Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
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May 1976 |
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
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July 1990 |
Perspective: Quantum mechanical methods in biochemistry and biophysics
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October 2016 |
New faster CHARMM molecular dynamics engine
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December 2013 |
The energy landscape of adenylate kinase during catalysis
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January 2015 |
Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase
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September 2015 |
Die Berechnung optischer und elektrostatischer Gitterpotentiale
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January 1921 |
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
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June 1993 |
Zonal methods for the parallel execution of range-limited N-body simulations
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January 2007 |
Classical Electrostatics for Biomolecular Simulations
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August 2013 |
Preface
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September 1994 |
OpenMP: an industry standard API for shared-memory programming
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January 1998 |
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
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September 2015 |
Fast Parallel Algorithms for Short-Range Molecular Dynamics
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March 1995 |
CHARMM: The biomolecular simulation program
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July 2009 |
Scalable molecular dynamics with NAMD
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January 2005 |
A smooth particle mesh Ewald method
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November 1995 |
Ewald mesh method for quantum mechanical calculations
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March 2012 |
Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions
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December 2000 |
An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald
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May 2014 |
Multipolar Ewald Methods, 1: Theory, Accuracy, and Performance
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January 2015 |
Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction
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January 2004 |
Direct dynamics calculations with NDDO (neglect of diatomic differential overlap) molecular orbital theory with specific reaction parameters
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June 1991 |
Exploring SCC-DFTB Paths for Mapping QM/MM Reaction Mechanisms †
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July 2007 |
Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations
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June 2014 |
Parameterization of NDDO wavefunctions using genetic algorithms. An evolutionary approach to parameterizing potential energy surfaces and direct dynamics calculations for organic reactions
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February 1995 |
Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms
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January 2007 |
Description of Phosphate Hydrolysis Reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Theory. 1. Parameterization
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November 2008 |
AM1 Specific Reaction Parameters for Reactions of Hydroxide Ion with Halomethanes in Complex Environments: Development and Testing
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September 2013 |
Quantum mechanical study of solvent effects in a prototype S N 2 reaction in solution: Cl − attack on CH 3 Cl
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February 2014 |
AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems
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September 2014 |
Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications
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March 2014 |
Specific parametrisation of a hybrid potential to simulate reactions in phosphatases
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January 2006 |
A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase-1
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January 2007 |
Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus
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April 2003 |
Computational chemistry on Fujitsu vector–parallel processors: Development and performance of applications software
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July 2000 |
GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations
- Maia, Julio Daniel Carvalho; Urquiza Carvalho, Gabriel Aires; Mangueira, Carlos Peixoto
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Journal of Chemical Theory and Computation, Vol. 8, Issue 9
https://doi.org/10.1021/ct3004645
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August 2012 |
Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU–GPU Computing Platform
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June 2012 |
Unified Approach for Molecular Dynamics and Density-Functional Theory
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November 1985 |
Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals
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June 2001 |
Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: Convergence toward Born–Oppenheimer trajectories
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December 2004 |
Acceleration of Semiempirical Quantum Mechanical Calculations by Extended Lagrangian Molecular Dynamics Approach
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July 2013 |
An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations
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October 2004 |
Extension of MNDO to d Orbitals: Parameters and Results for the Second-Row Elements and for the Zinc Group
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January 1996 |
Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches
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September 2014 |
Convergence acceleration of iterative sequences. the case of scf iteration
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July 1980 |
ImprovedSCF convergence acceleration
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January 1982 |
Fast semiempirical calculations: Fast Semiempirical Calculations
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June 1982 |
Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation
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June 2009 |
Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method
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July 2011 |
Fock matrix dynamics
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March 2004 |
Accelerated, energy-conserving Born–Oppenheimer molecular dynamics via Fock matrix extrapolation
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January 2005 |
New Developments in Molecular Orbital Theory
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April 1951 |
Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters
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January 2016 |
Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I
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October 1955 |
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
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July 1983 |
The implementation of a fast and accurate QM/MM potential method in Amber
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January 2008 |
COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient
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January 1993 |
Smooth Solvation Method for d-Orbital Semiempirical Calculations of Biological Reactions. 1. Implementation
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May 2005 |
Beyond the MNDO model: Methodical considerations and numerical results
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July 1993 |
Orthogonalization corrections for semiempirical methods
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April 2000 |
Ground states of molecules. 38. The MNDO method. Approximations and parameters
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June 1977 |
Ground states of molecules. 39. MNDO results for molecules containing hydrogen, carbon, nitrogen, and oxygen
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June 1977 |
Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model
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June 1985 |
Optimization of parameters for semiempirical methods I. Method
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March 1989 |
Optimization of parameters for semiempirical methods II. Applications
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March 1989 |
Optimization of parameters for semiempirical methods. III Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi
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April 1991 |
A combinedab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl? exchange reaction and gas phase protonation of polyethers
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December 1986 |
A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations
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June 1998 |
Comparison of simple potential functions for simulating liquid water
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July 1983 |
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
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April 1998 |
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
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January 2000 |
Development and current status of the CHARMM force field for nucleic acids
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January 2000 |
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
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August 2004 |
Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog
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September 1997 |
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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March 1977 |
Parametrization and Benchmark of DFTB3 for Organic Molecules
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November 2012 |
Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications
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August 2014 |
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
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February 1977 |
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
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October 1992 |
Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution
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September 2003 |
The Scalasca performance toolset architecture
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January 2010 |
Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
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September 1998 |
A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method
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January 2001 |
A Perspective on Enzyme Catalysis
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August 2003 |
Connecting Protein Conformational Dynamics with Catalytic Function As Illustrated in Dihydrofolate Reductase
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January 2013 |
Enzymatic transition states and dynamic motion in barrier crossing
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July 2009 |
At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
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January 2010 |
Perspectives on Electrostatics and Conformational Motions in Enzyme Catalysis
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January 2015 |
Role of Dynamics in Enzyme Catalysis: Substantial versus Semantic Controversies
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December 2014 |
Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step
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September 2015 |
Revisiting the finite temperature string method for the calculation of reaction tubes and free energies
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May 2009 |
Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI
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February 2011 |
A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes
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May 2016 |
Escaping free-energy minima
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September 2002 |