Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

<p>Abstract</p> <p>Background</p> <p>Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI) is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles.</p> <p>Results</p> <p>In this paper, we propose a computational method to predict DDI using support vector machines (SVMs), based on domains represented as interaction profile hidden Markov models (ipHMM) where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB). Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD). Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to <it>InterPreTS </it>(Interaction Prediction through Tertiary Structure), an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure.</p> <p>Conclusions</p> <p>We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on the web at <url>http://liao.cis.udel.edu/pub/svdsvm</url>. Implemented in Matlab and supported on Linux and MS Windows.</p

El consumo de productos ecológicos en España : marketing y publicidad

La realidad del mercado ecológico en España es que es un sector fuerte en producción y débil en comercialización interna. Este hecho ha provocado que el consumo en España esté muy por debajo de sus posibilidades en comparación con otros países europeos. Al mismo tiempo, la distribución del producto ecológico se centra en canales de venta especializados, cuya cuota de mercado es muy inferior a la del canal de venta convencional. En este contexto, el conocimiento del producto ecológico por parte del consumidor y distribuidor convencionales es limitado, y la presencia de estos productos en mercados, tiendas, supermercados, etc., escasa e irregular. Estudiar el aumento de la demanda; el perfil del consumidor, sus variables sociodemográficas, su actitud hacia la ecología y su preocupación por tener una vida más saludable, y como se centra la publicidad y el marketing en los productos ecológicos ha sido el principal objetivo de este trabajo. Analizada la literatura y recopilados todos los datos, hemos podido analizarlos y verificar que tanto la producción como el consumo de productos ecológicos se está afianzando cada vez más y es una tendencia que va a seguir creciendo en los próximos años, debido a que las características de este tipo productos generan muchas ventajas frente a uno convencional, ya que no solo proporciona beneficios para la salud del consumidor sino también para el entorno natural y humano donde se producen

Thermodynamic Properties Of In1-xBxP Semiconducting Alloys: A First-Principles Study

We have carried out first-principles total-energy calculations in order to study the electronic structure and thermodynamic properties of In 1-xBxP semiconducting alloys using the GGA and LDA formalisms within density functional theory (DFT) with a plane-wave ultrasoft pseudopotential scheme. We have also taken into account the correlation effects of the 3d-In orbitals within the LDA+U method to calculate the band-gap energy. We use special quasirandom structures to investigate the effect of the substituent concentration on structural parameter, band gap energy, mixing enthalpy and phase diagram of In1-xBxP alloys for x = 0, 0.25, 0.50, 0.75 and 1. It is found that the lattice parameters of the In 1-xBxP alloys decrease with B-concentration, showing a negative deviation from Vegard's law, while the bulk modulus increases with composition x, showing a large deviation from the linear concentration dependence (LCD). The calculated band structure presents a similar behavior for any B-composition using LDA, PBE or LDA+U approach. Our results predict that the band-gap shows a x-dependent nonlinear behavior. Calculated band gaps also shows a transition from (Γ→Γ)-direct to (Γ→Δ)- indirect at x = 0.611 and 0.566 for LDA and PBE functionals, respectively. Our calculations predict that the In1-xBxP alloy to be stable at unusual high temperature for both LDA and PBE potentials. © 2014 Elsevier B.V. All rights reserved

Computational study of Mn-doped GaN polar and non-polar surfaces

First-principles calculations were carried out in order to study the magnetic, electronic and structural properties of the Mn-doped polar GaN(0 0 0 1) and non-polar GaN(101¯0) and GaN(112¯0) surfaces, with the aim of refining the growth of thin films of this material. The results indicate that the surfaces present magnetization of approximately 4.0 μβ/Mn atom, in agreement with the recently reported theoretical and experimental results. Calculations of surface formation energy indicate that Mn atoms are incorporated into top surface layers (first and second) of GaN, being the MnGa incorporation in the polar surface more energetically favourable than in the nonpolar surfaces. In addition, it was observed that the magnetic coupling between the Mn impurities depends on the surface orientation, which could be useful for the design of magnetic nanodevices

Theoretical prediction of the electronic and thermodynamic properties of YN-ZrN solid solutions

In this study, the results of structural parameters, electronic structure, and thermodynamic properties of the ZrxY1-xN solid solutions are presented. The effect of zirconium composition on lattice constant, and bulk modulus shows nonlinear dependence on concentration. Deviations of the lattice constant from Vegard's law and deviations of the bulk modulus from linear concentration dependence were found. Our findings indicate that the ZrxY1-xN solid solutions are metallic for x = 0.25, 0.5, 0.75. The calculated excess mixing enthalpy is positive over the entire zirconium composition range. The positive mixing enthalpies for ZrxY1-xN alloys indicate the existence of miscibility gaps and spinodal decompositions. The effect of temperature on the volume, bulk modulus, Debye temperature, and the heat capacity for ZrxY1-xN alloys were analyzed using the quasi-harmonic Debye model. Results show that the heat capacity is slightly sensitive to composition as temperature increases

Structural parameters, band-gap bowings and phase diagrams of zinc-blende Sc1-xInxP ternary alloys: A FP-LAPW study

Using first-principles total-energy calculations, we investigate the structural, electronic and thermodynamic properties of the cubic Sc 1-xInxP semiconducting alloys. The calculations are based on the fullpotential linearized-augmented plane wave (FP-LAPW) method within density functional theory (DFT). The exchange-correlation effect is treated by both local-density approximation (LDA) and generalizedgradient approximation (GGA). In the latter approach, both Perdew-Burke-Ernzerhof (PBE) and EngelVosko (EV) functional of the exchange-correlation energy were used. The effect of atomic composition on structural parameters, band-gap energy, mixing enthalpy and phase diagram was analyzed for x = 0, 0.25, 0.5, 0.75, 1. Lattice constant, bulk modulus, and band-gap energy for zinc-blende Sc1-xIn xP alloys show nonlinear dependence on the aluminium composition x. Deviations of the lattice constant from Vegard's law, and deviations of the bulk modulus and band-gap energy from linear concentration dependence (LCD) were found

Effects of scandium composition on the structural, electronic, and thermodynamic properties of SCxY1-x metallic alloys

The aim of this work is to analyse the compositional dependence of the structural, electronic and thermodynamic properties of alloys. Density functional calculations have been carried out to reveal compositional dependence of the structural, electronic and thermodynamic properties of alloys. The lattice constants of the binary compounds are in fairly good agreement with the available experimental data. The variation of calculated lattice constant with scandium concentration is almost linear, and shows a slight deviation from Vegards law. The effect of scandium composition on bulk modulus gives nonlinear dependence on concentration x. A small deviation of the bulk modulus from linear concentration dependence was observed. The metallic nature of binary precursor compounds ScP and YP was confirmed. Our findings indicate that the alloys are metallic for 0.25, 0.5, 0.75. The calculated excess mixing enthalpy is positive over the entire scandium composition range. The positive mixing enthalpies indicate meta-stability of the alloys at high temperatures. The effect of temperature on the volume, bulk modulus, Debye temperature and the heat capacity for alloys were analysed using the quasi-harmonic Debye model. Results show that the heat capacity is slightly sensitive to composition as temperature increases

Theoretical study of structural stability, elastic, electronic and thermodynamic properties of ScxGa1−x P compounds by ab initio calculations

We carried out a theoretical study on the structural stability, elastic, electronic and thermodynamic properties of the ScxGa1 x P compound (x ¼ 0, 0.25, 0.50, 0.75 and 1) in the ZnS and NaCl crystallographic phases. For this purpose, we performed ab initio calculations using the DFT within LDA and GGA approximations. To solve the Kohn-Sham equations, we implemented the accurate full-potential linearized augmented plane wave method. From the results obtained, it can be noted that for the 0x0.30 range, the most stable structure of ScxGa1 x P is the ZnS phase, and for the 0.30<x1 interval, the most stable structure is the NaCl phase. The structural results also show a phase transition from the ZnS to NaCl at a pressure of ~ 2.84 GPa for a Sc concentration value of 25%. Electronic band structure analysis shows that in the ZnS phase, for a 25% of Sc concentration, ScxGa1 x P is a direct semiconductor, and from 50% to 100% concentrations in the NaCl phase, the compound exhibits a metallic behavior. Calculated phase diagrams predict ScxGa1 x P to be stable as homogeneous alloy phases at high temperature for both ZnS and NaCl phase

Structural, electronic and magnetic properties of Ti-doped polar and nonpolar GaN surfaces

Based on density functional theory, first-principles calculations were performed in order to study the titanium incorporation on polar and nonpolar GaN surfaces. The formation energy calculations indicate that Ti impurity atoms prefer to incorporate in surface layers (first and second) of GaN. It is also concluded that the incorporation of Ti atoms in Ga-substitutional sites are more energetically favorable compared with N-substitutional or interstitial sites on the polar and nonpolar GaN surfaces. For Ti-rich growth conditions, formation energy calculations show the formation of TixN layers on the a and c GaN surfaces, which corroborates recent experimental observations. Results also display that the 3d-Ti states are the responsible for the metallization of the surface on the c and m planes, forming an intermetallic alloy (TixN), which could be used as low-resistance ohmic contacts for GaN. In addition, the magnetic properties with Ti doping show magnetization of about 1.0 μB/Ti atom for the nonpolar GaN surfaces

La Acumulación De Basuras Como Material Geotécnico I: Fundamentos Técnicos

Human wastes constitute an evergrowing by-product of civilization. Several catastrophic landslides have taken place in these so-called sanitary land fills. It is apparent that geotechnical and environmental engineers follow divergent paths to solve the related technical problems. Part I of this paper addresses the development of mechanical sciences leading to Soil Mechanics (1925) and Rock Mechanics (1960). Part II is dedicated to show how these sciences and arts or geomechanics are applied to huge accumulations of garbage of what could be referred to as anthropic waste deposits.