On the low-temperature phase of the three-state antiferromagnetic Potts model on the simple cubic lattice

The three-state antiferromagnetic Potts model on the simple cubic lattice is investigated using the cluster variation method in the cube and the star-cube approximations. The broken-sublattice-symmetry phase is found to be stable in the whole low-temperature region, contrary to previous results obtained using a modified cluster variation method. The tiny free energy difference between the broken-sublattice-symmetry and the permutationally-symmetric-sublattices phases is calculated in the two approximations and turns out to be smaller in the (more accurate) star-cube approximation than in the cube one.Comment: 4 pages REVTeX + 2 PostScript figures, to be published in Phys. Rev. E as a Rapid Communicatio

Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?

The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures

NNcon: improved protein contact map prediction using 2D-recursive neural networks

Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008. Both NNcon server and software are available at http://casp.rnet.missouri.edu/nncon.html

NNcon: improved protein contact map prediction using 2D-recursive neural networks

Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008. Both NNcon server and software are available at http://casp.rnet.missouri.edu/nncon.html

Electronic Structure of a Hydrogenic Acceptor Impurity in Semiconductor Nano-structures

The electronic structure and binding energy of a hydrogenic acceptor impurity in 2, 1, and 0-dimensional semiconductor nano-structures (i.e. quantum well (QW), quantum well wire (QWW), and quantum dot (QD)) are studied in the framework of effective-mass envelope-function theory. The results show that (1) the energy levels monotonically decrease as the quantum confinement sizes increase; (2) the impurity energy levels decrease more slowly for QWWs and QDs as their sizes increase than for QWs; (3) the changes of the acceptor binding energies are very complex as the quantum confinement size increases; (4) the binding energies monotonically decrease as the acceptor moves away from the nano-structures’ center; (5) as the symmetry decreases, the degeneracy is lifted, and the first binding energy level in the QD splits into two branches. Our calculated results are useful for the application of semiconductor nano-structures in electronic and photoelectric devices

Coulomb gap in a model with finite charge transfer energy

The Coulomb gap in a donor-acceptor model with finite charge transfer energy $\Delta$ describing the electronic system on the dielectric side of the metal-insulator transition is investigated by means of computer simulations on two- and three-dimensional finite samples with a random distribution of equal amounts of donor and acceptor sites. Rigorous relations reflecting the symmetry of the model presented with respect to the exchange of donors and acceptors are derived. In the immediate neighborhood of the Fermi energy $\mu$ the the density of one-electron excitations $g(\epsilon)$ is determined solely by finite size effects and $g(\epsilon)$ further away from $\mu$ is described by an asymmetric power law with a non-universal exponent, depending on the parameter $\Delta$.Comment: 10 pages, 6 figures, submitted to Phys. Rev.

Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives

BACKGROUND: Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the predicted 3D structures. The correlated mutations (CM) method serves as the most promising approach and it has been used to predict amino acids pairs that are distant in the primary sequence but form contacts in the native 3D structure of homologous proteins. RESULTS: Here we report a new implementation of the CM method with an added set of selection rules (filters). The parameters of the algorithm were optimized against fifteen high resolution crystal structures with optimization criterion that maximized the confidentiality of the predictions. The optimization resulted in a true positive ratio (TPR) of 0.08 for the CM without filters and a TPR of 0.14 for the CM with filters. The protocol was further benchmarked against 65 high resolution structures that were not included in the optimization test. The benchmarking resulted in a TPR of 0.07 for the CM without filters and to a TPR of 0.09 for the CM with filters. CONCLUSION: Thus, the inclusion of selection rules resulted to an overall improvement of 30%. In addition, the pair-wise comparison of TPR for each protein without and with filters resulted in an average improvement of 1.7. The methodology was implemented into a web server that is freely available to the public. The purpose of this implementation is to provide the 3D structure predictors with a tool that can help with ranking alternative models by satisfying the largest number of predicted contacts, as well as it can provide a confidence score for contacts in cases where structure is known

Hydrophilicity Matching – A Potential Prerequisite for the Formation of Protein-Protein Complexes in the Cell

A binding event between two proteins typically consists of a diffusional search of binding partners for one another, followed by a specific recognition of the compatible binding sites resulting in the formation of the complex. However, it is unclear how binding partners find each other in the context of the crowded, constantly fluctuating, and interaction-rich cellular environment. Here we examine the non-specific component of protein-protein interactions, which refers to those physicochemical properties of the binding partners that are independent of the exact details of their binding sites, but which can affect their localization or diffusional search for one another. We show that, for a large set of high-resolution experimental 3D structures of binary, transient protein complexes taken from the DOCKGROUND database, the binding partners display a surprising, statistically significant similarity in terms of their total hydration free energies normalized by a size-dependent variable. We hypothesize that colocalization of binding partners, even within individual cellular compartments such as the cytoplasm, may be influenced by their relative hydrophilicity, potentially in response to local hydrophilic gradients