Related papers: Quantitative Protein Dynamics from Dominant Foldin…
The folding of a peptide chain into a three dimensional structure is a thermodynamically driven process such that the chain naturally evolves to form domains of similar amino acids. The formation of this domain occurs by curling the one…
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native…
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…
Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
The dynamics of two 12-monomer heteropolymers on the square lattice is studied exactly within the master equation approach. The time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time…
This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
We simulate neutral evolution of proteins imposing conservation of the thermodynamic stability of the native state in the framework of an effective model of folding thermodynamics. This procedure generates evolutionary trajectories in…
A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
In this conceptual paper we propose to explore the analogy between ontic/epistemic description of quantum phenomena and interrelation between dynamics of conformational and functional states of proteins. Another new idea is to apply theory…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…
A variety of enhanced statistical and numerical methods are now routinely used to extract comprehensible and relevant thermodynamic information from the vast amount of complex, high-dimensional data obtained from intensive molecular…
We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…