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namd2 NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry (2005) vol. 26(16) pp. 1781–1802
gromacs GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

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van der Spoel, et al. (2005) J. Comput. Chem. 26: 1701-1718.

Hess, et al. (2008) J. Chem. Theory Comput. 4: 435-447.

Pronk, et al. (2013) Bioinformatics 29 845-854.
Rosetta Rosetta is the premier software suite for modeling macromolecular structures. 原始文獻:
  • Fleishman et al. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science (New York, NY) (2011) vol. 332 (6031) pp. 816-21 Wang et al. Modeling disordered regions in proteins using rosetta. PloS one (2011) vol. 6 (7) pp. e22060 DiMaio et al. Refinement of protein structures into low-resolution density maps using rosetta. Journal of molecular biology (2009) vol. 392 (1) pp. 181-90 Ramelot et al. Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins (2009) vol. 75 (1) pp. 147-67
  • Rigden et al. Molecular replacement using ab initio polyalanine models generated with ROSETTA. Acta crystallographica Section D, Biological crystallography (2008) vol. 64 (Pt 12) pp. 1288-91