D. Fedorov

发表

Role of the key mutation in the selective binding of avian and human influenza hemagglutinin to sialosides revealed by quantum-mechanical calculations.

Kazuo Kitaura, Dmitri G Fedorov, K. Kitaura, 2010, Journal of the American Chemical Society.

Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method.

Kazuo Kitaura, Dmitri G Fedorov, K. Kitaura, 2004, The Journal of chemical physics.

On the accuracy of the 3-body fragment molecular orbital method (FMO) applied to density functional theory

Kazuo Kitaura, Dmitri G. Fedorov, K. Kitaura, 2004 .

The importance of three-body terms in the fragment molecular orbital method.

Kazuo Kitaura, Dmitri G Fedorov, K. Kitaura, 2004, The Journal of chemical physics.

Multiconfiguration self-consistent-field theory based upon the fragment molecular orbital method.

Kazuo Kitaura, Dmitri G Fedorov, K. Kitaura, 2005, The Journal of chemical physics.

Multilayer formulation of the fragment molecular orbital method (FMO).

K. Kitaura, D. Fedorov, Toyokazu Ishida, 2005, The journal of physical chemistry. A.

Coupled-cluster theory based upon the fragment molecular-orbital method.

Kazuo Kitaura, Dmitri G Fedorov, K. Kitaura, 2005, The Journal of chemical physics.

All electron quantum chemical calculation of the entire enzyme system confirms a collective catalytic device in the chorismate mutase reaction.

Kazuo Kitaura, Toyokazu Ishida, Dmitri G Fedorov, 2006, The journal of physical chemistry. B.

The three-body fragment molecular orbital method for accurate calculations of large systems

Kazuo Kitaura, Dmitri G. Fedorov, K. Kitaura, 2006 .

CHAPTER 1 – Theoretical development of the fragment molecular orbital (FMO) method

Kazuo Kitaura, Dmitri G. Fedorov, K. Kitaura, 2006 .

Time-dependent density functional theory based upon the fragment molecular orbital method.

Kazuo Kitaura, Mahito Chiba, Dmitri G Fedorov, 2007, The Journal of chemical physics.

Extending the power of quantum chemistry to large systems with the fragment molecular orbital method.

Kazuo Kitaura, Dmitri G Fedorov, K. Kitaura, 2007, The journal of physical chemistry. A.

Time-dependent density functional theory with the multilayer fragment molecular orbital method

K. Kitaura, D. Fedorov, Mahito Chiba, 2007 .

Ab initio NMR chemical shift calculations on proteins using fragment molecular orbitals with electrostatic environment

Shinichiro Nakamura, Kazuo Kitaura, Dmitri G. Fedorov, 2007 .

Molecular recognition mechanism of FK506 binding protein: An all‐electron fragment molecular orbital study

Kazuo Kitaura, Dmitri G Fedorov, K. Kitaura, 2007, Proteins.

The fragment molecular orbital method for geometry optimizations of polypeptides and proteins.

Masami Uebayasi, Kazuo Kitaura, Toyokazu Ishida, 2007, The journal of physical chemistry. A.

Theoretical analysis of the intermolecular interaction effects on the excitation energy of organic pigments: solid state quinacridone.

Kazuo Kitaura, Mahito Chiba, Dmitri G Fedorov, 2008, The journal of physical chemistry. A.

Covalent bond fragmentation suitable to describe solids in the fragment molecular orbital method.

Jan H. Jensen, Kazuo Kitaura, Jan H Jensen, 2008, The journal of physical chemistry. A.

Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method

Kazuo Kitaura, Dmitri G. Fedorov, K. Kitaura, 2009 .

Structural and interaction analysis of helical heparin oligosaccharides with the fragment molecular orbital method

Kazuo Kitaura, Dmitri G. Fedorov, K. Kitaura, 2009 .

The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems

Kazuo Kitaura, Dmitri G. Fedorov, K. Kitaura, 2009 .

Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems

Yuto Komeiji, Yuji Mochizuki, Dmitri G. Fedorov, 2009 .

A combined effective fragment potential-fragment molecular orbital method. I. The energy expression and initial applications.

M. Gordon, K. Kitaura, D. Fedorov, 2009, The Journal of chemical physics.

Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method

Jan H. Jensen, Kazuo Kitaura, Dmitri G. Fedorov, 2009 .

Excited state geometry optimizations by time-dependent density functional theory based on the fragment molecular orbital method

K. Kitaura, D. Fedorov, T. Nagata, 2009 .

Importance of the hybrid orbital operator derivative term for the energy gradient in the fragment molecular orbital method

Kazuo Kitaura, Dmitri G. Fedorov, K. Kitaura, 2010 .

Effective fragment molecular orbital method: a merger of the effective fragment potential and fragment molecular orbital methods.

Jan H. Jensen, Casper Steinmann, Jan H Jensen, 2010, The journal of physical chemistry. A.

Fragment-Molecular-Orbital-Method-Based ab Initio NMR Chemical-Shift Calculations for Large Molecular Systems

K. Kitaura, M. Sakurai, S. Yokojima, 2010 .

Systematic study of the embedding potential description in the fragment molecular orbital method.

K. Kitaura, L. Slipchenko, D. Fedorov, 2010, The journal of physical chemistry. A.

Binding of influenza A virus hemagglutinin to the sialoside receptor is not controlled by the homotropic allosteric effect.

Kazuo Kitaura, Dmitri G Fedorov, K. Kitaura, 2010, The journal of physical chemistry. B.

Fully analytic energy gradient in the fragment molecular orbital method.

Kazuo Kitaura, Mark S Gordon, Dmitri G Fedorov, 2011, The Journal of chemical physics.

Geometry Optimization of the Active Site of a Large System with the Fragment Molecular Orbital Method

Yuri Alexeev, Kazuo Kitaura, Dmitri G. Fedorov, 2011 .

A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin.

Kazuo Kitaura, Mark S Gordon, Dmitri G Fedorov, 2011, The Journal of chemical physics.

Mathematical Formulation of the Fragment Molecular Orbital Method

K. Kitaura, D. Fedorov, T. Nagata, 2011 .

Recent Development of the Fragment Molecular Orbital Method in GAMESS

D. Fedorov, 2021, Recent Advances of the Fragment Molecular Orbital Method.

Multi-Level Parallelization of the Fragment Molecular Orbital Method in GAMESS

Spencer R Pruitt, M. Gordon, D. Fedorov, 2021 .

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

Dmitri G. Fedorov, D. Fedorov, 2017 .

Energy decomposition analysis in solution based on the fragment molecular orbital method.

K. Kitaura, D. Fedorov, 2012, The journal of physical chemistry. A.

The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

Jan H. Jensen, Casper Steinmann, Dmitri G. Fedorov, 2012, PloS one.

GAMESS as a free quantum-mechanical platform for drug research.

Yuri Alexeev, Michael P Mazanetz, Michael P. Mazanetz, 2012, Current topics in medicinal chemistry.

Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method.

Kazuo Kitaura, Hui Li, Dmitri G Fedorov, 2012, The Journal of chemical physics.

Geometry optimizations of open-shell systems with the fragment molecular orbital method.

Mark S Gordon, Spencer R Pruitt, Dmitri G Fedorov, 2012, The journal of physical chemistry. A.

Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method.

K. Kitaura, D. Fedorov, T. Nagata, 2011, The Journal of chemical physics.

Fragment molecular orbital method: application to molecular dynamics simulation, ‘ab initio FMO-MD’

Yuichi Inadomi, Yutaka Ueno, Yuto Komeiji, 2003 .

An experimental and theoretical study of the spin–orbit interaction for CO+(A 2Π3/2,1/2, v+=0–41) and O2+(X 2Π3/2,1/2g, v+=0–38)

M. Gordon, Yang Song, D. Fedorov, 1999 .

Recent developments in the general atomic and molecular electronic structure system.

Michael W. Schmidt, Alistair P. Rendell, Bryce M. Westheimer, 2020, The Journal of chemical physics.

Polarization energies in the fragment molecular orbital method

D. Fedorov, 2022, J. Comput. Chem..

Partitioning of the Vibrational Free Energy.

D. Fedorov, 2021, The journal of physical chemistry letters.

Analytic first and second derivatives of the energy in the fragment molecular orbital method combined with molecular mechanics

D. Fedorov, H. Nakata, 2020 .

Three-Body Energy Decomposition Analysis Based on the Fragment Molecular Orbital Method.

D. Fedorov, 2020, The journal of physical chemistry. A.

Partition Analysis for Density-Functional Tight-Binding.

D. Fedorov, 2020, The journal of physical chemistry. A.

Fragmentation methods: a route to accurate calculations on large systems.

Spencer R Pruitt, M. Gordon, L. Slipchenko, 2012, Chemical reviews.

Exploring chemistry with the fragment molecular orbital method.

Kazuo Kitaura, Dmitri G Fedorov, K. Kitaura, 2012, Physical chemistry chemical physics : PCCP.

Efficient parallel implementations of QM/MM-REMD (quantum mechanical/molecular mechanics-replica-exchange MD) and umbrella sampling: isomerization of H2O2 in aqueous solution.

Yuji Sugita, Cheol Ho Choi, Dmitri G Fedorov, 2013, The journal of physical chemistry. B.

Analytic second derivatives of the energy in the fragment molecular orbital method.

Shinichiro Nakamura, Kazuo Kitaura, Satoshi Yokojima, 2013, The Journal of chemical physics.

Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method.

M. Gordon, Kurt R. Brorsen, D. Fedorov, 2014, Journal of chemical theory and computation.

Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method.

Stephan Irle, Yoshio Nishimoto, Dmitri G Fedorov, 2014, Journal of chemical theory and computation.

Efficient vibrational analysis for unrestricted Hartree–Fock based on the fragment molecular orbital method

Shinichiro Nakamura, Kazuo Kitaura, Dmitri G. Fedorov, 2014 .

Unrestricted density functional theory based on the fragment molecular orbital method for the ground and excited state calculations of large systems.

K. Kitaura, M. Sakurai, S. Yokojima, 2014, The Journal of chemical physics.

Use of an auxiliary basis set to describe the polarization in the fragment molecular orbital method

K. Kitaura, D. Fedorov, 2014 .

Extension of the fragment molecular orbital method to treat large open-shell systems in solution

K. Kitaura, Shinichiro Nakamura, D. Fedorov, 2015 .

Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method.

Stephan Irle, Yoshio Nishimoto, S. Irle, 2015, The journal of physical chemistry letters.

Third-order density-functional tight-binding combined with the fragment molecular orbital method

Stephan Irle, Dmitri G. Fedorov, Yoshio Nishimoto, 2015 .

Analytic second derivative of the energy for density-functional tight-binding combined with the fragment molecular orbital method.

Yoshio Nishimoto, Dmitri G Fedorov, D. Fedorov, 2016, The Journal of chemical physics.

Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method.

Yuri Alexeev, Kazuo Kitaura, Mark S Gordon, 2016, Journal of chemical theory and computation.

Many-body expansion of the Fock matrix in the fragment molecular orbital method.

K. Kitaura, D. Fedorov, 2017, The Journal of chemical physics.

Adaptive frozen orbital treatment for the fragment molecular orbital method combined with density-functional tight-binding.

D. Fedorov, Y. Nishimoto, 2018, The Journal of chemical physics.

Pair Interaction Energy Decomposition Analysis for Density Functional Theory and Density-Functional Tight-Binding with an Evaluation of Energy Fluctuations in Molecular Dynamics.

K. Kitaura, D. Fedorov, 2018, The journal of physical chemistry. A.

Simulations of infrared and Raman spectra in solution using the fragment molecular orbital method.

D. Fedorov, H. Nakata, 2019, Physical chemistry chemical physics : PCCP.

The use of many-body expansions and geometry optimizations in fragment-based methods.

K. Kitaura, D. Fedorov, I. Nakanishi, 2014, Accounts of chemical research.

Spin-orbit multireference multistate perturbation theory

D. Fedorov, J. Finley, 2001 .

Multi-Focus Imaging using Local Focus Estimation and Mosaicking

B. S. Manjunath, Dmitri G. Fedorov, Baris Sumengen, 2006, 2006 International Conference on Image Processing.

Geometry Optimization, Transition State Search, and Reaction Path Mapping Accomplished with the Fragment Molecular Orbital Method.

D. Fedorov, H. Nakata, 2020, Methods in molecular biology.

Empirical corrections and pair interaction energies in the fragment molecular orbital method

Jan H. Jensen, Jimmy C. Kromann, J. H. Jensen, 2018, Chemical Physics Letters.

Analysis of solute-solvent interactions using the solvation model density combined with the fragment molecular orbital method

D. Fedorov, 2018, Chemical Physics Letters.

Group molecular orbital approach to solve the Huzinaga subsystem self-consistent-field equations.

K. Kitaura, D. Fedorov, T. Shimazaki, 2017, The Journal of chemical physics.

Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein-Ligand Binding in Solution.

K. Kitaura, D. Fedorov, 2016, The journal of physical chemistry. A.

Efficient Geometry Optimization of Large Molecular Systems in Solution Using the Fragment Molecular Orbital Method.

D. Fedorov, H. Nakata, 2016, The journal of physical chemistry. A.

Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method.

K. Kitaura, Shinichiro Nakamura, D. Fedorov, 2015, Journal of chemical theory and computation.

Applications of the Fragment Molecular Orbital Method to Drug Research

Ewa I. Chudyk, Michael P. Mazanetz, D. Fedorov, 2015 .

Hybrid RHF/MP2 Geometry Optimizations with the Effective Fragment Molecular Orbital Method

Anders S. Christensen, J. H. Jensen, D. Fedorov, 2013, PloS one.

Simulations of Raman Spectra Using the Fragment Molecular Orbital Method.

K. Kitaura, S. Yokojima, Shinichiro Nakamura, 2014, Journal of chemical theory and computation.

Effective ion mobility calculations for macromolecules by scattering on electron clouds.

A. Shvartsburg, D. Fedorov, Y. Alexeev, 2014, The journal of physical chemistry. A.

Derivatives of the approximated electrostatic potentials in unrestricted Hartree–Fock based on the fragment molecular orbital method and an application to polymer radicals

K. Kitaura, S. Yokojima, Shinichiro Nakamura, 2014, Theoretical Chemistry Accounts.

Efficient molecular dynamics simulations of multiple radical center systems based on the fragment molecular orbital method.

Michael W. Schmidt, M. Gordon, K. Kitaura, 2014, The journal of physical chemistry. A.

Syddansk Universitet Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method : Towards all ab initio

Svendsen, D. Fedorov, Casper Steinmann, 2013 .

Hexamers and witchamers: Which hex do you choose?

Spencer R Pruitt, Sarom S. Leang, M. Gordon, 2013 .

Open-shell pair interaction energy decomposition analysis (PIEDA): formulation and application to the hydrogen abstraction in tripeptides.

K. Kitaura, L. Slipchenko, J. S. Francisco, 2013, The Journal of chemical physics.

Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

Jan H. Jensen, J. H. Jensen, D. Fedorov, 2012, PloS one.

Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method combined with effective potentials

K. Kitaura, D. Fedorov, T. Nagata, 2012, Theoretical Chemistry Accounts.

Unrestricted Hartree-Fock based on the fragment molecular orbital method: energy and its analytic gradient.

K. Kitaura, S. Yokojima, Shinichiro Nakamura, 2012, The Journal of chemical physics.

The Fragment Molecular Orbital–Based Time- Dependent Density Functional Theory for Excited States in Large Systems

K. Kitaura, D. Fedorov, Mahito Chiba, 2009 .

Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method

M. Babu, M. Bodkin, Iñaki Morao, 2020, Journal of chemical theory and computation.

Multiscale Simulations on Charge Transport in Covalent Organic Frameworks Including Dynamics of Transfer Integrals from the FMO-DFTB/LCMO Approach

K. Welke, S. Irle, Hirotaka Kitoh-Nishioka, 2017 .

A study of the relative importance of one and two-electron contributions to spin–orbit coupling

M. Gordon, D. Fedorov, 2000 .

Exploring GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method.

Ewa I. Chudyk, M. Bodkin, Iñaki Morao, 2018, Methods in molecular biology.

Pharmaceutical Industry—Academia Cooperation

P. Coveney, M. Bodkin, Iñaki Morao, 2021, Recent Advances of the Fragment Molecular Orbital Method.

Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method.

M. Bodkin, Iñaki Morao, A. Heifetz, 2020, Methods in molecular biology.

Characterising GPCR-ligand interactions using a fragment molecular orbital-based approach.

M. Bodkin, Iñaki Morao, A. Heifetz, 2019, Current opinion in structural biology.

Aptamer-Conjugated Superparamagnetic Ferroarabinogalactan Nanoparticles for Targeted Magnetodynamic Therapy of Cancer

Yury E. Glazyrin, T. Zamay, Y. Glazyrin, 2020, Cancers.

Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers

Kelvin H.-C. Chen, D. V. Veprintsev, V. de Franciscis, 2022, Chemistry.

Accurate Scoring in Seconds with the Fragment Molecular Orbital and Density-Functional Tight-Binding Methods.

Iñaki Morao, A. Heifetz, D. Fedorov, 2020, Methods in molecular biology.

Hotspot Identification and Drug Design of Protein-Protein Interaction Modulators Using the Fragment Molecular Orbital Method

M. Bodkin, A. Heifetz, D. Fedorov, 2022, J. Chem. Inf. Model..

New symmetric families of silicon quantum dots and their conglomerates as a tunable source of photoluminescence in nanodevices

M. Gordon, L. Chernozatonskii, P. Sorokin, 2007, 0709.2279.

Analyzing Interactions with the Fragment Molecular Orbital Method.

D. Fedorov, 2020, Methods in molecular biology.

Photodissociation of alkyl and aryl iodides and effect of fluorination: Analysis of proposed mechanisms and vertical excitations by spin–orbit ab initio study

K. Hirao, D. Fedorov, J. Finley, 2002 .

FMO-MD: An Ab Initio-Based Molecular Dynamics of Large Systems

K. Kitaura, D. Fedorov, 2009 .

High-capacity electrode material BC 3 for lithium batteries proposed by ab initio simulations

D. Fedorov, P. Avramov, A. Kuzubov, 2012 .

Theoretical study of spin-orbit coupling constants for O2+(A 2Π3/2,1/2u,v+=0–17 and a 4Π5/2,3/2,1/2,−1/2u,v+=0–25)

M. Gordon, Yang Song, D. Fedorov, 2001 .

Spin–orbit coupling with model core potentials

D. Fedorov, M. Klobukowski, 2002 .

Theoretical study of the unusual potential energy curve of the A 1Σ+ state of AgH

K. Hirao, Per-Olof Widmark, H. Witek, 2002 .

Theoretical study of spin-orbit coupling in molecules

D. Fedorov, 1999 .

Natural Spinors Reveal How the Spin-Orbit Coupling Affects the Jahn-Teller Distortions in the Hexafluorotungstate(V) Anion.

Michael W. Schmidt, D. Fedorov, M. Klobukowski, 2012, Journal of chemical theory and computation.

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides

V. Sládek, D. Fedorov, 2022, International journal of molecular sciences.

Characterising protein-protein interactions with the fragment molecular orbital method

V. Sládek, A. Heifetz, D. Fedorov, 2020 .

Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method.

V. Sládek, A. Heifetz, D. Fedorov, 2020, Methods in molecular biology.

Fluorescence and photoinduced proton transfer in the protolytic forms of fluorescein: Experimental and computational study

D. Fedorov, S. Ovchinnikov, F. Tomilin, 2020 .

Detailed Electronic Structure Studies Revealing the Nature of Protein–Ligand Binding

K. Kitaura, D. Fedorov, I. Nakanishi, 2009 .

A systematic study of minima in alanine dipeptide

Vladimir Mironov, Yuri Alexeev, Vikram Khipple Mulligan, 2018, J. Comput. Chem..

An ab initio study of excited states of U and UF

K. Hirao, D. Fedorov, T. Nakajima, 2003 .

Pair interaction energy decomposition analysis

Kazuo Kitaura, Dmitri G. Fedorov, K. Kitaura, 2007, J. Comput. Chem..

Spin-orbit coupling in molecules: Chemistry beyond the adiabatic approximation

Michael W. Schmidt, M. Gordon, D. Fedorov, 2003 .

Reducing the scaling of the fragment molecular orbital method using the multipole method

Dmitri G. Fedorov, Cheol Ho Choi, D. Fedorov, 2012 .

Band-gap unification of partially Si-substituted single-wall carbon nanotubes

P. Sorokin, D. Fedorov, P. Avramov, 2006, 0709.2573.

Spin-Orbit Splittings in the Third-Row Transition Elements: Comparison of Effective Nuclear Charge and Full Breit-Pauli Calculations

Michael W. Schmidt, M. Gordon, D. Fedorov, 2001 .

Unusual shift in the visible absorption spectrum of an active ctenophore photoprotein elucidated by time-dependent density functional theory

E. Vysotski, D. Fedorov, P. Avramov, 2021, Photochemical & Photobiological Sciences.

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

A. V. Krat, T. Zamay, O. Kolovskaya, 2021, Molecular therapy. Nucleic acids.

Intrinsic Edge Asymmetry in Narrow Zigzag Hexagonal Heteroatomic Nanoribbons Causes their Subtle Uniform Curvature

Yoshihiro Matsumoto, Dmitri G. Fedorov, Pavel Sorokin, 2012 .

Fragment molecular orbital study of the electronic excitations in the photosynthetic reaction center of Blastochloris viridis

Yuichi Inadomi, Hiroaki Umeda, Satoshi Sekiguchi, 2009, J. Comput. Chem..

Effects of Spin-Orbit Coupling on Covalent Bonding and the Jahn-Teller Effect Are Revealed with the Natural Language of Spinors.

Michael W. Schmidt, Tao Zeng, Mariusz Klobukowski, 2011, Journal of chemical theory and computation.

Multireference study of spin-orbit coupling in the hydrides of the 6p-block elements using the model core potential method.

D. Fedorov, M. Klobukowski, Tao Zeng, 2010, The Journal of chemical physics.

Application of the Fragment Molecular Orbital Method to Organic Charge Transport Materials in Xerography: A Feasibility Study and a Charge Mobility Analysis

K. Kitaura, D. Fedorov, I. Fujino, 2021 .

Locating minimum energy crossings of different spin states using the fragment molecular orbital method.

D. Fedorov, Y. Alexeev, Danil S. Kaliakin, 2019, Journal of chemical theory and computation.

Accuracy of the three‐body fragment molecular orbital method applied to Møller–Plesset perturbation theory

Kazuya Ishimura, Peter Pulay, Shigeru Nagase, 2007, J. Comput. Chem..

Bisque: a platform for bioimage analysis and management

Ambuj K. Singh, B. S. Manjunath, Boguslaw Obara, 2009, Bioinform..

Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method.

Michael W. Schmidt, Shinichiro Nakamura, Kazuo Kitaura, 2015, The Journal of chemical physics.

Quantum dots embedded into silicon nanowires effectively partition electron confinement

L. Chernozatonskii, S. Ovchinnikov, P. Sorokin, 2008 .

A theoretical study of the reaction of Ti + with ethane

M. Gordon, D. Fedorov, J. Moc, 2000 .

Open-Shell Formulation of the Fragment Molecular Orbital Method.

Spencer R Pruitt, M. Gordon, K. Kitaura, 2010, Journal of chemical theory and computation.

Band structure and chemical bonding in Cu2O and Ag2O oxides

D. Fedorov, A. B. Gordienko, Y. Zhuravlev, 2007 .

Atomic and Electronic Structure of New Hollow-Based Symmetric Families of Silicon Nanoclusters

M. Gordon, L. Chernozatonskii, P. Sorokin, 2007 .

Diffusion energy profiles in silica mesoporous molecular sieves modelled with the fragment molecular orbital method

Mark S. Gordon, Dmitri G. Fedorov, M. Gordon, 2013 .

The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding.

B. Sumpter, S. Irle, V. Vuong, 2019, Journal of chemical theory and computation.

Performance of dynamically weighted multiconfiguration self-consistent field and spin-orbit coupling calculations of diatomic molecules of Group 14 elements.

D. Fedorov, M. Klobukowski, Tao Zeng, 2011, The Journal of chemical physics.

Model core potentials of p-block elements generated considering the Douglas-Kroll relativistic effects, suitable for accurate spin-orbit coupling calculations.

D. Fedorov, M. Klobukowski, Tao Zeng, 2010, The Journal of chemical physics.

Octahedral point-charge model and its application to fragment molecular orbital calculations of chemical shifts

Shinichiro Nakamura, Minoru Sakurai, Kazuo Kitaura, 2014 .

Three‐body expansion of the fragment molecular orbital method combined with density‐functional tight‐binding

Dmitri G. Fedorov, Yoshio Nishimoto, D. Fedorov, 2017, J. Comput. Chem..

The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model.

Yoshio Nishimoto, Dmitri G Fedorov, D. Fedorov, 2016, Physical chemistry chemical physics : PCCP.

The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)

Hui Li, Mark S. Gordon, Jan H. Jensen, 2006, J. Comput. Chem..

Two-component natural spinors from two-step spin-orbit coupled wave functions.

Michael W. Schmidt, Tao Zeng, Mariusz Klobukowski, 2011, The Journal of chemical physics.

Model core potentials for studies of scalar-relativistic effects and spin-orbit coupling at Douglas-Kroll level. I. Theory and applications to Pb and Bi.

D. Fedorov, M. Klobukowski, Tao Zeng, 2009, The Journal of chemical physics.

A Novel, Computationally Efficient Multipolar Model Employing Distributed Charges for Molecular Dynamics Simulations.

Markus Meuwly, Dmitri G Fedorov, Shampa Raghunathan, 2014, Journal of chemical theory and computation.

Deformation mechanism of the explosive degradation of heavy metal azides under pulsed treatments

D. Fedorov, V. Lisitsyn, Y. Zhuravlev, 2006 .

Bisque: Advances in Bioimage Databases

Ambuj K. Singh, B. S. Manjunath, Kristian Kvilekval, 2012, IEEE Data Eng. Bull..

Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation

Hui Li, Mark S. Gordon, Takeshi Nagata, 2009, J. Comput. Chem..

Planteome & BisQue: Automating Image Annotation with Ontologies using Deep-Learning Networks

B. S. Manjunath, Sinisa Todorovic, Kristian Kvilekval, 2018, ICBO.

Plant Image Segmentation and Annotation with Ontologies in BisQue

B. S. Manjunath, Xu Xu, Sinisa Todorovic, 2016, ICBO/BioCreative.

Dissociation Potential Curves of Low-Lying States in Transition Metal Hydrides. 2. Hydrides of Groups 3 and 5

M. Gordon, D. Fedorov, H. Umeda, 2004 .

Symmetry in Spin-Orbit Coupling

M. Gordon, D. Fedorov, 2002 .

Free Energy Decomposition Analysis Based on the Fragment Molecular Orbital Method.

D. Fedorov, Taiji Nakamura, 2022, The journal of physical chemistry letters.

Analysis of Guest Adsorption on Crystal Surfaces Based on the Fragment Molecular Orbital Method.

D. Fedorov, Taiji Nakamura, Tomoko Yokaichiya, 2022, The journal of physical chemistry. A.

A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO)

Mark S. Gordon, Kazuo Kitaura, Dmitri G. Fedorov, 2004, J. Comput. Chem..

An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method.

Kenneth M Merz, Kazuo Kitaura, Dmitri G Fedorov, 2012, The journal of physical chemistry letters.

Polarizable continuum model with the fragment molecular orbital‐based time‐dependent density functional theory

Kazuo Kitaura, Dmitri G. Fedorov, Mahito Chiba, 2008, J. Comput. Chem..

Electronic structure of solid solutions of argentum halide and heterojunctions based on them

A. S. Poplavnoi, D. Fedorov, Y. Zhuravlev, 2004 .

Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method.

D. Fedorov, H. Nakata, 2023, Journal of chemical theory and computation.

The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand Interactions

Michael J. Bodkin, Philip C. Biggin, Alexander Heifetz, 2016, J. Chem. Inf. Model..

Influence of tool wear on the heat-flux distribution and temperature at the contact surfaces in the end milling of OT4 titanium alloy

D. L. Skuratov, Dmitriy L. Skuratov, Dmitriy V. Evdokimov, 2016 .

A biosegmentation benchmark for evaluation of bioimage analysis methods

B. S. Manjunath, Boguslaw Obara, Kristian Kvilekval, 2009, BMC Bioinformatics.

Theoretical Background of the Fragment Molecular Orbital (FMO) Method and Its Implementation in GAMESS

Kazuo Kitaura, Dmitri G. Fedorov, K. Kitaura, 2009 .

Electron density from the fragment molecular orbital method combined with density-functional tight-binding

D. Fedorov, 2021 .

Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems.

D. Fedorov, Taiji Nakamura, Tomoko Yokaichiya, 2021, The journal of physical chemistry letters.

Solvent Screening in Zwitterions Analyzed with the Fragment Molecular Orbital Method.

D. Fedorov, 2019, Journal of chemical theory and computation.

Rapid and accurate assessment of GPCR–ligand interactions Using the fragment molecular orbital‐based density‐functional tight‐binding method

Alexander Heifetz, Dmitri G. Fedorov, Roger Robinson, 2017, J. Comput. Chem..

Using the fragment molecular orbital method to investigate agonist–orexin-2 receptor interactions

Philip C. Biggin, Matteo Aldeghi, Dmitri G. Fedorov, 2016, Biochemical Society transactions.

Towards a quantitative description of excitonic couplings in photosynthetic pigment–protein complexes: quantum chemistry driven multiscale approaches

T. Renger, D. Fedorov, Christian Friedl, 2022, Physical chemistry chemical physics : PCCP.

FMOxFMO: Elucidating Excitonic Interactions in the Fenna-Matthews-Olson Complex with the Fragment Molecular Orbital Method.

L. Slipchenko, D. Fedorov, H. Nakata, 2019, Journal of chemical theory and computation.

Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin

Yuto Komeiji, Kazuo Kitaura, Dmitri G. Fedorov, 2007, J. Comput. Chem..

Analytic gradient for the relativistic elimination of small components (RESCs) approach

K. Hirao, D. Fedorov, T. Nakajima, 2001 .

Implementation of replica-exchange umbrella sampling in GAMESS

Yuko Okamoto, Stephan Irle, Shingo Ito, 2018, Comput. Phys. Commun..

Radical damage in lipids investigated with the fragment molecular orbital method

L. Slipchenko, D. Fedorov, H. Nakata, 2016 .

Theoretical study of the unusual potential energy curve of the A [sup 1] (cid:6) [sup +] state of AgH

K. Hirao, H. Witek, A. Viel, 2018 .

Multithreaded parallelization of the energy and analytic gradient in the fragment molecular orbital method

Yuri Alexeev, Dmitri G. Fedorov, D. Fedorov, 2019, International Journal of Quantum Chemistry.

Molecular Electrostatic Potential and Electron Density of Large Systems in Solution Computed With the Fragment Molecular Orbital Method.

D. Fedorov, Y. Alexeev, V. Mironov, 2019, The journal of physical chemistry. A.

Three‐body expansion of the fragment molecular orbital method combined with density‐functional tight‐binding

D. Fedorov, Y. Nishimoto, 2017, Journal of Computational Chemistry.

Development of the Analytic Second Derivatives for the Fragment Molecular Orbital Method

D. Fedorov, H. Nakata, 2021 .

The catalytic activity and adsorption in faujasite and ZSM-5 zeolites: the role of differential stabilization and charge delocalization.

D. Fedorov, Taiji Nakamura, 2022, Physical chemistry chemical physics : PCCP.

Publisher’s Note: “Coupled-cluster theory based upon the fragment molecular-orbital method” [J. Chem. Phys. 123, 134103 (2005)]

K. Kitaura, D. Fedorov, 2006 .

Atypical quantum confinement effect in silicon nanowires.

L. Chernozatonskii, P. Sorokin, D. Fedorov, 2008, The journal of physical chemistry. A.

Analysis of Site Energies and Excitonic Couplings: The Role of Symmetry and Polarization.

D. Fedorov, 2024, The journal of physical chemistry. A.

The fragment molecular orbital method combined with density-functional tight-binding and periodic boundary conditions.

D. Fedorov, Y. Nishimoto, 2021, The Journal of chemical physics.