Biological Medicine

With the rapid development of life science theory and computational analysis methods, research on new drug has entered a new period. Emerging disciplines have infiltrated into the discovery and preliminary studies about the new drug research. The cross-penetration between computational science and pharmaceutical research is increasingly strengthened so that there are computer-aided drug design and computational biology which are significant potential for new research areas and technologies.

Molecular Dynamics (MD) simulations, as a branch of computational biology, provide a new way to study the protein dynamics behavior, the protein dynamics interactions and biological network analysis. MD has greatly expanded the breadth and depth of protein science and other life science. Currently, MD simulations which combine with various experimental methods have become an important approach to research life sciences issues.

NSCC-TJ which collaborates with Shanghai Institute of Materia Medica, Institute of Biophysics, Academy of Military Medical Sciences, Genomics Institute and other companies has carried out a series of cooperation projects in the field of molecular dynamics.

Application examples:

Shanghai Institute of Materia Medica used Gromaccs software to test small-scale and medium-scale simulation system (about 20,000 atoms). The truncation radius of test was set about 1,200 Picometers, used 512 computing cores and simulation speed was about 330 ns/day. Large-scale simulation system (approximately four hundred thousand atoms) test set the truncation radius of 1,200 Picometers and used 2048 computing cores and simulation speed was 85 ns / day.

Shanghai Institute of Materia Medica used the NAMD software to test which includes proteins, phospholipids and water, a total of about 967,172 atomic number system. The truncation radius of test was 1,200 Picometers, Particle Mesh Ewald, (PME) full electrostatic potential, the time step was set to 2fs, the temperature was 310K, the energy and pressure output is 0.1ps time, the simulation duration was 500 picoseconds. The various tests used the same initial file and a different number of CPU cores. The parallel computing speeds up as shown below.

Fig.1 drug test results on the TH-1A

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National Supercomputing Center in Tianjin Copyright 2009
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