Molecular modeling databases: A new way in the search of protein targets for drug development

DBMODELING is a relational database of annotated comparative protein structure models and their metabolic, pathway characterization. It is focused on enzymes identified in the genomes of Mycobacterium tuberculosis and Xylella fastidiosa. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. However, since the accuracy of structural models is highly dependent on sequence identity between template and target, it is necessary to make clear to the user that only models which show high structural quality should be used in such efforts. Molecular modeling of these genomes generated a database, in which all structural models were built using alignments presenting more than 30% of sequence identity, generating models with medium and high accuracy. All models in the database are publicly accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools. DBMODELING user interface provides users friendly menus, so that all information can be printed in one stop from any web browser. Furthermore, DBMODELING also provides a docking interface, which allows the user to carry out geometric docking simulation, against the molecular models available in the database. There are three other important homology model databases: MODBASE, SWISSMODEL, and GTOP. The main applications of these databases are described in the present article. © 2007 Bentham Science Publishers Ltd.

Preparação e caracterização de coacervatos e vidros a base de fosfato, dopados com európio

Pós-graduação em Química - IQ

Incorporação de tiofosfatos em vidros calcogenetos: estrutura e fenômenos fotoinduzidos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Dispositivos institucionais filantrópicos e socioeducativos de atenção à infância na assistência social

This study investigated Social Care as an institution that creates mechanisms for the production of subjectivity in the care of children and adolescents. For this, we used some analytical coordinates, both conjectural and structural, models of care for mapping care in confrontation in the field of Social Care. It was concluded that there was two contradictory paradigms, in the dialectical sense, organizing social care, one being the philanthropic mode and the other the socioeducative mode. The first, which is hegemonic in the field, corresponds to a care entity still organized from philanthropic care and is guided by a minority age logic, articulated by a discourse of criminalizing the lower classes. It is informally based on the legal concept of irregular situations, which would develop preventive, repressive, correctional and moralizing care practices. The construction of a socioeducative mode implies socioeducative care that aims for an effective increase in the rights of children and adolescents, based on their status as subjects and citizens, through democratic, dialogic, participatory, multi-disciplinary and fundamentally emancipatory institutional practices.

Espécies metalo-supramoleculares discretas polinucleares: sínteses e caracterização

Pós-graduação em Química - IQ

Síntese, caracterização e estudo do comportamento térmico dos oxanatos de lantanídeos(III) e de ítrio(III), no estado sólido

Pós-graduação em Química - IQ

Síntese, caracterização e estudo do comportamento térmico dos glicolatos de lantanídeos e ítrio no estado sólido

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The structural origin and biological function of pH-sensitivity in firefly luciferases

Firefly luciferases are called pH-sensitive because their bioluminescence spectra display a typical red-shift at acidic pH, higher temperatures, and in the presence of heavy metal cations, whereas other beetle luciferases (click beetles and railroadworms) do not, and for this reason they are called pH-insensitive. Despite many studies on firefly luciferases, the origin of pH-sensitivity is far from being understood. This subject is revised in view of recent results. Some substitutions of amino-acid residues influencing pH-sensitivity in firefly luciferases have been identified. Sequence comparison, site-directed mutagenesis and modeling studies have shown a set of residues differing between pH-sensitive and pH-insensitive luciferases which affect bioluminescence colors. Some substitutions dramatically affecting bioluminescence colors in both groups of luciferases are clustered in the loop between residues 223-235 (Photinus pyralis sequence). A network of hydrogen bonds and salt bridges involving the residues N229-S284-E311-R337 was found to be important for affecting bioluminescence colors. It is suggested that these structural elements may affect the benzothiazolyl side of the luciferin-binding site affecting bioluminescence colors. Experimental evidence suggest that the residual red light emission in pH-sensitive luciferases could be a vestige that may have biological importance in some firefly species. Furthermore, the potential utility of pH-sensitivity for intracellular biosensing applications is considered. © The Royal Society of Chemistry and Owner Societies.

Structural Health Monitoring based on AR models and PZT sensors

This paper presents a new approach for damage detection in Structural Health Monitoring (SHM) systems, which is based on the Electromechanical Impedance (EMI) principle and Autoregressive (AR) models. Typical applications of EMI in SHM are based on computing the Frequency Response Function (FRF). In this work the procedure is based on the EMI principle but the results are determined through the coefficients of AR models, which are computed from the time response of PZT transducers bonded to the monitored structure, and acting as actuator and sensors at the same time. The procedure is based on exciting the PZT transducers using a wide band chirp signal and getting its time response. The AR models are obtained in both healthy and damaged conditions and used to compute statistics indexes. Practical tests were carried out in an aluminum plate and the results have demonstrated the effectiveness of the proposed method. © 2012 IEEE.

Comparative analysis of strut-and-tie models using Smooth Evolutionary Structural Optimization

The strut-and-tie models are widely used in certain types of structural elements in reinforced concrete and in regions with complexity of the stress state, called regions D, where the distribution of deformations in the cross section is not linear. This paper introduces a numerical technique to determine the strut-and-tie models using a variant of the classical Evolutionary Structural Optimization, which is called Smooth Evolutionary Structural Optimization. The basic idea of this technique is to identify the numerical flow of stresses generated in the structure, setting out in more technical and rational members of strut-and-tie, and to quantify their value for future structural design. This paper presents an index performance based on the evolutionary topology optimization method for automatically generating optimal strut-and-tie models in reinforced concrete structures with stress constraints. In the proposed approach, the element with the lowest Von Mises stress is calculated for element removal, while a performance index is used to monitor the evolutionary optimization process. Thus, a comparative analysis of the strut-and-tie models for beams is proposed with the presentation of examples from the literature that demonstrates the efficiency of this formulation. © 2013 Elsevier Ltd.

Atmospheric Models Applied to DGPS and RTK Network in Brazil: Preliminary Results

Several positioning techniques have been developed to explore the GPS capability to provide precise coordinates in real time. However, a significant problem to all techniques is the ionosphere effect and the troposphere refraction. Recent researches in Brazil, at São Paulo State University (UNESP), have been trying to tackle these problems. In relation to the ionosphere effects it has been developed a model named Mod_Ion. Concerning tropospheric refraction, a model of Numerical Weather Prediction(NWP) has been used to compute the zenithal tropospheric delay (ZTD). These two models have been integrated with two positioning methods: DGPS (Differential GPS) and network RTK (Real Time Kinematic). These two positioning techniques are being investigated at São Paulo State University (UNESP), Brazil. The in-house DGPS software was already finalized and has provided very good results. The network RTK software is still under development. Therefore, only preliminary results from this method using the VRS (Virtual Reference Station) concept are presented.

Combining SERRS and electrochemistry to characterize sensors based on biomembrane mimetic models formed by phospholipids

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structural and Electronic Effects of Incorporating Mn in TiO2 Films Grown by Sputtering: Anatase versus Rutile

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Periodic study on the structural and electronic properties of bulk, oxidized and reduced SnO2(110) surfaces and the interaction with O-2

The structural and electronic properties of bulk and both oxidized and reduced SnO2(110) surfaces as well as the adsorption process of O-2 on the reduced surface have been investigated by periodic DFT calculations at B3LYP level. The lattice parameters, charge distribution, density of states and band structure are reported for the bulk and surfaces. Surface relaxation effects have been explicitly taken into account by optimizing slab models of nine and seven atomic layers representing the oxidized and reduced surfaces, respectively. The conductivity behavior of the reduced SnO2(110) surface is explained by a distribution of the electrons in the electronic states in the band gap induced by oxygen vacancies. Three types of adsorption approaches of O-2 on the four-fold tin at the reduced SuO(2)(110) surface have been considered. The most exothermic channel corresponds to the adsorption of O-2 parallel to the surface and to the four-fold tin row, and it is believed to be associated with the formation of a peroxo O-2(2-) species. The chemisorption of O-2 on reduced SnO2(110) surface causes a significant depopulation of states along the band gap and it is shown to trap the electrons in the chemisorbed complex producing an electron-depleted space-charge layer in the inner surface region of the material in agreement with some experimental evidences. (C) 2002 Elsevier B.V. B.V. All rights reserved.