Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems

Artificial Force Induced Reaction (AFIR) Method for Exploring Quantum Chemical Potential Energy Surfaces

(2016) Satoshi Maeda et al.   CHEMICAL RECORD

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase

(2016) Heather J. Kulik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region

(2016) Garima Jindal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The ONIOM Method and Its Applications

(2015) Lung Wa Chung et al.   CHEMICAL REVIEWS

Intrinsic reaction coordinate: Calculation, bifurcation, and automated search

(2014) Satoshi Maeda et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

A microiterative intrinsic reaction coordinate method for large QM/MM systems

(2013) Iakov Polyak et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Exploring Potential Energy Surfaces of Large Systems with Artificial Force Induced Reaction Method in Combination with ONIOM and Microiteration

(2012) Satoshi Maeda et al.   Journal of Chemical Theory and Computation

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

QM/MM Reweighting Free Energy SCF for Geometry Optimization on Extensive Free Energy Surface of Enzymatic Reaction

(2011) Takahiro Kosugi et al.   Journal of Chemical Theory and Computation

Enzymatic Methyl Transfer: Role of an Active Site Residue in Generating Active Site Compaction That Correlates with Catalytic Efficiency

(2011) Jianyu Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reaction path optimization and vibrational frequency analysis via ab initio QM/MM free energy gradient (FEG) method: application to isomerization process of glycine in aqueous solution

(2011) Norio Takenaka et al.   THEORETICAL CHEMISTRY ACCOUNTS

The ONIOM method: its foundation and applications to metalloenzymes and photobiology

(2011) Lung Wa Chung et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Finding Reaction Pathways for Multicomponent Reactions: The Passerini Reaction is a Four-Component Reaction

(2010) Satoshi Maeda et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Communications: A systematic method for locating transition structures of A+B→X type reactions

(2010) Satoshi Maeda et al.   JOURNAL OF CHEMICAL PHYSICS

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

An Automated and Systematic Transition Structure Explorer in Large Flexible Molecular Systems Based on Combined Global Reaction Route Mapping and Microiteration Methods

(2009) Satoshi Maeda et al.   Journal of Chemical Theory and Computation

Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods

(2008) Hao Hu et al.   Annual Review of Physical Chemistry

Transition States in a Protein Environment − ONIOM QM:MM Modeling of Isopenicillin N Synthesis

(2008) Marcus Lundberg et al.   Journal of Chemical Theory and Computation

Crystal Structures of Human 108V and 108M Catechol O-Methyltransferase

(2008) K. Rutherford et al.   JOURNAL OF MOLECULAR BIOLOGY