A simple knowledge-based method for DNA atomic structure prediction from nucleic sequence is presented. We used free B-DNA crystal structures to estimate the distribution of trinucleotide base pairs and tetranucleotide base-pair steps conformational coordinates. We used these distributions as a basis to predict the 3D position of the non-hydrogen atoms of the nucleic bases of any arbitrary DNA ...

background : the aim of this study was to generate in silico 3d-structure of the envelope protein of ahfv using homology modeling method to further predict its conformational epitopes and help other studies to investigate its structural features using the model. methods : a 3d-structure prediction was developed for the envelope protein of alkhumra haemorrhagic fever virus (ahfv), an emerging ti...

A method is presented for the study of rare events such as conformational changes arising in activated processes whose reaction coordinate is not known beforehand and for which the assumptions of transition state theory are invalid. The method samples the energy landscape adaptively and determines the isoprobability surfaces for the transition: by definition the trajectories initiated anywhere ...

We present a recently developed clustering method and specify it for the problem of identification of metastable conformations in non-equilibrium biomolecular time series. The approach is based on variational minimization of some novel regularized clustering functional. In context of conformational analysis, it allows to combine the features of standard geometrical clustering techniques (like t...

Single-molecule pump probe (SM2P) is a novel, fluorescence-based technique that allows the study of ultrafast processes on the single-molecule level. Exploiting SM2P we have observed large variations (from 1 ps to below 100 fs) in the energy redistribution times of chemically identical molecules in the same sample. Embedding the molecules in a different matrix or changing the excitation wavelen...

We simulate the nonlocal Stokesian hydrodynamics of an elastic filament which is active due a permanent distribution of stresslets along its contour. A bending instability of an initially straight filament spontaneously breaks flow symmetry and leads to autonomous filament motion which, depending on conformational symmetry, can be translational or rotational. At high ratios of activity to elast...