Titlebook: Computational Molecular Dynamics: Challenges, Methods, Ideas; Proceeding of the 2n Peter Deuflhard,Jan Hermans,Robert D. Skeel Conference p

粗糙滥制

liposuction

Conformational Transitions of Proteins from Atomistic Simulationsependent protein kinase (cAPK) with a continuum (Poisson) model for the electrostatics. In this paper, we will put the previous results into context and discuss possible extensions into the dynamic regime.

宏伟

Agronomy

Nikolai Zamarashkin,Dmitry Zheltkovrticle densities rather than positions. It is concluded that MD is a mature technique for classical simulations of all-atom systems in the nanosecond time range, but is still in its infancy in reaching reliably into longer time scales.

Bumptious

confide

Molecular Dynamics Simulations: The Limits and Beyondrticle densities rather than positions. It is concluded that MD is a mature technique for classical simulations of all-atom systems in the nanosecond time range, but is still in its infancy in reaching reliably into longer time scales.

提炼

New Techniques for the Construction of Residue Potentials for Protein Foldingfind appropriate weights with which the various terms enter the total potential. For nine small test proteins, the new potential has local minima within 1.3-4.7Å of the PDB geometry, with one exception that has an error of 8.5Å.

BUST

Moises Torres,Jaime Klapp,Andrei Tchernykhays to explanation of elastic properties of proteins. First attempts to deduce potentials of mean force by discounting irreversible work performed on the system are summarized. The non-equilibrium statistical mechanics underlying analysis of SMD data is outlined.

Fermentation

Fast Random Cactus Graph Generationst demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales.

Ostrich

Panel Discussion 1: Questions and Answersfact allows one to explain the hysteresis phenomena observed experimentally in the nucleic acid-water system. The problem of self-organization in the nucleic acid-water system is of great importance for revealing physical mechanisms of the functioning of nucleic acids and for many specific practical fields.