An incremental correlation approach to excited state energies based on natural transition/localized orbitals. , 2011, The Journal of chemical physics.
[29] Dieter Cremer,et al. Møller–Plesset perturbation theory: from small molecule methods to methods for thousands of atoms , 2011 .
[30] Yuji Mochizuki,et al. Configuration interaction singles method with multilayer fragment molecular orbital scheme , 2005 .
[31] S. Grimme,et al. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.
[32] Kaori Fukuzawa,et al. Large scale FMO-MP2 calculations on a massively parallel-vector computer , 2008 .
[33] Zhihai Liu,et al. Evaluation of the performance of four molecular docking programs on a diverse set of protein‐ligand complexes , 2010, J. Comput. Chem..
[34] Kiyoshi Tanaka,et al. Application of fragment molecular orbital scheme to silicon-containing systems , 2006 .
[35] Martin Head-Gordon,et al. Quadratic configuration interaction. A general technique for determining electron correlation energies , 1987 .
[36] E. Nobusawa,et al. Restriction of Amino Acid Change in Influenza A Virus H3HA: Comparison of Amino Acid Changes Observed in Nature and In Vitro , 2003, Journal of Virology.
[37] Yuichi Inadomi,et al. Fragment molecular orbital method: application to molecular dynamics simulation, ‘ab initio FMO-MD’ , 2003 .
[38] T. Yanai,et al. High-performance ab initio density matrix renormalization group method: applicability to large-scale multireference problems for metal compounds. , 2009, The Journal of chemical physics.
[39] J. Tomasi,et al. Quantum mechanical continuum solvation models. , 2005, Chemical reviews.
[40] Shinichiro Nakamura,et al. Analytic second derivatives of the energy in the fragment molecular orbital method. , 2013, The Journal of chemical physics.
[41] R. Feynman,et al. Quantum Mechanics and Path Integrals , 1965 .
[42] Examination of numerical accuracy on fragment-DFT calculations with integral values of total electron density functions , 2006 .
[43] W. Hackbusch,et al. Tensor representation techniques in post-Hartree–Fock methods: matrix product state tensor format , 2013 .
[44] K. Mori,et al. Computational Insights into Binding of Bisphosphates to Farnesyl Pyrophosphate Synthase , 2011, Current medicinal chemistry.
[45] Kazuo Kitaura,et al. Role of the key mutation in the selective binding of avian and human influenza hemagglutinin to sialosides revealed by quantum-mechanical calculations. , 2010, Journal of the American Chemical Society.
[46] A Eugene DePrince,et al. Coupled Cluster Theory on Graphics Processing Units I. The Coupled Cluster Doubles Method. , 2011, Journal of chemical theory and computation.
[47] Hirotoshi Mori,et al. Revised model core potentials for third-row transition–metal atoms from Lu to Hg , 2008 .
[48] Spencer R Pruitt,et al. Open-Shell Formulation of the Fragment Molecular Orbital Method. , 2010, Journal of chemical theory and computation.
[49] K. Kitaura,et al. Definition of molecular orbitals in fragment molecular orbital method , 2002 .
[50] Kazuya Ishimura,et al. A new parallel algorithm of MP2 energy calculations , 2006, J. Comput. Chem..
[51] H. Sekino,et al. Evaluation of NMR Chemical Shift by Fragment Molecular Orbital Method , 2007 .
[52] Curtis L. Janssen,et al. An efficient reformulation of the closed‐shell coupled cluster single and double excitation (CCSD) equations , 1988 .
[53] Takeshi Ishikawa,et al. Fragment Molecular Orbital method‐based Molecular Dynamics (FMO‐MD) as a simulator for chemical reactions in explicit solvation , 2009, J. Comput. Chem..
[54] Mark S. Gordon,et al. Accurate methods for large molecular systems. , 2009, The journal of physical chemistry. B.
[55] Lou Massa,et al. The kernel energy method of quantum mechanical approximation carried to fourth-order terms , 2008, Proceedings of the National Academy of Sciences.
[56] Claus Ehrhardt,et al. The coupled pair functional (CPF). A size consistent modification of the CI(SD) based on an energy functional , 1985 .
[57] D. Truhlar,et al. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals , 2008 .
[58] S. Whitney,et al. Manipulating ribulose bisphosphate carboxylase/oxygenase in the chloroplasts of higher plants. , 2003, Archives of biochemistry and biophysics.
[59] Hiroshi Chuman,et al. Correlation Analyses on Binding Affinity of Sialic Acid Analogues with Influenza Virus Neuraminidase-1 Using ab Initio MO Calculations on Their Complex Structures , 2010, J. Chem. Inf. Model..
[60] T. Nakano,et al. Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion , 2010 .
[61] D. Mazziotti,et al. Low-rank spectral expansions of two electron excitations for the acceleration of quantum chemistry calculations. , 2012, The Journal of chemical physics.
[62] Takashi Nakamura,et al. Roles of K151 and D180 in L‐2‐haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations , 2009, J. Comput. Chem..
[63] Kazuo Kitaura,et al. The importance of three-body terms in the fragment molecular orbital method. , 2004, The Journal of chemical physics.
[64] P Pulay,et al. Local Treatment of Electron Correlation , 1993 .
[65] R. Bartlett,et al. Many – Body Methods in Chemistry and Physics: Introduction , 2009 .
[66] Y. Mochizuki. A practical use of self-energy shift for the description of orbital relaxation , 2008 .
[67] Shigenori Tanaka,et al. Ab initio study of molecular interactions in higher plant and Galdieria partita Rubiscos with the fragment molecular orbital method. , 2007, Biochemical and biophysical research communications.
[68] Robert M Parrish,et al. Tensor hypercontraction density fitting. I. Quartic scaling second- and third-order Møller-Plesset perturbation theory. , 2012, The Journal of chemical physics.
[69] J. Skehel,et al. Structural evidence for recognition of a single epitope by two distinct antibodies , 2000, Proteins.
[70] Manabu Oumi,et al. A doubles correction to electronic excited states from configuration interaction in the space of single substitutions , 1994 .
[71] T. Okamoto,et al. A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD Simulation , 2013 .
[72] Y. Aoki,et al. An elongation method for large systems toward bio-systems. , 2012, Physical chemistry chemical physics : PCCP.
[73] Yuichi Inadomi,et al. Fragment molecular orbital study of the electronic excitations in the photosynthetic reaction center of Blastochloris viridis , 2009, J. Comput. Chem..
[74] Kaori Fukuzawa,et al. Higher-order correlated calculations based on fragment molecular orbital scheme , 2011 .
[75] Hiroshi Chuman,et al. Correlation Analyses on Binding Affinity of Substituted Benzenesulfonamides with Carbonic Anhydrase Using ab Initio MO Calculations on Their Complex Structures , 2010, J. Chem. Inf. Model..
[76] Y. Mochizuki,et al. Modification for spin-adapted version of configuration interaction singles with perturbative doubles , 2007 .
[77] R. Darnell,et al. Sequence-Specific RNA Binding by a Nova KH Domain Implications for Paraneoplastic Disease and the Fragile X Syndrome , 2000, Cell.
[78] Wei Li,et al. A refined cluster-in-molecule local correlation approach for predicting the relative energies of large systems. , 2012, Physical chemistry chemical physics : PCCP.
[79] Kazuo Kitaura,et al. Multiconfiguration self-consistent-field theory based upon the fragment molecular orbital method. , 2005, The Journal of chemical physics.
[80] K. Kitaura,et al. Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method combined with effective potentials , 2012, Theoretical Chemistry Accounts.
[81] Shigenori Tanaka,et al. Modern methods for theoretical physical chemistry of biopolymers , 2006 .
[82] Mark Whittaker,et al. Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method , 2011, J. Cheminformatics.
[83] Y. Mochizuki,et al. Theoretical study of hydration models of trivalent rare-earth ions using model core potentials , 2010 .
[84] Masha Sosonkina,et al. Fragment Molecular Orbital Method Adaptations for Heterogeneous Computing Platforms , 2012, ICCS.
[85] Martin Head-Gordon,et al. Higher order singular value decomposition in quantum chemistry , 2010 .
[86] Tatsuo Kurihara,et al. Bacterial hydrolytic dehalogenases and related enzymes: occurrences, reaction mechanisms, and applications. , 2008, Chemical record.
[87] J. Olsen,et al. A non-linear approach to configuration interaction: The low-rank CI method (LR CI) , 1987 .
[88] A. Pastore,et al. Novel RNA-binding motif: the KH module. , 1999, Biopolymers.
[89] Shigenori Tanaka,et al. Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method , 2008, Comput. Biol. Chem..
[90] S. M. Rothstein,et al. Molecular mechanics and all-electron fragment molecular orbital calculations on mutated polyglutamine peptides , 2010 .
[91] Garnet Kin-Lic Chan,et al. Canonical transformation theory from extended normal ordering. , 2007, The Journal of chemical physics.
[92] Kaori Fukuzawa,et al. Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations , 2009 .
[93] K. Kitaura,et al. Multilayer formulation of the fragment molecular orbital method (FMO). , 2005, The journal of physical chemistry. A.
[94] Seiichiro Ten-no,et al. Explicitly correlated wave functions: summary and perspective , 2012, Theoretical Chemistry Accounts.
[95] M. Head‐Gordon,et al. Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. , 2008, Physical chemistry chemical physics : PCCP.
[96] Kohji Itoh,et al. Correlation Analyses on Binding Affinity of Sialic Acid Analogues and Anti-Influenza Drugs with Human Neuraminidase Using ab Initio MO Calculations on Their Complex Structures - LERE-QSAR Analysis (IV) , 2011, J. Chem. Inf. Model..
[97] Koji Ando,et al. Fragment molecular orbital study on electron tunneling mechanisms in bacterial photosynthetic reaction center. , 2012, The journal of physical chemistry. B.
[98] Shigenori Tanaka,et al. Statistical correction to effective interactions in the fragment molecular orbital method , 2013 .
[99] K. Kitaura,et al. Energy decomposition analysis in solution based on the fragment molecular orbital method. , 2012, The journal of physical chemistry. A.
[100] Kazuo Kitaura,et al. Pair interaction energy decomposition analysis , 2007, J. Comput. Chem..
[101] Shigenori Tanaka,et al. Incorporation of solvation effects into the fragment molecular orbital calculations with the Poisson–Boltzmann equation , 2010 .
[102] T. Nakano,et al. An application of fragment interaction analysis based on local MP2 , 2008 .
[103] O. Sugino,et al. Symmetric tensor decomposition description of fermionic many-body wave functions. , 2012, Physical review letters.
[104] Hermann Stoll,et al. The correlation energy of crystalline silicon , 1992 .
[105] Kaori Fukuzawa,et al. Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid X receptor and its coactivator; part II: influence of mutations in transcriptional activation function 2 activating domain core on the molecular interactions. , 2008, The journal of physical chemistry. A.
[106] K. Kitaura,et al. Fragment-Molecular-Orbital-Method-Based ab Initio NMR Chemical-Shift Calculations for Large Molecular Systems , 2010 .
[107] Xiaolin Cheng,et al. Ab initio study of molecular interactions in cellulose Iα. , 2013, The journal of physical chemistry. B.
[108] Marcel Nooijen,et al. pCCSD: parameterized coupled-cluster theory with single and double excitations. , 2010, The Journal of chemical physics.
[109] Stefan Grimme,et al. Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction , 2006, J. Comput. Chem..
[110] Robert M Parrish,et al. Discrete variable representation in electronic structure theory: quadrature grids for least-squares tensor hypercontraction. , 2013, The Journal of chemical physics.
[111] S. Tanaka. Variational Quantum Monte Carlo with Inclusion of Orbital Correlations , 2013 .
[112] Yoshihiro Matsumoto,et al. Intrinsic Edge Asymmetry in Narrow Zigzag Hexagonal Heteroatomic Nanoribbons Causes their Subtle Uniform Curvature , 2012 .
[113] Edward F. Valeev,et al. Explicitly correlated R12/F12 methods for electronic structure. , 2012, Chemical reviews.
[114] H. Hieronymus,et al. A systems view of mRNP biology. , 2004, Genes & development.
[115] Kaori Fukuzawa,et al. Sialic acid recognition of the pandemic influenza 2009 H1N1 virus: binding mechanism between human receptor and influenza hemagglutinin. , 2011, Protein and peptide letters.
[116] K. Kitaura,et al. Systematic study of the embedding potential description in the fragment molecular orbital method. , 2010, The journal of physical chemistry. A.
[117] Feng Xu,et al. Fragment Molecular Orbital Molecular Dynamics with the Fully Analytic Energy Gradient. , 2012, Journal of chemical theory and computation.
[118] Jirí Cerný,et al. Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data. , 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.
[119] K. Fujimura,et al. The Role of Fluorine Atoms in a Fluorinated Prostaglandin Agonist , 2010, ChemMedChem.
[120] Kiyotaka Shiba,et al. A hexapeptide motif that electrostatically binds to the surface of titanium. , 2003, Journal of the American Chemical Society.
[121] Y. Mochizuki. A size-extensive modification of super-CI for orbital relaxation , 2005 .
[122] Kazuo Kitaura,et al. Extending the power of quantum chemistry to large systems with the fragment molecular orbital method. , 2007, The journal of physical chemistry. A.
[123] Takeshi Ishikawa,et al. Fragment molecular orbital calculation using the RI-MP2 method , 2009 .
[124] Kaori Fukuzawa,et al. Modeling of peptide–silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations , 2013 .
[125] Yuji Mochizuki,et al. Large scale MP2 calculations with fragment molecular orbital scheme , 2004 .
[126] T. Nakano,et al. Fragment molecular orbital calculations for excitation energies of blue- and yellow-fluorescent proteins , 2011 .
[127] Kaori Fukuzawa,et al. Accuracy of fragmentation in ab initio calculations of hydrated sodium cation , 2009 .
[128] Kaori Fukuzawa,et al. Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA) , 2010 .
[129] Noriyuki Kurita,et al. Molecular orbital analysis based on fragment molecular orbital scheme , 2003 .
[130] Takeshi Ishikawa,et al. Partial energy gradient based on the fragment molecular orbital method: Application to geometry optimization , 2010 .
[131] Yutaka Akiyama,et al. Fragment molecular orbital method: application to polypeptides , 2000 .
[132] Frédéric H.-T. Allain,et al. Sequence-specific binding of single-stranded RNA: is there a code for recognition? , 2006, Nucleic acids research.
[133] T. Nakano,et al. Dynamic polarizability calculation with fragment molecular orbital scheme , 2006 .
[134] Mark S. Gordon,et al. General atomic and molecular electronic structure system , 1993, J. Comput. Chem..
[135] Yuichi Inadomi,et al. Fragment Molecular Orbital (FMO) and FMO-MO Calculations of DNA: Accuracy Validation of Energy and Interfragment Interaction Energy , 2009 .
[136] K. Ando,et al. Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO-LCMO approach. , 2011, The Journal of chemical physics.
[137] Trygve Helgaker,et al. Ab Initio Methods for the Calculation of NMR Shielding and Indirect Spin-Spin Coupling Constants , 1999 .
[138] Y. Aoki,et al. Linear-scaled excited state calculations at linear response time-dependent Hartree–Fock theory , 2010 .
[139] P. Fulde,et al. An incremental coupled-cluster approach to metallic lithium , 2009 .
[140] Mark S Gordon,et al. Geometry optimizations of open-shell systems with the fragment molecular orbital method. , 2012, The journal of physical chemistry. A.
[141] Daniel Kats,et al. Sparse tensor framework for implementation of general local correlation methods. , 2013, The Journal of chemical physics.
[142] Yuto Komeiji,et al. Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin , 2007, J. Comput. Chem..
[143] Kazuo Kitaura,et al. Coupled-cluster theory based upon the fragment molecular-orbital method. , 2005, The Journal of chemical physics.
[144] K. Kitaura,et al. Unrestricted Hartree-Fock based on the fragment molecular orbital method: energy and its analytic gradient. , 2012, The Journal of chemical physics.
[145] Kazuo Kitaura,et al. Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method , 2009 .
[146] Kaori Fukuzawa,et al. Development of the four-body corrected fragment molecular orbital (FMO4) method , 2012 .
[147] Junwei Zhang,et al. VISCANA: Visualized Cluster Analysis of Protein-Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening , 2006, J. Chem. Inf. Model..
[148] Yang,et al. Direct calculation of electron density in density-functional theory. , 1991, Physical review letters.
[149] Shinichiro Nakamura,et al. Octahedral point-charge model and its application to fragment molecular orbital calculations of chemical shifts , 2014 .
[150] Alistair P. Rendell,et al. A direct coupled cluster algorithm for massively parallel computers , 1997 .
[151] Arieh Warshel,et al. Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches , 1993 .
[152] Kaori Ueno-Noto,et al. CHEMICAL DESCRIPTION OF THE INTERACTION BETWEEN GLYCAN LIGAND AND SIGLEC-7 USING AB INITIO FMO METHOD AND CLASSICAL MD SIMULATION , 2013 .
[153] Noriyuki Kurita,et al. DENSITY FUNCTIONAL CALCULATIONS ON THE INTERACTION BETWEEN CATABOLITE ACTIVATOR PROTEIN AND CYCLIC AMP USING THE FRAGMENT MOLECULAR ORBITAL METHOD , 2005 .
[154] Yuto Komeiji,et al. FMO-MD simulations on the hydration of formaldehyde in water solution with constraint dynamics. , 2012, Chemistry.
[155] Martin Head-Gordon,et al. Scaled opposite-spin second order Møller-Plesset correlation energy: an economical electronic structure method. , 2004, The Journal of chemical physics.
[156] Paulus,et al. Electron correlations for ground-state properties of group-IV semiconductors. , 1995, Physical review. B, Condensed matter.
[157] H. Stoll. Can incremental expansions cope with high-order coupled-cluster contributions? , 2010 .
[158] Mark S. Gordon,et al. Diffusion energy profiles in silica mesoporous molecular sieves modelled with the fragment molecular orbital method , 2013 .
[159] U. Dräger,et al. Retinoids in embryonal development. , 2000, Physiological reviews.
[160] Nuclear-Electronic Orbital Method within the Fragment Molecular Orbital Approach† , 2010 .
[161] Tetsuya Sakurai,et al. Parallel Fock matrix construction with distributed shared memory model for the FMO‐MO method , 2010, J. Comput. Chem..
[162] Mahito Chiba,et al. Electronic excitation energy calculation by the fragment molecular orbital method with three-body effects. , 2010, The Journal of chemical physics.
[163] Jing Ma,et al. Linear scaling local correlation approach for solving the coupled cluster equations of large systems , 2002, J. Comput. Chem..
[164] Kazuo Kitaura,et al. A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin. , 2011, The Journal of chemical physics.
[165] M. Klobukowski,et al. Model potentials for molecular calculations. I. The sd‐MP set for transition metal atoms Sc through Hg , 2022 .
[166] Y. Mochizuki,et al. 4f-in-core model core potentials for trivalent lanthanides , 2011 .
[167] Jan H. Jensen,et al. Covalent bond fragmentation suitable to describe solids in the fragment molecular orbital method. , 2008, The journal of physical chemistry. A.
[168] F. Verstraete,et al. Complete-graph tensor network states: a new fermionic wave function ansatz for molecules , 2010, 1004.5303.
[169] Mark Whittaker,et al. Compound Design by Fragment‐Linking , 2011, Molecular informatics.
[170] T. Nakano,et al. Does amination of formaldehyde proceed through a zwitterionic intermediate in water? Fragment molecular orbital molecular dynamics simulations by using constraint dynamics. , 2010, Chemistry.
[171] Kazuo Kitaura,et al. CHAPTER 1 – Theoretical development of the fragment molecular orbital (FMO) method , 2006 .
[172] Yuto Komeiji,et al. Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient , 2011 .
[173] Yuto Komeiji,et al. Fragment molecular orbital method: analytical energy gradients , 2001 .
[174] Y. Aoki,et al. Theoretical study on static (hyper)polarizabilities for polyimide by the elongation finite-field method , 2009 .
[175] Kenneth M Merz,et al. Acceleration of Electron Repulsion Integral Evaluation on Graphics Processing Units via Use of Recurrence Relations. , 2013, Journal of chemical theory and computation.
[176] P. J. Andralojc,et al. Manipulation of Rubisco: the amount, activity, function and regulation. , 2003, Journal of experimental botany.
[177] Umpei Nagashima,et al. Ab Initio MO-MD Simulation Based on the Fragment MO Method. A Case of (−)-Epicatechin Gallate with STO-3G Basis Set , 2008 .
[178] Martin Karplus,et al. Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization , 1972 .
[179] M. Shiga,et al. Ab initio path integral Monte Carlo simulations for water trimer with electron correlation effects , 2012 .
[180] Takeshi Ishikawa,et al. Fragment molecular orbital calculations on large scale systems containing heavy metal atom , 2006 .
[181] Michiel Sprik,et al. Free energy from constrained molecular dynamics , 1998 .
[182] Masami Uebayasi,et al. The fragment molecular orbital method for geometry optimizations of polypeptides and proteins. , 2007, The journal of physical chemistry. A.
[183] Kazuo Kitaura,et al. Importance of the hybrid orbital operator derivative term for the energy gradient in the fragment molecular orbital method , 2010 .
[184] Kotoko Nakata,et al. Ab initio quantum mechanical study of the binding energies of human estrogen receptor α with its ligands: An application of fragment molecular orbital method , 2005, J. Comput. Chem..
[185] A. Becke. Density-functional thermochemistry. III. The role of exact exchange , 1993 .
[186] Mika Ito,et al. Ab initio quantum-chemical study on emission spectra of bioluminescent luciferases by fragment molecular orbital method , 2009 .
[187] A. Kitao,et al. A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method. , 2013, Physical chemistry chemical physics : PCCP.
[188] Kaori Fukuzawa,et al. Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme , 2011 .
[189] Kaori Fukuzawa,et al. Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)–RNA complex system , 2010 .
[190] Masato Kobayashi,et al. Extension of linear-scaling divide-and-conquer-based correlation method to coupled cluster theory with singles and doubles excitations. , 2008, The Journal of chemical physics.
[191] Tjerk P. Straatsma,et al. NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations , 2010, Comput. Phys. Commun..
[192] M. Head‐Gordon,et al. Systematic optimization of long-range corrected hybrid density functionals. , 2008, The Journal of chemical physics.
[193] Takeshi Ishikawa,et al. RI-MP2 Gradient Calculation of Large Molecules Using the Fragment Molecular Orbital Method. , 2012, The journal of physical chemistry letters.
[194] G. Chan,et al. Entangled quantum electronic wavefunctions of the Mn₄CaO₅ cluster in photosystem II. , 2013, Nature chemistry.
[195] Takao Otsuka,et al. Trimer effects in fragment molecular orbital-linear combination of molecular orbitals calculation of one-electron orbitals for biomolecules. , 2013, The Journal of chemical physics.
[196] Jun Zhang,et al. Third-Order Incremental Dual-Basis Set Zero-Buffer Approach: An Accurate and Efficient Way To Obtain CCSD and CCSD(T) Energies. , 2013, Journal of chemical theory and computation.
[197] T. Nakano,et al. Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme , 2007 .
[198] Shinichiro Nakamura,et al. Ab initio NMR chemical shift calculations on proteins using fragment molecular orbitals with electrostatic environment , 2007 .
[199] Kazuya Ishimura,et al. Accuracy of the three‐body fragment molecular orbital method applied to Møller–Plesset perturbation theory , 2007, J. Comput. Chem..
[200] Yuto Komeiji,et al. Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems , 2009 .
[201] D. Yamaki,et al. The extension of the fragment molecular orbital method with the many-particle Green's function. , 2006, The Journal of chemical physics.
[202] S. Tanaka. Modulation of excitation energy transfer by conformational oscillations in biomolecular systems , 2011 .
[203] Wei Li,et al. Local correlation calculations using standard and renormalized coupled-cluster approaches. , 2009, The Journal of chemical physics.
[204] Dick B Janssen,et al. Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities. , 2005, Environmental microbiology.
[205] Mark S. Gordon,et al. The Distributed Data Interface in GAMESS , 2000 .
[206] E. Nobusawa,et al. Accumulation of Amino Acid Substitutions Promotes Irreversible Structural Changes in the Hemagglutinin of Human Influenza AH3 Virus during Evolution , 2005, Journal of Virology.
[207] Mark S Gordon,et al. Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method. , 2012, Journal of chemical theory and computation.
[208] Kazuo Kitaura,et al. Time-dependent density functional theory based upon the fragment molecular orbital method. , 2007, The Journal of chemical physics.
[209] Kazuo Kitaura,et al. Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method. , 2012, The Journal of chemical physics.
[210] S. Miyachi,et al. Ribulose-1,5-bisphosphate carboxylase/oxygenase from thermophilic red algae with a strong specificity for CO2 fixation. , 1997, Biochemical and biophysical research communications.
[211] Mark S. Gordon,et al. New Multithreaded Hybrid CPU/GPU Approach to Hartree-Fock. , 2012, Journal of chemical theory and computation.
[212] J. V. Von Roenn,et al. Antitumor activity of oral 9-cis-retinoic acid in HIV-associated Kaposi's sarcoma , 2002, AIDS.
[213] R. Bartlett,et al. Singular value decomposition approach for the approximate coupled-cluster method , 2003 .
[214] L. Regan,et al. Structure and function of KH domains , 2008, The FEBS journal.
[215] Kaori Fukuzawa,et al. Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid X receptor and its coactivator: roles of helix 12 in the coactivator binding mechanism. , 2007, The journal of physical chemistry. B.
[216] Christine M. Isborn,et al. Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units , 2011, Journal of chemical theory and computation.
[217] D. Macfarlane,et al. Large-scale ab initio calculations of archetypical ionic liquids. , 2012, Chemical communications.
[218] Werner Kutzelnigg,et al. How many‐body perturbation theory (MBPT) has changed quantum chemistry , 2009 .
[219] Kaori Fukuzawa,et al. A configuration analysis for fragment interaction , 2005 .
[220] Hiroaki Tokiwa,et al. Theoretical study of intramolecular interaction energies during dynamics simulations of oligopeptides by the fragment molecular orbital-Hamiltonian algorithm method. , 2005, The Journal of chemical physics.
[221] Roland Lindh,et al. Utilizing high performance computing for chemistry: parallel computational chemistry. , 2010, Physical chemistry chemical physics : PCCP.
[222] Pekka Pyykkö,et al. Relativistic effects in structural chemistry , 1988 .
[223] S. Grimme. Improved second-order Møller–Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies , 2003 .
[224] Michael A Collins,et al. Accuracy and efficiency of electronic energies from systematic molecular fragmentation. , 2006, The Journal of chemical physics.
[225] M. Parrinello,et al. AB INITIO PATH INTEGRAL MOLECULAR DYNAMICS : BASIC IDEAS , 1996 .
[226] K. Umesono,et al. The nuclear receptor superfamily: The second decade , 1995, Cell.
[227] D. Jordan,et al. Species variation in the specificity of ribulose biphosphate carboxylase/oxygenase , 1981, Nature.
[228] Kaori Fukuzawa,et al. Possibility of mutation prediction of influenza hemagglutinin by combination of hemadsorption experiment and quantum chemical calculation for antibody binding. , 2009, The journal of physical chemistry. B.
[229] Spencer R Pruitt,et al. Fragmentation methods: a route to accurate calculations on large systems. , 2012, Chemical reviews.
[230] Yuji Mochizuki,et al. Acceleration of fragment molecular orbital calculations with Cholesky decomposition approach , 2010 .
[231] K. Kitaura,et al. Mathematical Formulation of the Fragment Molecular Orbital Method , 2011 .
[232] K. Kitaura,et al. Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method. , 2011, The Journal of chemical physics.
[233] Robert M Parrish,et al. Tensor hypercontraction. II. Least-squares renormalization. , 2012, The Journal of chemical physics.
[234] Hui Li,et al. Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation , 2009, J. Comput. Chem..
[235] Heather Netzloff,et al. Ab initio energies of nonconducting crystals by systematic fragmentation. , 2007, The Journal of chemical physics.
[236] Daniel Kats,et al. Communication: The distinguishable cluster approximation. , 2013, The Journal of chemical physics.
[237] Michael J. Frisch,et al. Toward a systematic molecular orbital theory for excited states , 1992 .
[238] T. Sakurai,et al. A projection method for generalized eigenvalue problems using numerical integration , 2003 .
[239] Mark S. Gordon,et al. A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO) , 2004, J. Comput. Chem..
[240] G. Varani,et al. Recent advances in RNA-protein recognition. , 2001, Current opinion in structural biology.
[241] Takeshi Ishikawa,et al. Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits). , 2009, The journal of physical chemistry. B.
[242] Kazuo Kitaura,et al. Analytic gradient for the embedding potential with approximations in the fragment molecular orbital method , 2012 .
[243] Kaori Fukuzawa,et al. Application of the fragment molecular orbital method for determination of atomic charges on polypeptides , 2007 .
[244] K. Kitaura,et al. The Fragment Molecular Orbital–Based Time- Dependent Density Functional Theory for Excited States in Large Systems , 2009 .
[245] Le Chang,et al. Protein‐specific force field derived from the fragment molecular orbital method can improve protein–ligand binding interactions , 2013, J. Comput. Chem..
[246] Yuto Komeiji,et al. Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method. , 2007, Biophysical chemistry.
[247] Kazuo Kitaura,et al. Polarizable continuum model with the fragment molecular orbital‐based time‐dependent density functional theory , 2008, J. Comput. Chem..
[248] The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method. , 2009, The Journal of chemical physics.
[249] Nicholas J Mayhall,et al. Many-Overlapping-Body (MOB) Expansion: A Generalized Many Body Expansion for Nondisjoint Monomers in Molecular Fragmentation Calculations of Covalent Molecules. , 2012, Journal of chemical theory and computation.
[250] Takeshi Ishikawa,et al. A fully quantum mechanical simulation study on the lowest n-π* state of hydrated formaldehyde , 2007 .
[251] Low-rank configuration interaction with orbital optimization - the LR SCF approach , 1988 .
[252] R. Bartlett,et al. Coupled-cluster theory in quantum chemistry , 2007 .
[253] Wei Li,et al. Improved design of orbital domains within the cluster-in-molecule local correlation framework: single-environment cluster-in-molecule ansatz and its application to local coupled-cluster approach with singles and doubles. , 2010, The journal of physical chemistry. A.
[254] K. Kitaura,et al. Open-shell pair interaction energy decomposition analysis (PIEDA): formulation and application to the hydrogen abstraction in tripeptides. , 2013, The Journal of chemical physics.
[255] Koji Yasuda,et al. Two‐electron integral evaluation on the graphics processor unit , 2008, J. Comput. Chem..
[256] Markus Reiher,et al. New electron correlation theories for transition metal chemistry. , 2011, Physical chemistry chemical physics : PCCP.
[257] Kaori Ueno-Noto,et al. A theoretical study of the physicochemical mechanisms associated with DNA recognition modulation in artificial zinc-finger proteins. , 2011, The journal of physical chemistry. B.
[258] Frederick R Manby,et al. Tensor factorizations of local second-order Møller-Plesset theory. , 2010, The Journal of chemical physics.
[259] Kaori Fukuzawa,et al. Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design. , 2013, Journal of molecular graphics & modelling.
[260] Takeshi Ishikawa,et al. Fragment molecular orbital calculations on red fluorescent protein (DsRed) , 2007 .
[261] M. Gordon,et al. A combined effective fragment potential-fragment molecular orbital method. I. The energy expression and initial applications. , 2009, The Journal of chemical physics.
[262] Poul Jørgensen,et al. The divide-expand-consolidate family of coupled cluster methods: numerical illustrations using second order Møller-Plesset perturbation theory. , 2012, The Journal of chemical physics.
[263] Kazuo Kitaura,et al. Exploring chemistry with the fragment molecular orbital method. , 2012, Physical chemistry chemical physics : PCCP.
[264] Umpei Nagashima,et al. A parallelized integral-direct second-order Møller–Plesset perturbation theory method with a fragment molecular orbital scheme , 2004 .
[265] Heather J Kulik,et al. Ab initio quantum chemistry for protein structures. , 2012, The journal of physical chemistry. B.
[266] J. Olsen,et al. Linear and nonlinear response functions for an exact state and for an MCSCF state , 1985 .
[267] Hui Li,et al. The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO) , 2006, J. Comput. Chem..
[268] G. Voth,et al. Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations. , 2013, Journal of chemical theory and computation.
[269] Yuri Alexeev,et al. GAMESS as a free quantum-mechanical platform for drug research. , 2012, Current topics in medicinal chemistry.
[270] Alán Aspuru-Guzik,et al. Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units , 2010, Computing in Science & Engineering.
[271] J. Schwabe,et al. Mechanism of the nuclear receptor molecular switch. , 2004, Trends in biochemical sciences.
[272] K. Kitaura,et al. Time-dependent density functional theory with the multilayer fragment molecular orbital method , 2007 .
[273] Shridhar R. Gadre,et al. Molecular tailoring approach in conjunction with MP2 and Ri‐MP2 codes: A comparison with fragment molecular orbital method , 2010, J. Comput. Chem..
[274] N. H. Beebe,et al. Simplifications in the generation and transformation of two‐electron integrals in molecular calculations , 1977 .
[275] Noriyuki Kurita,et al. Fragment molecular orbital method with density functional theory and DIIS convergence acceleration , 2003 .
[276] Kaori Fukuzawa,et al. Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations. , 2011, Journal of molecular graphics & modelling.
[277] Branislav Jansík,et al. Linear scaling coupled cluster method with correlation energy based error control. , 2010, The Journal of chemical physics.
[278] Kiyoyuki Terakura,et al. Molecular orbital calculation of biomolecules with fragment molecular orbitals , 2009 .
[279] M. Levitt,et al. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.
[280] R. J. Spreitzer. Questions about the complexity of chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase , 1999, Photosynthesis Research.
[281] Kaori Fukuzawa,et al. Antigen–antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation , 2011 .
[282] Shigenori Tanaka,et al. Intra‐ and intermolecular interactions between cyclic‐AMP receptor protein and DNA: Ab initio fragment molecular orbital study , 2006, J. Comput. Chem..
[283] Kazuo Kitaura,et al. Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method. , 2004, The Journal of chemical physics.
[284] Jan H. Jensen,et al. Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method , 2009 .
[285] Michio Katouda. Application of resolution of identity approximation of second-order Møller–Plesset perturbation theory to three-body fragment molecular orbital method , 2011 .
[286] Nicholas J Mayhall,et al. Molecules-in-Molecules: An Extrapolated Fragment-Based Approach for Accurate Calculations on Large Molecules and Materials. , 2011, Journal of chemical theory and computation.
[287] Michael Dolg,et al. Implementation and performance of a domain-specific basis set incremental approach for correlation energies: applications to hydrocarbons and a glycine oligomer. , 2008, The Journal of chemical physics.
[288] Y. Komeiji,et al. Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) , 2012 .
[289] Shigenori Tanaka,et al. Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method , 2009 .
[290] Dmitri G. Fedorov,et al. Reducing the scaling of the fragment molecular orbital method using the multipole method , 2012 .
[291] Takeshi Ishikawa,et al. How does an S(N)2 reaction take place in solution? Full ab initio MD simulations for the hydrolysis of the methyl diazonium ion. , 2008, Journal of the American Chemical Society.
[292] Michael Dolg,et al. Fully automated implementation of the incremental scheme: application to CCSD energies for hydrocarbons and transition metal compounds. , 2007, The Journal of chemical physics.
[293] Feng Long Gu,et al. Describing electron correlation effects in the framework of the elongation method—Elongation‐MP2: Formalism, implementation and efficiency , 2009, J. Comput. Chem..
[294] Tetsuya Sakurai,et al. A parallel eigensolver using contour integration for generalized eigenvalue problems in molecular simulation , 2010 .
[295] Kazuo Kitaura,et al. On the accuracy of the 3-body fragment molecular orbital method (FMO) applied to density functional theory , 2004 .
[296] M. Reiher,et al. Decomposition of density matrix renormalization group states into a Slater determinant basis. , 2007, The Journal of chemical physics.
[297] Shigenori Tanaka,et al. Fragment molecular orbital calculations under periodic boundary condition , 2011 .
[298] Christof Hättig,et al. Explicitly correlated electrons in molecules. , 2012, Chemical reviews.
[299] Kazuo Kitaura,et al. The three-body fragment molecular orbital method for accurate calculations of large systems , 2006 .
[300] Ryo Maezono,et al. Fragmentation Method Combined with Quantum Monte Carlo Calculations(Atomic and molecular physics) , 2007 .
[301] Kaori Fukuzawa,et al. Partial geometry optimization with FMO-MP2 gradient: Application to TrpCage , 2012 .
[302] Sriram Krishnamoorthy,et al. GPU-Based Implementations of the Noniterative Regularized-CCSD(T) Corrections: Applications to Strongly Correlated Systems. , 2011, Journal of chemical theory and computation.
[303] Nicholas C. Handy,et al. Size-consistent Brueckner theory limited to double substitutions , 1989 .
[304] K. Kitaura,et al. Excited state geometry optimizations by time-dependent density functional theory based on the fragment molecular orbital method , 2009 .
[305] Roland Lindh,et al. Density fitting with auxiliary basis sets from Cholesky decompositions , 2009 .