Molecular simulations with high-performance computers

In this article, we present the work carried out in our group on various fields of theoretical biochemistry. Our main fields of research are as follows: i) design of an algorithm for de novo prediction of protein structure from amino-acid sequence using energetic criteria, ii) theoretical modeling of the structure and dynamics of neurohypophyseal-hormone receptors, iii) quantum-mechanical investigation of reactions in organic chemistry and biochemistry, and iv) theoretical conformational analysis of small peptides using experimental information. The performance of different machines, depending on the kind of calculations with special focus on the exploitation of parallelism as well as the applicability and performance of various commercial, free, and our home- made software (AMBER. GAUSSIAN, ECEPPAK, GAMESS, SYBYE, MSI/Biosym) available at TASK and the importance of graphical processing of the data are discussed.