Diseño e implementación de la biblioteca virtual de la Facultad de Ciencias Médicas de Bayamo

Las páginas web constituyen un medio facilitador del conocimiento. El trabajo se realizó con el objetivo de diseñar e implementar una biblioteca virtual para favorecer el proceso de gestión de la información del Departamento de Información Científica-Técnica y Biblioteca de la Facultad de Ciencias Médicas de Bayamo. Para el desarrollo del contenido del sitio se emplearon: observación, encuestas y entrevistas. Para desarrollar el producto se llevaron a cabo cinco procesos: planificación inicial del sitio, definición, diseño y estándares, puesta en marcha y plan de mantenimiento. Para la confección de la página se empleó el gestor de contenidos WordPress, así como PHP, MySQL, Apache, XAMPP y Windows como lenguaje de programación, motor de bases de datos, servidor Web, paquete de software libre y sistema operativo respectivamente. Se concluye que la implementación de la biblioteca virtual, facilita el proceso de gestión de la información, despierta el interés por la investigación y contribuye a la alfabetización informacional de los usuarios de salud que ingresen a la web. Facilitará la visibilidad, la gestión técnica bibliotecaria; la divulgación, difusión, y uso de los servicios y recursos de información disponibles.

Web pages constitute a means of facilitating knowledge. The work was carried out with the objective of designing and implementing a virtual library to favor the information management process of the Department of Scientific and Technical Information and the Library of the Faculty of Medical Sciences of Bayamo. Observation, surveys and interviews were used in the development of the content of the site. Five processes were carried out to develop the product: initial planning of the site, definition, design and standards, commissioning, and maintenance plan. To create the page, the content manager WordPress was used; PHP, MySQL, Apache, XAMPP and Windows were used as the programming language, database engine, Web server, free software package and operating system, respectively. It is concluded that the implementation of the virtual library facilitates the information management process, awakens the interest in research, and contributes to the information literacy of health users who enter the web. It will facilitate visibility, library technical management, disclosure, dissemination, and use of available information services and resources.

Virtual screening of ultra-large chemical libraries identifies cell-permeable small-molecule inhibitors of a "non-druggable" target, STAT3 N-terminal domain.

STAT3 N-terminal domain is a promising molecular target for cancer treatment and modulation of immune responses. However, STAT3 is localized in the cytoplasm, mitochondria, and nuclei, and thus, is inaccessible to therapeutic antibodies. Its N-terminal domain lacks deep pockets on the surface and represents a typical "non-druggable" protein. In order to successfully identify potent and selective inhibitors of the domain, we have used virtual screening of billion structure-sized virtual libraries of make-on-demand screening samples. The results suggest that the expansion of accessible chemical space by cutting-edge ultra-large virtual compound databases can lead to successful development of small molecule drugs for hard-to-target intracellular proteins.

Forty years of combinatorial technology.

Combinatorial technology has been facilitating the synthesis and screening of large molecular libraries containing millions of organic compounds ever since its introduction 40 years ago. It has changed the paradigms of pharmaceutical research from focusing on single compounds to focusing on immense collections of compounds. It inspired the development of dynamic combinatorial libraries, fragment-based drug discovery and virtual library screening. Combinatorial technology was revitalized by the development of DNA encoding. Amplification of DNA oligomers plus next-generation sequencing has made it possible to successfully screen billions of compounds in a single process.

One-pot parallel synthesis of 1,3,5-trisubstituted 1,2,4-triazoles.

An implementation of the three-component one-pot approach to unsymmetrical 1,3,5-trisubstituted-1,2,4-triazoles into combinatorial chemistry is described. The procedure is based on the coupling of amidines with carboxylic acids and subsequent cyclization with hydrazines. After the preliminary assessment of the reagent scope, the method had 81% success rate in parallel synthesis. It was shown that over a billion-sized chemical space of readily accessible ("REAL") compounds may be generated based on the proposed methodology. Analysis of physicochemical parameters shows that the library contains significant fractions of both drug-like and "beyond-rule-of-five" members. More than 10 million of accessible compounds meet the strictest lead-likeness criteria. Additionally, 195 Mln of sp3-enriched compounds can be produced. This makes the proposed approach a valuable tool in medicinal chemistry.

Design of Novel Drug-like Molecules Using Informatics Rich Secondary Metabolites Analysis of Indian Medicinal and Aromatic Plants.

BACKGROUND: Several medicinal plants are being used in Indian medicine systems from ancient times. However, in most cases, the specific molecules or the active ingredients responsible for the medicinal or therapeutic properties are not yet known. OBJECTIVE: This study aimed to report a computational protocol as well as a tool for generating novel potential drug candidates from the bioactive molecules of Indian medicinal and aromatic plants through the chemoinformatics approach. METHODS: We built a database of the Indian medicinal and aromatic plants coupled with associated information (plant families, plant parts used for the medicinal purpose, structural information, therapeutic properties, etc.) We also developed a Java-based chemoinformatics open-source tool called DoMINE (Database of Medicinally Important Natural products from plantaE) for the generation of virtual library and screening of novel molecules from known medicinal plant molecules. We employed chemoinformatics approaches to in-silico screened metabolites from 104 Indian medicinal and aromatic plants and designed novel drug-like bioactive molecules. For this purpose, 1665 ring containing molecules were identified by text mining of literature related to the medicinal plant species, which were later used to extract 209 molecular scaffolds. Different scaffolds were further used to build a focused virtual library. Virtual screening was performed with cluster analysis to predict drug-like and lead-like molecules from these plant molecules in the context of drug discovery. The predicted drug-like and lead-like molecules were evaluated using chemoinformatics approaches and statistical parameters, and only the most significant molecules were proposed as the candidate molecules to develop new drugs. RESULTS AND CONCLUSION: The supra network of molecules and scaffolds identifies the relationship between the plant molecules and drugs. Cluster analysis of virtual library molecules showed that novel molecules had more pharmacophoric properties than toxicophoric and chemophoric properties. We also developed the DoMINE toolkit for the advancement of natural product-based drug discovery through chemoinformatics approaches. This study will be useful in developing new drug molecules from the known medicinal plant molecules. Hence, this work will encourage experimental organic chemists to synthesize these molecules based on the predicted values. These synthesized molecules need to be subjected to biological screening to identify potential molecules for drug discovery research.

Bibliotecas digitais e virtuais à luz da literatura brasileira: da construção ao acesso / Digital and virtual libraries in the light of brazilian literature: from construction to access

RESUMO Os reflexos das tecnologias da informação e comunicação nas bibliotecas é tema recorrente na literatura da área de Biblioteconomia e Ciência da Informação. Este artigo constitui uma revisão de literatura sobre o tema "Bibliotecas Digitais" e "Bibliotecas Virtuais", haja vista verificar os principais assuntos discorridos na literatura, por conseguinte, apresentar aspectos quantitativos que caracterizam a produção científica sobre o tema. A pesquisa é descritiva, qualiquantitativa e foram selecionados artigos da Base de Dados de Periódicos em Ciência da Informação, SciELO e Portal de Periódicos CAPES, publicados em português, de 2010 a 2014, mediante a técnica de coleta do tipo levantamento e análise de conteúdo. Os procedimentos realizados no estudo permitiram a identificação de 21 artigos que contemplam diferentes assuntos relacionados ao tema: estruturação das bibliotecas, produtos e serviços oferecidos, educação e formação, e acesso e usabilidade da biblioteca. Os dados quantitativos analisados demonstraram haver preferência pelo termo "Bibliotecas Digitais" ao termo "Bibliotecas Virtuais", com predominância dos assuntos "estruturação de bibliotecas" e "acesso e usabilidade". Os trabalhos foram publicados de forma equilibrada, ao longo dos anos, predomínio da autoria coletiva, e houve distribuição uniforme entre boa parte dos periódicos brasileiros da Ciência da Informação/Biblioteconomia. Como principal limitação, destaca-se o uso de artigos em português, o que instiga a realização de estudos futuros em artigos publicados em inglês e espanhol, e delimitando o tempo para anos mais recentes.

RESUMEN Los reflejos de las tecnologías de la información y la comunicación en las bibliotecas son un tema recurrente en la literatura de bibliotecas y ciencias de la información. Este artículo es una revisión de la literatura sobre el tema "Bibliotecas digitales" y "Bibliotecas virtuales", con el fin de verificar los principales temas discutidos en la literatura, por lo tanto, presenta aspectos cuantitativos que caracterizan la producción científica sobre el tema. La investigación es descriptiva, cualitativa y cuantitativa, y los artículos de la Base de datos periódica de ciencias de la información, SciELO y Portal Capes, publicados en portugués, de 2010 a 2014, se seleccionaron utilizando la técnica de recopilación de encuestas y el análisis de contenido. Los procedimientos realizados en el estudio permitieron la identificación de 21 artículos que cubren diferentes temas relacionados con el tema: estructuración de la biblioteca, productos y servicios ofrecidos, educación y capacitación, y acceso a la biblioteca y usabilidad. Los datos cuantitativos analizados mostraron una preferencia por el término "Bibliotecas digitales" sobre el término "Bibliotecas virtuales", con predominio de los temas "estructuración de bibliotecas" y "acceso y usabilidad". Las obras se publicaron de manera equilibrada, a lo largo de los años, predominando la autoría colectiva, y hubo una distribución uniforme entre la mayoría de las revistas brasileñas de Ciencias de la Información / Bibliotecología. La principal limitación es el uso de artículos en portugués, lo que impulsa futuros estudios en artículos publicados en inglés y español, limitando el tiempo a años más recientes.

ABSTRACT The reflexes of information and communication technologies in libraries is a recurring theme in the library and information science literature. This article is a literature review on the topic "Digital Libraries" and "Virtual Libraries", in order to verify the main subjects discussed in the literature, therefore, presenting quantitative aspects that characterize the scientific production on the subject. The research is descriptive, qualitative and quantitative, and articles from the Information Science Periodical Database, SciELO and Portal Capes, published in Portuguese, from 2010 to 2014, were selected using the survey collection technique and content analysis. The procedures performed in the study allowed the identification of 21 articles that cover different subjects related to the theme: library structuring, products and services offered, education and training, and library access and usability. The quantitative data analyzed showed a preference for the term "Digital Libraries" over the term "Virtual Libraries", with predominance of the subjects "library structuring" and "access and usability". The works were published in a balanced way, over the years, predominance of collective authorship, and there was a uniform distribution among most Brazilian journals of Information Science / Library Science. The main limitation is the use of articles in Portuguese, which prompts future studies in articles published in English and Spanish, limiting the time to more recent years.

Virtual Screening Techniques in Drug Discovery: Review and Recent Applications.

The discovery of bioactive molecules is an expensive and time-consuming process and new strategies are continuously searched for in order to optimize this process. Virtual Screening (VS) is one of the recent strategies that has been explored for the identification of candidate bioactive molecules. The number of new techniques and software that can be applied in this strategy has grown considerably in recent years, so, before their use, it is necessary to understand the basics an also the limitations behind each one to get the most out of them. It is also necessary to assess the real contributions of this strategy so that more significant progress can be made in the future. In this context, this review aims to discuss some important points related to VS, including the use of virtual ligand and biotarget libraries, structurebased and ligand-based VS techniques, as well as to present recent cases where this strategy was successfully applied.

Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein-Protein Interactions.

Peptide cyclization can improve stability, conformational constraint, and compactness. However, apart from beta-turn structures, which are well incorporated into cyclic peptides (CPs), many primary peptide structures and functions are markedly altered by cyclization. Accordingly, to mimic linear peptide interfaces with cyclic peptides, it can be beneficial to screen combinatorial cyclic peptide libraries. Computational methods have been developed to screen CPs, but face a number of challenges. Here, we review methods to develop in silico computational libraries, and the potential for screening naturally occurring libraries of CPs. The simplest and most rapid computational pharmacophore methods that estimate peptide three-dimensional structures to be screened versus targets are relatively easy to implement, and while the constraint on structure imposed by cyclization makes them more effective than the same approaches with linear peptides, there are a large number of limiting assumptions. In contrast, full molecular dynamics simulations of cyclic peptide structures not only are costly to implement, but also require careful attention to interpretation, so that not only is the computation time rate limiting, but the interpretation time is also rate limiting due to the analysis of the typically complex underlying conformational space of CPs. A challenge for the field of computational cyclic peptide screening is to bridge this gap effectively. Natural compound libraries of short cyclic peptides, and short cyclized regions of proteins, encoded in the genomes of many organisms present a potential treasure trove of novel functionality which may be screened via combined computational and experimental screening approaches.

CHIPMUNK: A Virtual Synthesizable Small-Molecule Library for Medicinal Chemistry, Exploitable for Protein-Protein Interaction Modulators.

A common issue during drug design and development is the discovery of novel scaffolds for protein targets. On the one hand the chemical space of purchasable compounds is rather limited; on the other hand artificially generated molecules suffer from a grave lack of accessibility in practice. Therefore, we generated a novel virtual library of small molecules which are synthesizable from purchasable educts, called CHIPMUNK (CHemically feasible In silico Public Molecular UNiverse Knowledge base). Altogether, CHIPMUNK covers over 95 million compounds and encompasses regions of the chemical space that are not covered by existing databases. The coverage of CHIPMUNK exceeds the chemical space spanned by the Lipinski rule of five to foster the exploration of novel and difficult target classes. The analysis of the generated property space reveals that CHIPMUNK is well suited for the design of protein-protein interaction inhibitors (PPIIs). Furthermore, a recently developed structural clustering algorithm (StruClus) for big data was used to partition the sub-libraries into meaningful subsets and assist scientists to process the large amount of data. These clustered subsets also contain the target space based on ChEMBL data which was included during clustering.

The octet rule in chemical space: generating virtual molecules.

We present a generator of virtual molecules that selects valid chemistry on the basis of the octet rule. Also, we introduce a mesomer group key that allows a fast detection of duplicates in the generated structures. Compared to existing approaches, our model is simpler and faster, generates new chemistry and avoids invalid chemistry. Its versatility is illustrated by the correct generation of molecules containing third-row elements and a surprisingly adept handling of complex boron chemistry. Without any empirical parameters, our model is designed to be valid also in unexplored regions of chemical space. One first unexpected finding is the high prevalence of dipolar structures among generated molecules.

Exploring α7-Nicotinic Receptor Ligand Diversity by Scaffold Enumeration from the Chemical Universe Database GDB.

Virtual analogues (1167860 compounds) of the nicotinic α7-receptor (α7 nAChR) ligands PNU-282,987 and SSR180711 were generated from the chemical universe database GDB-11 by extracting all aliphatic diamine analogues of the aminoquinuclidine and 1,4-diazabicyclo[3.2.2]nonane scaffolds of these ligands and converting them to the corresponding aryl amides using five different aromatic acyl groups. The library was ranked by docking to the nicotinic binding site of the acetylcholine binding protein (AChBP, 1UW6.pdb) using Autodock and Glide. Thirty-eight ligands derived from the best docking hits were synthesized and tested for modulation of the acetylcholine signal at the human α7 nAChR receptor expressed in Xenopus oocytes, leading to competitive and noncompetitive antagonists with IC50 = 5-7 µM. These experiments demonstrate the first example of using GDB in a fragment-based approach by diversifying the scaffold of known drugs.

Saúde reprodutiva: uma contribuição para avaliação de biblioteca virtual / Reproductive health: a contribution to the evaluation of a virtual library

As bibliotecas virtuais foram implementadas numa tentativa de organizar a informação científica encontrada na internet. Dentre elas, destaca-se a Biblioteca Virtual de Saúde Reprodutiva (BVSR), cujo princípio é oferecer informações com qualidade aos pesquisadores da área da saúde reprodutiva. O objetivo deste trabalho é apresentar um estudo de avaliação de uso da BVSR, destacando as expectativas, dificuldades e sugestões dos seus usuários. Foi utilizado método de natureza qualitativa, com a técnica de grupo focal, aplicada por meio de salas de bate-papo na internet, em pesquisadores da área. Os resultados mostram as expectativas do pesquisador em relação à informação, apontando para discussões relacionadas à falta de tempo e à necessidade de obter a informação com precisão e rapidez. O uso da BVSR para pesquisas é maior de acordo com a confiabilidade das instituições mantenedoras. Algumas sugestões levantadas pelos pesquisadores foram: necessidade de maior divulgação, edição de boletins eletrônicos, disponibilização de um canal de comunicação entre a BVSR e os usuários, a fim de promover a construção de coletivos inteligentes.

Virtual libraries have been implemented in an attempt to organize scientific information found in the Internet, including the Biblioteca Virtual de Saúde Reprodutiva (BVSR), or Virtual Library on Reproductive Health. The aim is to provide quality information to researchers in the reproductive health field. The current study evaluates the use of the BVSR, emphasizing the users' expectations, difficulties, and suggestions. The study adopted a qualitative methodology. The focus group technique was applied to Internet chat groups through which reproductive health researchers communicated. Users expressed their expectations regarding information, highlighting the lack of time and the need to quickly obtain precise data. Use of virtual libraries for research increases where there is more trust in the institutions responsible for maintaining them. Researchers suggested the following: greater dissemination of the BVSR, publication of an electronic newsletter, and creation of a communications channel between the BVSR and users in order to foster intelligent collective communication.

EPrints y la creación de repositorios virtuales. Estudio de un caso. La biblioteca virtual de la Facultad de Matemática y Computación de la Universidad de La Habana / EPrints and the creation of virtual repositories. Study of a case. The virtual library of Mathematics and the Information Science Faculty of the University of Havana

Desarrollada con EPrints, un software que facilita la creación de repositorios virtuales, la biblioteca virtual de la Facultad de Matemática y Computación de la Universidad de La Habana es un recurso útil, tanto a profesores e investigadores como a los estudiantes de dicha institución. Se exponen brevemente la organización del trabajo en el repositorio, así como las principales opciones disponibles para la gestión de los documentos: almacenamiento, navegación y búsqueda.

Developed with EPrints, software that facilitates the creation of virtual repositories, the Virtual Library of the Information Science and Mathematics Faculty of the University of Havana is a very useful resource for its professors, researchers and students. The organization of the work at the repository is exposed, as well as the main options available for document management: storing, navigation and search.

SciELO: una metodología para la publicación electrónica

Se describe la Metodología SciELO (Scientific Electronic Library Online) para la difusión por la vía electrónica de publicaciones periódicas científicas. Se abordan temas como la transición de la publicación impresa en papel hacia la publicación electrónica, el proceso de comunicación científica, los principios que orientaron el desarrollo de la metodología, su aplicación en el sitio SciELO, sus módulos y componentes, los instrumentos en los cuales se basa, etcétera. Se discuten asimismo las potencialidades y tendencias disponibles en esta esfera en Brasil y en América Latina, y se indican cuestiones y propuestas que la metodología deberá abordar y solucionar. Se concluye que la Metodología SciELO es una solución eficiente, flexible y amplia para la publicación científica electrónica.

It describes the SciELO Methodology Scientific Electronic Library Online for electronic publishing of scientific periodicals, examining issues such as the transition from traditional printed publication to electronic publishing, the scientific communication process, the principles which founded the methodology development, its application in the building of the SciELO site, its modules and components, the tools use for its construction etc. The article also discusses the potentialities and trends for the area in Brazil and Latin America, pointing out questions and proposals which should be investigated and solved by the methodology. It concludes that the SciELO Methodology is an efficient, flexible and wide solution for the scientific electronic publishing.