Continuum solvent models predict a quadratic charge dependence (linear response) of the free energy of a system of charged solutes. The relation between this prediction and the structure of the solvation shell around the solutes is discussed. Studies of the derivative of the free energy with respect to the charges for different reference states are shown to be a convenient way of testing the li...

Central in a variational implicit-solvent description of biomolecular solvation is an effective free-energy functional of the solute atomic positions and the solute-solvent interface (i.e., the dielectric boundary). The free-energy functional couples together the solute molecular mechanical interaction energy, the solute-solvent interfacial energy, the solute-solvent van der Waals interaction e...

Computer simulations have been demonstrated to be important for unraveling atomic mechanisms in biological systems. In this study, we show how combining unbiased molecular dynamic simulations with appropriate analysis tools can successfully describe metal-based drug interactions with DNA. To elucidate the noncovalent affinity of cisplatin's family to DNA, we performed extensive all-atom molecul...

Anti-angiogenic agents are biological drugs used for treatment of retinal neovascular degenerative diseases. In this study, we aimed at in silico analysis of interaction of vascular endothelial growth factor A (VEGFA), the main mediator of angiogenesis, with binding domains of anti-angiogenic agents used for treatment of retinal diseases, such as ranibizumab, bevacizumab and aflibercept. The an...

Hybrid quantum/molecular mechanics models (QM/MM methods) are widely used in material and molecular simulations when MM do not provide sufficient accuracy but pure QM computationa...

Novel techniques are revealing the movements and forces associated with single interactions of motor proteins, such as myosin and kinesin, and also of processive enzymes, such as RNA polymerase.

1. Poisson schemes 1 2. Hamiltonian reduction in the symplectic case 6 3. Deformations and quantizations of Poisson schemes 9 4. Symplectic singularities 13 5. Symplectic resolutions 18 6. Poisson deformations. 19 7. Purity 22 8. Tilting generators 25 9. Algebraic cycles and cohomological purity 28 10. Appendix 1: On rational singularities 31 11. Appendix 2: Reminder on GIT and stability 33 12....

Fragment density functional theory (DFT) calculation of NMR chemical shifts for several proteins (Trp-cage, Pin1 WW domain, the third IgG-binding domain of Protein G (GB3) and human ubiquitin) has been carried out. The present study is based on a recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach but the solvent effects are included by using the...

Tyrosinase is a type-3 copper enzyme that is widely distributed in plants, fungi, insects, and mammals. Developing high potent inhibitors against tyrosinase is of great interest in diverse fields including tobacco curing, food processing, bio-insecticides development, cosmetic development, and human healthcare-related research. In the crystal structure of Agaricus bisporus mushroom tyrosinase, ...