Title :
SMD: visual steering of molecular dynamics for protein design
Author :
Leech, Jonathan ; Prins, Jan E. ; Hermans, Jan
Author_Institution :
North Carolina Univ., Chapel Hill, NC, USA
Abstract :
SMD, a system for interactively steering molecular dynamics calculations of protein molecules, includes computation, visualization, and communication components. Biochemists can “tug” molecules into different shapes by specifying external forces in the graphical interface, which are added to internal forces representing atomic bonds and nonbonded interactions. SMD provides a new tool for biochemists to use in exploring the structure of proposed designs, as well as in more general applications such as exploring the molecular dynamics model itself. Its primary use is in modeling single large biomolecules in a bath of water acting as the solvent
Keywords :
biology computing; chemistry computing; data visualisation; graphical user interfaces; interactive systems; molecular configurations; molecular dynamics method; proteins; SMD system; atomic bonds; biochemists; communication components; external forces; graphical interface; interactive steering; internal forces; molecular dynamics calculations; molecular dynamics model; nonbonded interactions; protein design; protein molecules; single large biomolecules; visual steering; visualization; Bonding; Crystallography; Data analysis; Molecular biophysics; Nuclear magnetic resonance; Protein engineering; Proteins; Sequences; Shape; Solvents; Terminology; Testing; Visualization;
Journal_Title :
Computational Science & Engineering, IEEE
