NOn-Linear rigid Block NMA approach (NOLB) a new conceptually simple and computationally efficient method for non-linear normal mode analysis.
The key observation of our method is that the angular velocity of a residue can be interpreted as the result of an implicit force, such that the motion of the residue can be considered as a pure rotation about a certain center.
To assessed the method with three types of tests, visual inspection of the motions, the energy and topology comparisons between the linear and non-linear deformations, and the memory and CPU consumption of our method. There are, generally, three basic types of internal motions that a molecular system may exhibit. These are bending, stretching and twisting and shown below for a coiled-coil water-soluble protein from the cytoplasmic domain of a bacterial chemoreceptor (pdb code 2ch7).
Alexandre Hoffmann & Sergei Grudinin,Nano-D team, Inria/CNRS Grenoble, France e-mail: Sergei.Grudinin @ inria.fr
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NOLB for MacOS (v. 0.5)
NOLB for Linux (v. 0.5, supported GLIBC version >= 2.10)
GUI will be made available soon at https://www.samson-connect.net
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