ARTIST: an activated method in internal coordinate space for sampling protein energy landscapes

Proteins
Mi-Ran YunP Derreumaux

Abstract

We present the first applications of an activated method in internal coordinate space for sampling all-atom protein conformations, the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method differs from all previous internal coordinate-based studies aimed at folding or refining protein structures in that conformational changes result from identifying and crossing well-defined saddle points connecting energy minima. Our simulations of four model proteins containing between 4 and 47 amino acids indicate that this method is efficient for exploring conformational space in both sparsely and densely packed environments, and offers new perspectives for applications ranging from computer-aided drug design to supramolecular assembly.

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Citations

Jan 28, 2012·The Journal of Chemical Physics·L Dupuis, Normand Mousseau
Apr 22, 2006·The Journal of Chemical Physics·Jed W PiteraWilliam C Swope
Mar 17, 2007·The Journal of Chemical Physics·Mi-Ran YunP Derreumaux
Jan 25, 2008·Journal of Pharmaceutical Sciences·Carlton A TaftCarlos Henrique Tomich De Paula Da Silva
Mar 27, 2007·Current Opinion in Structural Biology·Hongxing Lei, Yong Duan
Aug 8, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Marco BaiesiLorenzo Tattini
Dec 11, 2012·Journal of Chemical Theory and Computation·Halim KusumaatmajaDavid J Wales

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