bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of protein–protein interaction using conformational space annealing
Authors: Lee Kyoungrim , Sim Jaehyun , Lee Jooyoung 
Published: June 2005

AbstractWe apply conformational space annealing (CSA), an efficient global optimization method, to the study of protein–protein interaction. The CSA is incorporated into the Tinker molecular modeling package along with a B‐spline method for CAPRI Round 5 experiments. We have used an energy function for the protein–protein interaction that consists of electrostatic interaction, van der Waals interaction, and solvation energy terms represented by the occupancy desolvation method. The parameters of the AMBER94 all‐atom empirical force field are used. Each energy term is calculated by precalculated grid potentials and B‐spline method approximation. The ligand protein is placed inside a sphere of 50 Å radius centered at an appropriate location, and the CSA rigid docking studies are carried out to find stable complexes. Up to 10 complexes are selected using the K‐mean clustering method and biological information when available. These complexes are energy‐minimized for further refinement by considering the flexibility of interacting proteins. The results show that the CSA method has a potential for the study of protein–protein interaction. Proteins 2005;60:257–262. © 2005 Wiley‐Liss, Inc.
Incorporation of flexibility into rigid‐body docking: Applications in rounds 3–5 of CAPRI
Authors: Smith Graham R. , Fitzjohn Paul W. , Page Christopher S. , Bates Paul A. 
Published: June 2005

AbstractWe have submitted models for all 9 targets in Rounds 3–5 of CAPRI and have predicted at least 30% of the correct contacts for 4 of the targets and at least 10% of the correct contacts for another 4 targets. We have employed a variety of techniques but have had the greatest success by combining established rigid‐body docking with a variety of initial conformations generated by molecular dynamics. Proteins 2005;60:263–268. © 2005 Wiley‐Liss, Inc.
Docking essential dynamics eigenstructures
Authors: Mustard Diana , Ritchie David W. 
Published: June 2005

AbstractThis article describes our attempts to dock the targets in CAPRI Rounds 3–5 using Hex 4.2, and it introduces a novel essential dynamics approach to generate multiple feasible conformations for docking. In the blind trial, the basic Hex algorithm found 1 high‐accuracy solution for CAPRI Target 12, and several further medium‐ and low‐accuracy solutions for Targets 11, 12, 13, and 14. Subsequent a posteriori docking of the targets using essential dynamics “eigenstructures” was found to give consistently better predictions than rigidly docking only the unbound or model‐built starting structures. Some suggestions to improve this promising new approach are presented. Proteins 2005;60:269–274. © 2005 Wiley‐Liss, Inc.
Scoring docking models with evolutionary information
Authors: Tress Michael , de Juan David , Graña Osvaldo , Gómez Manuel J. , Gómez‐Puertas Paulino , González Jose M. , López Gonzalo , Valencia Alfonso 
Published: June 2005

AbstractWe have developed methods for the extraction of evolutionary information from multiple sequence alignments for use in the study of the evolution of protein interaction networks and in the prediction of protein interaction. For Rounds 3, 4, and 5 of the CAPRI experiment, we used scores derived from the analysis of multiple sequence alignments to submit predictions for 7 of the 12 targets. Our docking models were generated with Hex and GRAMM, but all our predictions were selected using methods based on multiple sequence alignments and on the available experimental evidence. With this approach, we were able to predict acceptable level models for 4 of the targets, and for a fifth target, we located the residues involved in the binding surface. Here we detail our successes and highlight several of the limitations and problems that we faced while dealing with particular docking cases. Proteins 2005;60:275–280. © 2005 Wiley‐Liss, Inc.
Protein–protein docking using 3D‐Dock in rounds 3, 4, and 5 of CAPRI
Authors: Carter Phil , Lesk Victor I. , Islam Suhail A. , Sternberg Michael J.E. 
Published: June 2005

AbstractIn rounds 3–5 of CAPRI, the community‐wide experiment on the comparative evaluation of protein–protein docking for structure prediction, we applied the 3D‐Dock software package to predict the atomic structures of nine biophysical interactions. This approach starts with an initial grid‐based shape complementarity search. The product of this is a large number of potential interacting conformations that are subsequently ranked by interface residue propensities and interaction energies. Refinement through detailed energetics and optimization of side‐chain positions using a rotamer library is also performed. For rounds 3, 4, and 5 of the CAPRI evaluation, where possible, we clustered functional residues on the surfaces of the monomers as an indication of binding sites, using sequence based evolutionary conservations. In certain targets this provided a very useful tool for identifying the areas of interaction. During round 5, we also applied the techniques of side‐chain trimming and geometrical clustering described in the literature. Of the nine target complexes in rounds 3–5, we predicted conformations that contained at least some correct contact residues for seven of these systems. For two of the targets, we submitted predictions that were considered as medium‐quality. These were a nidogen–laminin complex for target 8 (T08) and a serine‐threonine phosphatase bound to a targeting subunit (T14). For a further three target systems, we produced models that were rated as acceptable predictions. Proteins 2005;60:281–288. © 2005 Wiley‐Liss, Inc.
Development and testing of an automated approach to protein docking
Authors: Tovchigrechko Andrei , Vakser Ilya A. 
Published: June 2005

AbstractA new version of GRAMM was applied to Targets 14, 18, and 19 in CAPRI Round 5. The predictions were generated without manual intervention. Ten top‐ranked matches for each target were submitted. The docking was performed by a rigid‐body procedure with a smoothed potential function to accommodate conformational changes. The first stage was a global search on a fine grid with a projection of a smoothed Lennard–Jones potential. The top predictions from the first stage were subjected to the conjugate gradient minimization with the same smoothed potential. The resulting local minima were reranked according to the weighted sum of Lennard–Jones potential, pairwise residue–residue statistical preferences, cluster occupancy, and the degree of the evolutionary conservation of the predicted interface. For Targets 14 and 18, the conformation of the complex was predicted with root‐mean‐square deviation (RMSD) of the ligand interface atoms 0.68 Å and 1.88 Å correspondingly. For Target 19, the interface areas on both proteins were correctly predicted. The performance of the procedure was also analyzed on the benchmark of bound–unbound protein complexes. The results show that, on average, conformations of only 3 side‐chains need to be optimized during docking of unbound structures before the backbone changes become a limiting factor. The GRAMM‐X docking server is available for public use at http://www.bioinformatics.ku.edu. Proteins 2005;60:296–301. © 2005 Wiley‐Liss, Inc.
Progress in computation and amide hydrogen exchange for prediction of protein–protein complexes
Authors: Law Dennis , Hotchko Matthew , Ten Eyck Lynn 
Published: June 2005

AbstractThe macromolecular docking problem that must be solved for experimental biologists is prediction of the structures of complexes for which the components are known or reliably modeled in the unbound state, but the structure of the complex is unknown. The current state of the art in macromolecular docking is such that solving this problem usually requires supplementary experimental chemical and/or biological information to evaluate computational predictions. Amide 1H/2H exchange measured by mass spectroscopy is a promising approach for obtaining such information, because it can reveal interfacial regions of each member of the complex and identify regions of conformational flexibility in the structure. In a previous article (Anand et al., Proc Natl Acad Sci USA 2003;100:13264–13269), we used 1H/2H exchange data to predict the structure of a complex between regulatory and catalytic subunits of protein kinase A. Comparison of the prediction with a recent crystal structure determination (Kim et al., Science 2005;307:690–696) showed large conformational change in the regulatory subunit on formation of the complex. Analysis of the prediction, previous CAPRI results, novel data processing methods for the 1H/2H exchange data, and new fragment docking computations give grounds for cautious optimism that this method can be useful even in cases of substantial conformational change. Proteins 2005;60:302–307. © 2005 Wiley‐Liss, Inc.
Improving CAPRI predictions: Optimized desolvation for rigid‐body docking
Authors: Fernández‐Recio Juan , Abagyan Ruben , Totrov Maxim 
Published: June 2005

AbstractThe ICM Docking and Interface Side‐Chain Optimization (ICM‐DISCO) showed promising predictive results during the first CAPRI experiment by successfully finding medium‐ or high‐accuracy models in 3 of the 7 targets. A key factor was the ability to recognize near‐native rigid‐body geometries in a relatively low number of alternative docking poses, together with the successful refinement of the rigid‐body docking interfaces. Since then, we have focused on improving the scoring function to optimally discriminate the near‐native rigid‐body conformations. For that, we have defined a new desolvation descriptor for rigid‐body docking, based on atomic solvation parameters (ASPs) derived from octanol–water transfer experiments. This and other new approaches have been gradually incorporated into our docking procedure during our participation on the second CAPRI experiment. Overall, we produced reasonable models for 8 of the 9 official targets. Especially encouraging were those cases in which a homology model of 1 of the subunits had to be used during the docking simulations. And not less gratifying has been the successful prediction of antibody–antigen targets in a completely automatic, unrestrained fashion. In summary, our success rate (89%) shows a consistent improvement over the previous CAPRI rounds, and suggests that a correct desolvation description is key for improved protein–protein docking predictions. Proteins 2005;60:308–313. © 2005 Wiley‐Liss, Inc.
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
Authors: Zhang Chi , Liu Song , Zhou Yaoqi 
Published: June 2005

AbstractWe entered the CAPRI experiment during the middle of Round 4 and have submitted predictions for all 6 targets released since then. We used the following procedures for docking prediction: (1) the identification of possible binding region(s) of a target based on known biological information, (2) rigid‐body sampling around the binding region(s) by using the docking program ZDOCK, (3) ranking of the sampled complex conformations by employing the DFIRE‐based statistical energy function, (4) clustering based on pairwise root‐mean‐square distance and the DFIRE energy, and (5) manual inspection and relaxation of the side‐chain conformations of the top‐ranked structures by geometric constraint. Reasonable predictions were made for 4 of the 6 targets. The best fraction of native contacts within the top 10 models are 89.1% for Target 12, 54.3% for Target 13, 29.3% for Target 14, and 94.1% for Target 18. The origin of successes and failures is discussed. Proteins 2005;60:314–318. © 2005 Wiley‐Liss, Inc.
Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition
Authors: Ma Xiao Hui , Li Chun Hua , Shen Long Zhu , Gong Xin Qi , Chen Wei Zu , Wang Cun Xin 
Published: June 2005

AbstractAn efficient biologically enhanced sampling geometric docking method is presented based on the FTDock algorithm to predict the protein–protein binding modes. The active site data from different sources, such as biochemical and biophysical experiments or theoretical analyses of sequence data, can be incorporated in the rotation–translation scan. When discretizing a protein onto a 3‐dimensional (3D) grid, a zero value is given to grid points outside a sphere centered on the geometric center of specified residues. In this way, docking solutions are biased toward modes where the interface region is inside the sphere. We also adopt a multiconformational superposition scheme to represent backbone flexibility in the proteins. When these procedures were applied to the targets of CAPRI, a larger number of hits and smaller ligand root‐mean‐square deviations (RMSDs) were obtained at the conformational search stage in all cases, and especially Target 19. With Target 18, only 1 near‐native structure was retained by the biologically enhanced sampling geometric docking method, but this number increased to 53 and the least ligand RMSD decreased from 8.1 Å to 2.9 Å after performing multiconformational superposition. These results were obtained after the CAPRI prediction deadlines. Proteins 2005;60:319–323. © 2005 Wiley‐Liss, Inc.
Simazine dynamics in a vineyard soil at Casablanca valley, Chile
Authors: Alister Claudio , Lopez Ramiro , Kogan Marcelo 
Published: June 2005

AbstractField dissipation, soil movement and laboratory leaching studies were performed to elucidate the effect of two rainfall amounts in the behaviour and environmental fate of simazine under climatic conditions at Casablanca Valley, Chile. Dissipation and soil movement were studied in a field vineyard with a sandy loam soil (Inceptisol; 74.08% sand; 14.87% silt and 11.04% clay). Simazine was applied to bare soil at 2.0 kg AI ha−1, and its concentration was measured using immunoassay (ELISA) at 0, 10, 20, 40 and 90 days after application under two rainfall amounts, natural field conditions (39 mm) and modified conditions (39 + 180 mm). Simazine leaching was studied using soil core PVC lysimeters (0.9 m height; 0.22 m diameter). Field dissipation data were adjusted with a bi‐exponential model. Half‐life (DT50) values varied between 31.3 (±2.5) and 19.0 (±4.2) days under natural and modified conditions, respectively. Simazine Kd varied from 0.42 to 2.15 (Koc 32.6–216.2) in the soil profile. Simazine was detected at a 90‐cm soil depth in concentrations of 0.0085 (±0.0043) mg kg−1 and 0.0321 (±0.001) mg kg−1 under field and modified conditions, respectively. The maximum simazine leachate concentrations were 0.013 (±0.00084) mg litre−1 (0.012% of total applied simazine) and 0.0084 (±0.00082) mg litre−1 (0.11% of total applied simazine) for field and modified conditions respectively. These data indicate that water quantity has a significant effect on the DT50 and the amount of simazine that moved through the soil profile, but not on the soil depth reached by this herbicide. Copyright © 2005 Society of Chemical Industry
AC‐Stark effect in a semi‐spherical quantum dot
Authors: Rodríguez Arezky H. , Meza‐Montes L. , Trallero‐Giner C. , Ulloa S. E. 
Published: June 2005

AbstractWe present a theoretical approach to study the effects of an ac‐field applied to quantum dots with semi‐spherical symmetry. Using the Floquet formalism for this periodically driven system, the time‐dependent Hamiltonian in the effective mass approximation is solved. We show that the Hilbert space of solutions is separated into orthogonal subspaces with different z‐component of the angular momentum. We give an explicit analytical representation for electronic states as a function of the intensity and frequency of the electric field. Under the two level approximation, two particular cases are studied: the low‐ and high‐frequency regimes, which result of comparing the ac‐field frequency to the characteristic level splitting at zero field. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Chirality assignments in carbon nanotubes based on resonant Raman scattering
Authors: Thomsen C. , Telg H. , Maultzsch J. , Reich S. 
Published: June 2005

AbstractResonant Raman scattering is a well‐known method for investigating the optical transitions in solids [1]. Here we show that the fully symmetric radial breathing mode (RBM) of carbon nanotubes can be used to derive an assignment of their chiral indices. Our assignment is based on a plot of the resonance maxima for the radial breathing modes as a function of laser excitation energy versus inverse ωRBM, a so‐called Kataura plot. Different from recent luminescence measurements [2], the chirality of both semiconducting and metallic nanotubes can be investigated. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
XPS, SEM and XRD investigations of CdSe films prepared by chemical bath deposition
Authors: Vargas‐Hernández C. , Lara V. C. , Vallejo J. E. , Jurado J. F. , Giraldo O. 
Published: June 2005

AbstractChemical bath deposition (CBD), a direct low cost technique that involves a cadmium salt solution, a complexing agent and a chalcogen source, was used to prepare CdSe semiconductor films. The most favourable conditions for acceptable quality CdSe films grown on glass were obtained. Commercially available microscope glass slides (with a size of 1 cm × 1 cm × 1 mm) were used as substrates to deposit CdSe films. CdSe films were deposited in a freshly prepared aqueous solution containing CdSO4 (0.2–0.4 M), NH4OH (3.8–14 M) as a complexing agent for slow release of Cd2+ ions, and Na2SeSO3 (0.118 and 0.16) as a source of Se2– ions. The solutions were prepared in deionized water. The glass slides were immersed in a mixture of CdSO4–NH4OH for 5 min before the solution of Na2SeSO3 was added. The bath temperature varied from 20 to 60 °C. Structural and morphological quality of the films was analyzed by XRD, SEM, EDS, and XPS. The results show that the crystallinity of the CdSe films as‐deposited is improved by increasing temperature. The initial growth stages of CdSe films at 20 and 60 °C start on CdOx and Cd(OH)2 buffer layers respectively. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Tunneling and ferroelectric properties of SRO/PZT/Pt capacitor structures
Authors: Delgado E. , Cortes A. , Lopera W. , Osorio J. , Prieto P. 
Published: June 2005

AbstractTunneling measurements at different temperatures were carried out in SrRuO3/Pb(Zr0.52Ti0.48)O3/Pt capacitor structures grown on (100) SrTiO3 single‐crystal substrates using a high‐oxygen pressure on axis sputtering technique. Crystalline quality and structure were measured by X‐ray diffractometry (XRD). The surface roughness and morphology were studied by atomic force microscopy (AFM). Electrical characterization was carried out by P–E hysteresis loops and fatigue measurements on different capacitors. Capacitor structures with electrode areas of 5.0 × 10–4 and 6.5 × 10–3 cm2 revealed remanent polarizations around of 30 µC/cm2 at room temperature. Current–voltage characteristics (I–V curves) demonstrated slight hysteretic behavior while the bias voltage dependence of the dynamic conductance measurements presented a parabolic characteristic, indicating electron tunneling. A Brinkman fit of the normalized conductance curves as a function of temperature gives barrier thicknesses below 2 nm. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Cd desorption induced by Zn exposure during atomic layer epitaxy of CdxZn1–xTe
Authors: Larramendi E. M. , de Melo O. , Hernández‐Calderón I. 
Published: June 2005

AbstractThe substitution of surface Cd atoms by Zn atoms during the growth of CdxZn1–xTe by atomic layer epitaxy has been studied as a function of substrate temperature and Zn exposure time by means of the analysis of the photoluminescence spectra of CdxZn1–xTe/ZnTe quantum wells. For substitution and desorption of Cd induced by Zn exposure an activation energy of 1.5 eV was found. The complexity of this desorption process was denoted by the fourth order of the kinetic reaction in the 250–280 °C temperature range. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantum islands formation and optical properties of CdZnTe/ZnTe quantum wells grown by atomic layer epitaxy
Authors: Larramendi E. M. , de Melo O. , Hernández‐Calderón I. 
Published: June 2005

AbstractIn this work we report on optical properties of CdZnTe/ZnTe quantum wells (QWs) grown by atomic layer epitaxy (ALE) and the formation of quantum island during the QWs growth. The photoluminescence (PL) emission of QWs at lower temperature (250 °C) consists of two peaks. From studying the dependence of the PL integrated emission with the excitation intensity, it is found that theses both PL features have different nature. The high‐energy sharp peak is associated to the excitonic recombination in the CdZnTe/ZnTe alloy quantum well while the low‐energy contributions (wide peak) are assigned to the recombination in the quantum islands (compositional fluctuations with high Cd molar fraction embedded inside the active zone of the QW). The temperature dependence of the PL FWHM, energy, and intensity confirm the enhancement of the quantum efficiency of optical recombination in quantum islands. The formation of quantum islands is more likely at lower growth temperature as evidenced by the optical properties of the QWs grown at different temperatures. Since the QWs growth is following an ALE procedure (Cd–Te–Zn–Te cycles), the existence of a Cd desorption induced by Zn exposure (Cd atoms are replaced by Zn atoms) leads to the formation of the compositional fluctuations (islands) on the growing surface at lower temperatures. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of applied magnetic fields on direct and indirect excitons in coupled semiconductor quantum wells
Authors: Reyes‐Gómez E. , Oliveira L. E. , de Dios‐Leyva M. 
Published: June 2005

AbstractWe have investigated magnetic‐field effects on the direct‐ and indirect‐exciton dispersions and on the exciton effective mass in the plane perpendicular to the applied field, within the variational framework and effective‐mass approximation, for coupled GaAs–(Ga,Al)As quantum wells. The simple hydrogen‐like envelope wave function we have used provides the expected behavior for the exciton dispersion law in a wide range of the center‐of‐mass momenta, and leads to an analytical expression for the exciton effective mass. Theoretical results for the magnetic‐field dependent exciton dispersion and effective mass are in quite good agreement with available experimental measurements. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the phase diagram of a two‐dimensional electron gas near integer fillings and fractions such as 1/5 and 1/7
Authors: Claro Francisco , Cabo Alejandro , March Norman H. 
Published: June 2005

AbstractThe phase diagram of the 2DEG at high magnetic fields is discussed in the light of recent experiments showing the presence of crystalline phases around integer as well as certain fractional fillings. We suggest that a Hall crystal is a proper competing phase compatible with the odd denominator rule that characterizes the fractional quantum Hall effect, and that near integer filling a pinned crystal coexists with an incompressible fluid with no longitudinal resistance. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)