Geometric simulation of flexible motion in proteins.
This chapter describes the use of physically simplified analysis and simulation methods-pebble-game rigidity analysis, coarse-grained elastic network modeling, and template-based geometric simulation-to explore flexible motion in protein structures. Substantial amplitudes of flexible motion can be explored rapidly in an all-atom model, retaining realistic covalent bonding, steric exclusion, and a user-defined network of noncovalent polar and hydrophobic interactions, using desktop computing resources. Detailed instructions are given for simulations using FIRST/FRODA software installed on a UNIX/Linux workstation. Other implementations of similar methods exist, particularly NMSim and FRODAN, and are available online. Topics covered include rigidity analysis and constraints, geometric simulation of flexible motion, targeting between known structures, and exploration of motion along normal mode eigenvectors.
Department of Physics, University of Bath, Bath, UK.
Stephen A
SA
Wells
D030562:Databases, Protein; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins