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Modeling of inhibitor–metalloenzyme interactions and selectivity using molecular mechanics grounded in quantum chemistry
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journal
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April 1998 |
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Conformational properties of a model alanyl dipeptide and of alanine-derived oligopeptides: Effects of solvation in water and in organic solvents—A combined SIBFA/continuum reaction field, ab initio self-consistent field, and density functional theory investigation
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journal
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May 1998 |
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Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase:ab initio and SIBFA molecular mechanics calculations
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journal
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January 2000 |
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A molecular mechanics/continuum reaction field investigation of the interactions between polar amino acid side chains in water and organic solvents
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journal
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December 1995 |
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Ab initio quality one-electron properties of large molecules: Development and testing of molecular tailoring approach
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journal
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February 2003 |
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CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
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journal
|
January 2003 |
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Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
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journal
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July 2001 |
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CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
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journal
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January 2004 |
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Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations
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journal
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August 2005 |
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Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides
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journal
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January 2006 |
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LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library
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journal
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July 2013 |
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Exploiting space-group symmetry in fragment-based molecular crystal calculations
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journal
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October 2014 |
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Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles
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journal
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January 2016 |
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AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions
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journal
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October 1981 |
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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
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journal
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July 1983 |
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An all atom force field for simulations of proteins and nucleic acids: An All Atom Force Field
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journal
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April 1986 |
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Empirical energy functions for energy minimization and dynamics of nucleic acids
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journal
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October 1986 |
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Electrostatic interaction of a solute with a continuum. Improved description of the cavity and of the surface cavity bound charge distribution.
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journal
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September 1987 |
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The MM3 force field for amides, polypeptides and proteins
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journal
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March 1991 |
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Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules
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journal
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February 1994 |
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The relaxation of molecular crystal structures using a distributed multipole electrostatic model
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journal
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May 1995 |
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Energetics of Zn2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded onab initio self-consistent field supermolecular computations
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journal
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July 1995 |
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Interactions within the alcohol dehydrogenase Zn(II)-metalloenzyme active site: Interplay between subvalence, electron correlation/dispersion, and charge transfer/induction effects
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journal
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June 2010 |
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Intermolecular interactions: Reproduction of the results of ab initio supermolecule computations by an additive procedure
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journal
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March 1979 |
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Computations of intermolecular interactions: Expansion of a charge-transfer energy contribution in the framework of an additive procedure. Applications to hydrogen-bonded systems
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journal
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July 1982 |
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Cation-ligand interactions: Reproduction of extended basis set Ab initio SCF computations by the SIBFA 2 additive procedure
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journal
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December 1985 |
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Intermolecular interactions: Elaboration on an additive procedure including an explicit charge-transfer contribution
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journal
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January 1986 |
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Polarizable Force Fields
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book
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August 2012 |
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Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies
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book
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March 2012 |
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Advancement of Polarizable Force Field and Its Use for Molecular Modeling and Design
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book
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November 2014 |
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Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison withab initio SCF computations
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journal
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January 1984 |
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Continuum solvation of large molecules described by QM/MM: a semi-iterative implementation of the PCM/EFP interface
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journal
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March 2003 |
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Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies
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journal
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March 2012 |
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Improving the specificity of organophosphorus hydrolase to acephate by mutagenesis at its binding site: a computational study
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journal
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May 2021 |
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Distributed multipole analysis, or how to describe a molecular charge distribution
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journal
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October 1981 |
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Frozen fragment reduced variational space analysis of hydrogen bonding interactions. Application to the water dimer
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journal
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August 1987 |
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Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects
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journal
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February 1981 |
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Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes
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journal
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March 1982 |
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The three-body fragment molecular orbital method for accurate calculations of large systems
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journal
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December 2006 |
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Fragment molecular orbital method: use of approximate electrostatic potential
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journal
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January 2002 |
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Fragment molecular orbital method: an approximate computational method for large molecules
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journal
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November 1999 |
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Polarizable force fields
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journal
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April 2001 |
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Modeling Polymorphic Molecular Crystals with Electronic Structure Theory
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journal
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March 2016 |
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Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method
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journal
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March 2016 |
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Ab Initio Atom–Atom Potentials Using C am CASP: Theory and Application to Many-Body Models for the Pyridine Dimer
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journal
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August 2016 |
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Beyond Born–Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields
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journal
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July 2016 |
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Analytic Gradients for the Effective Fragment Molecular Orbital Method
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journal
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September 2016 |
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Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
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journal
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December 2016 |
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Derivation and Implementation of the Gradient of the R –7 Dispersion Interaction in the Effective Fragment Potential Method
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journal
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January 2016 |
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Multipole Moments in the Effective Fragment Potential Method
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journal
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February 2017 |
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Dispersion Interactions in QM/EFP
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journal
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December 2017 |
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Efficient and Accurate Fragmentation Methods
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journal
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May 2014 |
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Transferable Next-Generation Force Fields from Simple Liquids to Complex Materials
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journal
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February 2015 |
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Accidental Degeneracy in Crystalline Aspirin: New Insights from High-Level ab Initio Calculations
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journal
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April 2012 |
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Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent
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journal
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November 1994 |
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Fragmentation Methods: A Route to Accurate Calculations on Large Systems
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journal
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August 2011 |
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Energy-Based Molecular Fragmentation Methods
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journal
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April 2015 |
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Accurate Molecular Crystal Lattice Energies from a Fragment QM/MM Approach with On-the-Fly Ab Initio Force Field Parametrization
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journal
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October 2011 |
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Accurate Prediction of Noncovalent Interaction Energies with the Effective Fragment Potential Method: Comparison of Energy Components to Symmetry-Adapted Perturbation Theory for the S22 Test Set
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journal
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July 2012 |
|
Fully Integrated Effective Fragment Molecular Orbital Method
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journal
|
April 2013 |
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Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins
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journal
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August 2013 |
|
Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations
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journal
|
August 2013 |
|
Extension of the Universal Force Field to Metal–Organic Frameworks
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journal
|
January 2014 |
|
The R –7 Dispersion Interaction in the General Effective Fragment Potential Method
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journal
|
March 2014 |
|
GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations
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journal
|
March 2014 |
|
A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations
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journal
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September 2014 |
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Toward a Separate Reproduction of the Contributions to the Hartree−Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential
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journal
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March 2007 |
|
Polarizable Force Fields: History, Test Cases, and Prospects
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journal
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September 2007 |
|
Design of a Next Generation Force Field: The X-POL Potential
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journal
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August 2007 |
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Spatially Homogeneous QM/MM for Systems of Interacting Molecules with on-the-Fly ab Initio Force-Field Parametrization
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journal
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December 2009 |
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Molecular Tailoring Approach for Simulation of Electrostatic Properties
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journal
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September 1994 |
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Improvements of the continuum model. 1. Application to the calculation of the vaporization thermodynamic quantities of nonassociated liquids
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journal
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March 1988 |
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UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
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journal
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December 1992 |
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Derivation of Class II Force Fields. 2. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules
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journal
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March 1994 |
|
Molecular mechanics. The MM3 force field for hydrocarbons. 1
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journal
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November 1989 |
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Molecular mechanics. The MM3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics
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journal
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November 1989 |
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Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons
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journal
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November 1989 |
|
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
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journal
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March 1988 |
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Optimized intermolecular potential functions for amides and peptides. Structure and properties of liquid amides
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journal
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February 1985 |
|
A new force field for molecular mechanical simulation of nucleic acids and proteins
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journal
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February 1984 |
|
Specificity of Acyl Transfer from 2-Mercaptobenzamide Thioesters to the HIV-1 Nucleocapsid Protein
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journal
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September 2007 |
|
The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry
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journal
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January 2001 |
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Modeling Copper(I) Complexes: SIBFA Molecular Mechanics versus ab Initio Energetics and Geometrical Arrangements
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journal
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June 2002 |
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Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation
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journal
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May 2003 |
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Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution
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journal
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December 2003 |
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Modeling Styrene−Styrene Interactions †
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journal
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January 2006 |
|
Methanol−Water Mixtures: A Microsolvation Study Using the Effective Fragment Potential Method
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journal
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August 2006 |
|
Unravelling the Origin of Intermolecular Interactions Using Absolutely Localized Molecular Orbitals
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journal
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September 2007 |
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Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods †
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journal
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August 2010 |
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Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model
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journal
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January 2011 |
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Benzene−Pyridine Interactions Predicted by the Effective Fragment Potential Method
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journal
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May 2011 |
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Effective Fragment Potential Study of the Interaction of DNA Bases
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journal
|
October 2011 |
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Physically-Motivated Force Fields from Symmetry-Adapted Perturbation Theory
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journal
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February 2013 |
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First-Principles Many-Body Force Fields from the Gas Phase to Liquid: A “Universal” Approach
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journal
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April 2014 |
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S/G-1: An ab Initio Force-Field Blending Frozen Hermite Gaussian Densities and Distributed Multipoles. Proof of Concept and First Applications to Metal Cations
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journal
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June 2014 |
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Surface Affinity of the Hydronium Ion: The Effective Fragment Potential and Umbrella Sampling
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journal
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December 2014 |
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Modeling π–π Interactions with the Effective Fragment Potential Method: The Benzene Dimer and Substituents
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journal
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June 2008 |
|
Incorporation of a QM/MM Buffer Zone in the Variational Double Self-Consistent Field Method
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journal
|
November 2008 |
|
Water−Benzene Interactions: An Effective Fragment Potential and Correlated Quantum Chemistry Study †
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journal
|
March 2009 |
|
Alanine: Then There Was Water
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journal
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June 2009 |
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Model, Multiply Hydrogen-Bonded Water Oligomers ( N = 3−20). How Closely Can a Separable, ab Initio-Grounded Molecular Mechanics Procedure Reproduce the Results of Supermolecule Quantum Chemical Computations?
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journal
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November 1997 |
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Complexes of Pentahydrated Zn 2+ with Guanine, Adenine, and the Guanine−Cytosine and Adenine−Thymine Base Pairs. Structures and Energies Characterized by Polarizable Molecular Mechanics and ab Initio Calculations
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journal
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December 1999 |
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Predicting Organic Crystal Lattice Energies with Chemical Accuracy
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journal
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December 2010 |
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What Governs the Proton Ordering in Ice XV?
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journal
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September 2013 |
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Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
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journal
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January 2006 |
|
Practical quantum mechanics-based fragment methods for predicting molecular crystal properties
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journal
|
January 2012 |
|
Rapid computation of intermolecular interactions in molecular and ionic clusters: self-consistent polarization plus symmetry-adapted perturbation theory
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journal
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January 2012 |
|
Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns
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journal
|
January 2015 |
|
Ab initio investigation of the aqueous solvation of the nitrate ion
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journal
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January 2015 |
|
Adjustment of the SIBFA method for potential maps to study hydrogen bonding vibrational frequencies
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journal
|
January 1991 |
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Intermolecular exchange-induction and charge transfer: Derivation of approximate formulas using nonorthogonal localized molecular orbitals
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journal
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May 2001 |
|
An integrated effective fragment—polarizable continuum approach to solvation: Theory and application to glycine
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journal
|
January 2002 |
|
Density functional theory based effective fragment potential method
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journal
|
April 2003 |
|
Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein–molecule interaction energy
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journal
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August 2003 |
|
Molecule intrinsic minimal basis sets. I. Exact resolution of ab initio optimized molecular orbitals in terms of deformed atomic minimal-basis orbitals
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journal
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February 2004 |
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Deviations from Pairwise Additivity in Intermolecular Potentials
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journal
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December 1967 |
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Interaction of the van der Waals Type Between Three Atoms
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journal
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June 1943 |
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Theoretical method for full ab initio calculation of DNA/RNA–ligand interaction energy
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journal
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June 2004 |
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Approximate ab initio energies by systematic molecular fragmentation
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journal
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April 2005 |
|
Intermolecular electrostatic energies using density fitting
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journal
|
July 2005 |
|
Towards a force field based on density fitting
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journal
|
March 2006 |
|
Charge transfer interaction in the effective fragment potential method
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journal
|
June 2006 |
|
Accuracy and efficiency of electronic energies from systematic molecular fragmentation
|
journal
|
September 2006 |
|
Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods
|
journal
|
November 2006 |
|
Gradients of the polarization energy in the effective fragment potential method
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journal
|
November 2006 |
|
Approximating quantum many-body intermolecular interactions in molecular clusters using classical polarizable force fields
|
journal
|
April 2009 |
|
Energy decomposition analysis of covalent bonds and intermolecular interactions
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journal
|
July 2009 |
|
Accurate treatment of nonbonded interactions within systematic molecular fragmentation
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journal
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January 2009 |
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Two- and three-body interatomic dispersion energy contributions to binding in molecules and solids
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journal
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June 2010 |
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An efficient, fragment-based electronic structure method for molecular systems: Self-consistent polarization with perturbative two-body exchange and dispersion
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journal
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March 2011 |
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Adjustment of the SIBFA Method for Potential Maps to Study Hydrogen Bonding Vibrational Frequencies
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conference
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January 1991 |
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An improved simple model for the van der Waals potential based on universal damping functions for the dispersion coefficients
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journal
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April 1984 |
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A new analysis of charge transfer and polarization for ligand–metal bonding: Model studies of Al 4 CO and Al 4 NH 3
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journal
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May 1984 |
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The exact multicenter multipolar part of a molecular charge distribution and its simplified representations
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journal
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April 1988 |
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Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
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journal
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June 1993 |
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Nonequilibrium solvation: An ab initio quantum‐mechanical method in the continuum cavity model approximation
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journal
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May 1993 |
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Natural energy decomposition analysis: An energy partitioning procedure for molecular interactions with application to weak hydrogen bonding, strong ionic, and moderate donor–acceptor interactions
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journal
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February 1994 |
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The fast Fourier Poisson method for calculating Ewald sums
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journal
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August 1994 |
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A smooth particle mesh Ewald method
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journal
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November 1995 |
|
Modeling intermolecular exchange integrals between nonorthogonal molecular orbitals
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journal
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May 1996 |
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An effective fragment method for modeling solvent effects in quantum mechanical calculations
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journal
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August 1996 |
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The dispersion interaction between quantum mechanics and effective fragment potential molecules
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journal
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June 2012 |
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Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model
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journal
|
January 1999 |
|
A study of water clusters using the effective fragment potential and Monte Carlo simulated annealing
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journal
|
February 2000 |
|
Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach
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journal
|
April 2000 |
|
A combined discrete/continuum solvation model: Application to glycine
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journal
|
July 2000 |
|
Charge transfer interaction using quasiatomic minimal-basis orbitals in the effective fragment potential method
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journal
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November 2013 |
|
A general intermolecular force field based on tight-binding quantum chemical calculations
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journal
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October 2017 |
|
Distributed multipole analysis Methods and applications
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journal
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January 2002 |
|
Dynamic polarizability, dispersion coefficient C 6 and dispersion energy in the effective fragment potential method
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journal
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January 2005 |
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Damping functions in the effective fragment potential method
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journal
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April 2009 |
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Distributed multipole analysis: Methods and applications
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journal
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December 1985 |
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Long-range and overlap effects on collision-induced properties
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journal
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November 1992 |
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Atom–atom potentials from ab initio calculations
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journal
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January 2007 |
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The Theory of Intermolecular Forces
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book
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January 2013 |
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Iterative Methods for Sparse Linear Systems
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book
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January 2003 |
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Accurate First Principles Model Potentials for Intermolecular Interactions
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journal
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April 2013 |
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The Fragment Molecular Orbital Method
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book
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January 2009 |
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Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry
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journal
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April 2013 |
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Ab Initio Atom-Atom Potentials Using CAMCASP: Theory and Application to Many-Body Models for the Pyridine Dimer
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journalarticle
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January 2016 |
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Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
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text
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January 2017 |
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Two- and three-body interatomic dispersion energy contributions to binding in molecules and solids
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text
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January 2010 |