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 Lilian Ramirez, Victoria Gisel Dumas and Marcelo Adrian Marti A practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules Jesus I. Mendieta-Moreno, Inigo Marcos-Alcalde, Daniel G. Trabada, Paulino Gomez Puertas, Jose Ortega and Jesus 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 Gomez, Fernanda Mendoza, Jose 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
