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 SystemsJuan Torras, Benjamin P. Roberts, Gustavo M. Seabra and Samuel B. TrickeyEfficient Calculation of Enzyme Reaction Free Energy Profiles using a Hybrid Differential Relaxation Algorithm: Application to Mycobacterial Zinc HydrolasesJuan Manuel Romero, Mariano Martin, Claudia Lilián Ramirez, Victoria Gisel Dumas and Marcelo Adrián MartiA practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in BiomoleculesJesús I. Mendieta-Moreno, Iñigo Marcos-Alcalde, Daniel G. Trabada, Paulino Gómez Puertas, José Ortega and Jesús MendietaExplicit Drug Re-Positioning: Predicting Novel Drug-Target Interactions of the Shelved Molecules with QM/MM Based ApproachesAnkur Omer, Venkatesan Suryanarayanan, Chandrabose Selvaraj, Sanjeev Kumar Singh and Poonam SinghEnzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism  and FunctionAmy Timmins and Sam P. de VisserThe Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations: Applications to Enzymatic ReactionsEric A. C. Bushnell, Victoria E. J. Berryman, James W. Gauld and Russell J. BoydQM and QM/MM Methods Compared: Case Studies on Reaction Mechanisms of MetalloenzymesTomasz 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 MasgrauExcited States and Photochemistry of Chromophores in the Photoactive Proteins Explored by the Combined Quantummechanical and Molecular Mechanical CalculationsLihong Liu, Ganglong Cui and Wei-Hai Fang