Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions

Dr. Tatyana Karabencheva-Christova works at the Department of Applied Sciences, University of Northumbria, UK.

PUPIL: a Software Integration System for Multi-scale QM/MM-MD Simulations and its Application to Biomolecular Systems
Juan Torras, Benjamin P. Roberts, Gustavo M. Seabra and Samuel B. Trickey
Efficient Calculation of Enzyme Reaction Free Energy Profiles using a Hybrid Differential Relaxation Algorithm: Application to Mycobacterial Zinc Hydrolases
Juan Manuel Romero, Mariano Martin, Claudia Lilián Ramirez, Victoria Gisel Dumas and Marcelo Adrián Marti
A practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules
Jesús I. Mendieta-Moreno, Iñigo Marcos-Alcalde, Daniel G. Trabada, Paulino Gómez Puertas, José Ortega and Jesús Mendieta
Explicit Drug Re-Positioning: Predicting Novel Drug-Target Interactions of the Shelved Molecules with QM/MM Based Approaches
Ankur Omer, Venkatesan Suryanarayanan, Chandrabose Selvaraj, Sanjeev Kumar Singh and Poonam Singh
Enzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism  and Function
Amy Timmins and Sam P. de Visser
The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations: Applications to Enzymatic Reactions
Eric A. C. Bushnell, Victoria E. J. Berryman, James W. Gauld and Russell J. Boyd
QM and QM/MM Methods Compared: Case Studies on Reaction Mechanisms of Metalloenzymes
Tomasz Borowski, Matthew Quesne and Maciej Szaleniec  
QM/MM Studies Reveal how Substrate-Substrate and Enzyme-Substrate Interactions  Modulate Retaining Glycosyltransferases Catalysis and Mechanism                               
Hansel Gómez, Fernanda Mendoza, José M. Lluch and Laura Masgrau
Excited States and Photochemistry of Chromophores in the Photoactive Proteins Explored by the Combined Quantummechanical and Molecular Mechanical Calculations
Lihong Liu, Ganglong Cui and Wei-Hai Fang