8,566 research outputs found
Protein Structure Determination Using Chemical Shifts
In this PhD thesis, a novel method to determine protein structures using
chemical shifts is presented.Comment: Univ Copenhagen PhD thesis (2014) in Biochemistr
An algorithm to enumerate all possible protein conformations verifying a set of distance constraints
International audienceBackground: The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only. Results: In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations. Conclusions: We described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides
Vibrational Density Matrix Renormalization Group
Variational approaches for the calculation of vibrational wave functions and
energies are a natural route to obtain highly accurate results with
controllable errors. However, the unfavorable scaling and the resulting high
computational cost of standard variational approaches limit their application
to small molecules with only few vibrational modes. Here, we demonstrate how
the density matrix renormalization group (DMRG) can be exploited to optimize
vibrational wave functions (vDMRG) expressed as matrix product states. We study
the convergence of these calculations with respect to the size of the local
basis of each mode, the number of renormalized block states, and the number of
DMRG sweeps required. We demonstrate the high accuracy achieved by vDMRG for
small molecules that were intensively studied in the literature. We then
proceed to show that the complete fingerprint region of the sarcosyn-glycin
dipeptide can be calculated with vDMRG.Comment: 21 pages, 5 figures, 4 table
- …