Search Results - subject:"protein folding"

SOME EXPERIENCES WITH SOLVING SEMIDEFINITE PROGRAMMING RELAXATIONS OF BINARY QUADRATIC OPTIMIZATION MODELS IN COMPUTATIONAL BIOLOGY

ENGAU, ALEXANDER - In: Asia-Pacific Journal of Operational Research (APJOR) 31 (2014) 04, pp. 1450022-1

We present two recent integer programming models in molecular biology and study practical reformulations to compute solutions to some of these problems. In extension of previously tested linearization techniques, we formulate corresponding semidefinite relaxations and discuss practical rounding...

Persistent link: https://www.econbiz.de/10010888468

Global energy minimisation and cotranslational protein folding of HP models

Wood, Graham; Patton, Yumi; Fisher, David - In: Journal of Global Optimization 52 (2012) 3, pp. 575-590

Persistent link: https://www.econbiz.de/10010539286

Multifractal analysis of polyalanines time series

Figueirêdo, P.H.; Nogueira, E.; Moret, M.A.; Coutinho, … - In: Physica A: Statistical Mechanics and its Applications 389 (2010) 10, pp. 2090-2095

Multifractal properties of the energy time series of short α-helix structures, specifically from a polyalanine family, are investigated through the MF-DFA technique (multifractal detrended fluctuation analysis). Estimates for the generalized Hurst exponent h(q) and its associated multifractal...

Persistent link: https://www.econbiz.de/10011059078

Folding kinetics of two-state proteins based on the model of general random walk in native contact number space

Guo, J.S.; Mi, D.; Sun, Y.Q. - In: Physica A: Statistical Mechanics and its Applications 389 (2010) 4, pp. 761-766

and the numbers of native contacts from “kinetic viewpoint”. The protein folding speed limit and stability in this model …

Persistent link: https://www.econbiz.de/10011064221

Spin correlations in a non-frustrated one-dimensional spin system, and formation of the ground state as a model of protein folding

Kikuchi, Takeshi - In: Physica A: Statistical Mechanics and its Applications 388 (2009) 2, pp. 129-136

-state Arrhenius-like kinetics, such as observed in protein folding. In this paper, we present that the correlation functions of the … states, and thus our result denotes the implication to the protein folding mechanism. …

Persistent link: https://www.econbiz.de/10010589608

Folding/unfolding kinetics of lattice proteins studied using a simple statistical mechanical model for protein folding, I: Dependence on native structures and amino acid sequences

Abe, Haruo; Wako, Hiroshi - In: Physica A: Statistical Mechanics and its Applications 388 (2009) 17, pp. 3442-3454

model for protein folding that we developed earlier. We calculated a characteristic relaxation rate for the free energy …

Persistent link: https://www.econbiz.de/10010591738

Use of the Metropolis algorithm to simulate the dynamics of protein chains

Tiana, G.; Sutto, L.; Broglia, R.A. - In: Physica A: Statistical Mechanics and its Applications 380 (2007) C, pp. 241-249

The Metropolis implementation of the Monte Carlo algorithm has been developed to study the equilibrium thermodynamics of many-body systems. Choosing small trial moves, the trajectories obtained applying this algorithm agree with those obtained by Langevin's dynamics. Applying this procedure to a...

Persistent link: https://www.econbiz.de/10011063256

A study of Barstar folding events using boundary value simulations

Yunger, Jacob - In: Physica A: Statistical Mechanics and its Applications 386 (2007) 2, pp. 791-798

From extensive biophysical studies of protein folding, two competing mechanisms emerged: hydrophobic collapse and the …

Persistent link: https://www.econbiz.de/10011064695

Elucidation of conserved long-range interaction networks in proteins and their significance in determining protein topology

Higman, Victoria A.; Greene, Lesley H. - In: Physica A: Statistical Mechanics and its Applications 368 (2006) 2, pp. 595-606

profound insights into the mechanism of protein folding and stability. Combining this avenue of research with principles being …

Persistent link: https://www.econbiz.de/10010590100

Overdamped thermal ratchets in one and more dimensions. Kinesin transport and protein folding

González-Candela, Ernesto; Romero-Rochín, Víctor - In: Physica A: Statistical Mechanics and its Applications 372 (2006) 2, pp. 249-262

The overdamped thermal ratchet driven by an external (Orstein–Uhlenbeck) noise is revisited. The ratchet we consider is unbounded in space and not necessarily periodic. We briefly discuss the conditions under which current is obtained by analyzing the corresponding Fokker–Planck equation and...

Persistent link: https://www.econbiz.de/10011057135