torek, 16. avgust 2016 Vabilo na predavanje prof. dr. Harukija Nakamure z naslovom Computational Approaches to Protein Interactions

Gostujoči profesor dr. Haruki Nakamura bo imel v sredo, 17.8.2016, ob 12:00 uri v Veliki predavalnici (Glagoljaška 8) predavanje z naslovom Computational Approaches to Protein Interactions.

Več o predavanju si lahko preberete v nadaljevanju.

Protein-ligand interactions govern very many biological phenomena, including protein-small compounds, protein-nucleic acids, and protein-protein interactions. In particular, electrostatic property of proteins is one of the most important factors for specific molecular recognitions on protein interfaces. Appropriate treatment of the electrostatic interaction is critical for computational analyses of PPI in a realistic manner. Since the potential function is long-range, it is not simple to handle the interactions in an effective manner: high accuracy, low computational cost, ease of the implementation, and freedom from artifacts. We have recently developed a novel algorithm, zero-multipole summation method, for evaluating the electrostatic energy of charged particle systems. Its simple pair wise form enables us to effectively apply the scheme to high-performance parallel computation with GPGPU systems. Several applications to homogeneous and inhomogeneous molecular systems have confirmed that it could replace the conventional Ewald method in order to perform rapid and accurate molecular dynamics simulations. This method is applied to simulate a protein-protein docking procedure in an ab-initio manner, based on the computed free energy landscape. Our software package, myPresto, is availble from http://presto.protein.osaka-u.ac.jp/myPresto4/, includng psygene-G and omegagne for GPGPUs.