Titlebook: Computational Methods for Macromolecules: Challenges and Applications; Proceedings of the 3 Tamar Schlick,Hin Hark Gan Conference proceedin

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Structural and Dynamical Characterization of Nucleic Acid Water and Ion Binding Siteshe purpose of characterizing water and ion binding features. Here, we give an outline of some of the methods we used in order to extract structural and dynamical information concerning the first water and ion coordination shell, from MD simulations conducted on RNA and DNA structures. Coordinates fo

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A Test Set for Molecular Dynamics Algorithms for molecular dynamics (MD) simulation. Common types of calculations and desirable features of algorithms are surveyed, and these are used to guide selection of representative models. By including essential features of certain classes of molecular systems, but otherwise limiting the physical and qu

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Overcoming Instabilities in Verlet-I/r-RESPA with the Mollified Impulse Methodlinear instabilities that arise as numerical artifacts in Verlet-I/r-RESPA. These methods allow for lengthening of the longest time step used in molecular dynamics (MD). We provide evidence that MOLLY methods can take a longest time step that is 50% greater than that of Verlet-I/r-RESPA, for a given

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Structure Calculation of Protein Segments Connecting Domains with Defined Secondary Structure: A Simino acids) that include parts of defined secondary structure motifs. Loop structure calculation can be considered a particular case of this more challenging problem. The new algorithm first finds conformations representative of the segment structure tethered to the protein at one terminus only, and

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Automatic Identification of Metastable Conformations via Self-Organized Neural Networksov operator. Naive discretization of this operator would suffer from combinatorial explosion. As a first remedy, a pre-identification of essential degrees of freedom out of the set of torsion angles had been applied up to now. The present paper suggests a different approach based on neural networks:

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