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...It is implemented on the graphics processing unit (GPU) using the OpenGL Shading Language (GLSL).
SimpleGVXR is a smaller library build on the top of gVirtualXRay. It provides wrappers to Python, R, Ruby, Tcl, C#, Java, and GNU Octave.
Weighted Implementation of Suboptimal Paths (WISP)
UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp
Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path...
ASCEND is a modelling environment and solver for large or small systems of non-linear equations, for use in engineering, thermodynamics, chemistry, physics, mathematics and biology. Solvers for both steady and dynamic (NLA & DAE) problems, are provid