Free energy landscape of a minimalist salt bridge model

Free-energy landscape of kinesin by a realistic lattice model.

Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Gō interactions. By means of the multi-self-overlap ensemble Monte Carlo method and the principal component analysis, the free-energy landscape is obtained. It is shown that kinesins have two subdomains that exhibit partial folding/unfolding at functionally important reg...

The energy landscape for solvent dynamics in electron transfer reactions: A minimalist model

Aging in a free-energy landscape model for glassy relaxation.

The aging properties of a simple free-energy landscape model for the primary relaxation in supercooled liquids are investigated. The intermediate scattering function and the rotational correlation functions are calculated for the generic situation of a quench from a high temperature to below the glass transition temperature. It is found that the reequilibration of molecular orientations takes l...

Mesoscopic model for free-energy-landscape analysis of DNA sequences.

A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores the sequence interacting more importantly with open base pairs of the DNA chain. We apply the model to promoter sequences of different organisms. The free ene...

ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2

UNLABELLED Component (bridge: ΔΔGbrd , background: ΔΔGprot , desolvation: ΔΔGdsolv ) and net (ΔΔGnet ) energy-terms of salt-bridge-structure (SBS) are auto-generated by the program ADSBET that makes use of general purpose Adaptive Poison Boltzmann Solver (APBS) method. While the procedure reports gross energy terms (Kcal Mol(-1) ), report on bond-multiplicity corrected normalized energyterms (K...