Loading...
Please wait, while we are loading the content...
Similar Documents
Development of physics-based energy functions that predict mediumresolution structures for proteins of the a, beta, and a/h structural classes
| Content Provider | CiteSeerX |
|---|---|
| Author | Pillardy, Jarosław Czaplewski, Cezary Liwo, Adam Wedemeyer, William J. Lee, Jooyoung Ripoll, Daniel R. Arłukowicz, Piotr Ołdziej, Stanisław Arnautova, Yelena A. Scheraga, Harold A. |
| Abstract | The development of three physics-based energy functions (force fields), designed to simulate the restricted free energy of proteins of the R, β, and R/β structural classes, is described. Each force field corresponds to a particular weighting of the united-residue (UNRES) interactions defined in earlier work. 1-6 To find the optimal weights for the R, β, and R/β force fields, both the Z-score and energy gap of the native versus nonnative structures are minimized simultaneously for four benchmark proteins: 1pou (for the R force field), 1tpm (for the β force field), and 1bdd and betanova (for the R/β force field). The simultaneous minimization was carried out by using a novel Monte Carlo method, Vector Monte Carlo (VMC). For R-helical proteins, another weighting of the UNRES interactions (denoted as the R0 force field) was developed; this fourth force field is described in a companion publication (Lee, J. et al. J. Phys. Chem. B 2001, 105, 7291). The structural implications of the final weights of the four force fields, i.e., the relative contributions of the various UNRES interactions to stabilizing common structural motifs of proteins, are analyzed. The R0, R, β, and R/β force fields were used in the CASP4 exercise for ab initio protein-structure prediction with reasonable success. Finally, using a simple model system it was shown that the VMC protocol does not require exhaustive sampling of medium- and high-energy structures in order to optimize the parameters of the potential energy adequately. I. |
| File Format | |
| Journal | J. Phys. Chem., B |
| Language | English |
| Access Restriction | Open |
| Subject Keyword | Force Field Physics-based Energy Function Structural Class Mediumresolution Structure Fourth Force Field Particular Weighting Simultaneous Minimization Simple Model System Benchmark Protein Various Unres Interaction Optimal Weight Novel Monte Carlo Method Exhaustive Sampling Relative Contribution R-helical Protein High-energy Structure Native Versus Nonnative Structure R0 Force Field Final Weight Companion Publication Reasonable Success Vmc Protocol Common Structural Motif Energy Gap Structural Implication Potential Energy Unres Interaction Vector Monte Carlo Restricted Free Energy Casp4 Exercise Ab Initio Protein-structure Prediction |
| Content Type | Text |
| Resource Type | Article |
