Related references
Note: Only part of the references are listed.Exploring paths of chemical transformations in molecular and periodic systems: An approach utilizing force
Satoshi Maeda et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2021)
Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations
Kiyoshi Yagi et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Polarizable QM/MM Approach with Fluctuating Charges and Fluctuating Dipoles: The QM/FQFμ Model
Tommaso Giovannini et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Exploration of Reaction Pathways and Chemical Transformation Networks
Gregor N. Simm et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2019)
Roles of Closed-and Open-Loop Conformations in Large-Scale Structural Transitions of L-Lactate Dehydrogenase
Kimichi Suzuki et al.
ACS OMEGA (2019)
Implementation and performance of the artificial force induced reaction method in the GRRM17 program
Satoshi Maeda et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2018)
Methods for exploring reaction space in molecular systems
Amanda L. Dewyer et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2018)
Software update: the ORCA program system, version 4.0
Frank Neese
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2018)
Toward Accurate QM/MM Reaction Barriers with Large QM Regions Using Domain Based Pair Natural Orbital Coupled Cluster Theory
Giovanni Bistoni et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
NAMD goes quantum: an integrative suite for hybrid simulations
Marcelo C. R. Melo et al.
NATURE METHODS (2018)
Simulating Electron Dynamics in Polarizable Environments
Xiaojing Wu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Automatic Generation of Auxiliary Basis Sets
Georgi L. Stoychev et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems
Kimichi Suzuki et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)
An optimized charge penetration model for use with the AMOEBA force field
Joshua A. Rockers et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)
Computational Catalysis Using the Artificial Force Induced Reaction Method
W. M. C. Sameera et al.
ACCOUNTS OF CHEMICAL RESEARCH (2016)
An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
Justin A. Lemkul et al.
CHEMICAL REVIEWS (2016)
Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions
Yu Takano et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2016)
The ONIOM Method and Its Applications
Lung Wa Chung et al.
CHEMICAL REVIEWS (2015)
Theoretical Investigation of Enantioselectivity of Cage-Like Supramolecular Assembly: The Insights into the Shape Complementarity and Host-Guest Interaction
Yusuke Ootani et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)
Application of a BOSS-Gaussian Interface for QM/MM Simulations of Henry and Methyl Transfer Reactions
Jonah Z. Vilseck et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)
QM/MM Calculations with deMon2k
Dennis R. Salahub et al.
MOLECULES (2015)
Advances in molecular quantum chemistry contained in the Q-Chem 4 program package
Yihan Shao et al.
MOLECULAR PHYSICS (2015)
Recent developments in QM/MM methods towards open-boundary multi-scale simulations
Soroosh Pezeshki et al.
MOLECULAR SIMULATION (2015)
Computational Catalysis-Past, Present, and Future
Walter Thiel
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)
The CHARMM-TURBOMOLE Interface for Efficient and Accurate QM/MM Molecular Dynamics, Free Energies, and Excited State Properties
Saleh Riahi et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)
Effect of Protein Environment within Cytochrome P450cam Evaluated Using a Polarizable-Embedding QM/MM Method
Nandun M. Thellamurege et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2014)
Large-Scale Density Functional Theory Transition State Searching in Enzymes
Greg Lever et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)
ChemShell-a modular software package for QM/MM simulations
Sebastian Metz et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2014)
Oxoferryl species in mononuclear non-heme iron enzymes: Biosynthesis, properties and reactivity from a theoretical perspective
Marcus Lundberg et al.
COORDINATION CHEMISTRY REVIEWS (2013)
A microiterative intrinsic reaction coordinate method for large QM/MM systems
Iakov Polyak et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2013)
Exploring Potential Energy Surfaces of Large Systems with Artificial Force Induced Reaction Method in Combination with ONIOM and Microiteration
Satoshi Maeda et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein
Christine M. Isborn et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
An overlap fitted chain of spheres exchange method
Robert Izsak et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions
Frederik Claeyssens et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2011)
Communications: A systematic method for locating transition structures of A plus B→X type reactions
Satoshi Maeda et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
Effects of Point Mutation on Enzymatic Activity: Correlation between Protein Electronic Structure and Motion in Chorismate Mutase Reaction
Toyokazu Ishida
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
QM/MM Methods for Biomolecular Systems
Hans Martin Senn et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2009)
An Automated and Systematic Transition Structure Explorer in Large Flexible Molecular Systems Based on Combined Global Reaction Route Mapping and Microiteration Methods
Satoshi Maeda et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
The implementation of a fast and accurate QM/MM potential method in Amber
Ross C. Walker et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)
Computational prediction of small-molecule catalysts
K. N. Houk et al.
NATURE (2008)
Very fast prediction and rationalization of pKa values for protein-ligand complexes
Delphine C. Bas et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)
Intrinsic motions along an enzymatic reaction trajectory
Katherine A. Henzler-Wildman et al.
NATURE (2007)
Exploiting QM/MM capabilities in geometry optimization:: A microiterative approach using electrostatic embedding
Johannes Kaestner et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
QM/MM: what have we learned, where are we, and where do we go from here?
Hai Lin et al.
THEORETICAL CHEMISTRY ACCOUNTS (2007)
The dynamic energy landscape of dihydrofolate reductase catalysis
David D. Boehr et al.
SCIENCE (2006)
Combining quantum mechanics methods with molecular mechanics methods in ONIOM
Thom Vreven et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
High-accuracy computation of reaction barriers in enzymes
Frederik Claeyssens et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2006)
GROMACS: Fast, flexible, and free
D Van der Spoel et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Very fast empirical prediction and rationalization of protein pKa values
H Li et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
The Amber biomolecular simulation programs
DA Case et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Isotope effects on the enzymatic and nonenzymatic reactions of chorismate
SK Wright et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Increased positive electrostatic potential in p-hydroxybenzoate hydroxylase accelerates hydroxylation but slows turnover
M Ortiz-Maldonado et al.
BIOCHEMISTRY (2004)
A DFT-based QM-MM approach designed for the treatment of large molecular systems:: Application to chorismate mutase
A Crespo et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2003)
Geometry optimization with QM/MM, ONIOM, and other combined methods.: I.: Microiterations and constraints
T Vreven et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Investigation of the S0→S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method
T Vreven et al.
THEORETICAL CHEMISTRY ACCOUNTS (2003)
The A245K mutation exposes another stage of the bacterial L-lactate dehydrogenase reaction mechanism
P Kedzierski et al.
BIOCHEMISTRY (2001)
Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase
R Yasuda et al.
NATURE (2001)
Share Paper
