Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase-2

Hydration and vibrational dynamics of betaine (N,N,N-trimethylglycine)

(2015) Tanping Li et al.   JOURNAL OF CHEMICAL PHYSICS

Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling

(2015) Tatiana Vasilevskaya et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras

(2015) Vladimir A. Mironov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Umbrella sampling of proton transfer in a creatine–water system

(2014) Olga Ivchenko et al.   CHEMICAL PHYSICS LETTERS

Averaging Techniques for Reaction Barriers in QM/MM Simulations

(2014) April M. Cooper et al.   CHEMPHYSCHEM

ChemShell-a modular software package for QM/MM simulations

(2013) Sebastian Metz et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

An AIMD Study of the CPD Repair Mechanism in Water: Reaction Free Energy Surface and Mechanistic Implications

(2011) Ali A. Hassanali et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

QM/MM Methods for Biomolecular Systems

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

Finite-temperature effects in enzymatic reactions — Insights from QM/MM free-energy simulations

(2009) Hans Martin Senn et al.   CANADIAN JOURNAL OF CHEMISTRY

A General Boundary Potential for Hybrid QM/MM Simulations of Solvated Biomolecular Systems

(2009) Tobias Benighaus et al.   Journal of Chemical Theory and Computation

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

DL-FIND: An Open-Source Geometry Optimizer for Atomistic Simulations†

(2009) Johannes Kästner et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations

(2009) Natalia Díaz et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Peptide Hydrolysis Catalyzed by Matrix Metalloproteinase 2: A Computational Study

(2008) Dr. Natalia Díaz et al.   JOURNAL OF PHYSICAL CHEMISTRY B