Screening ultra-large virtual libraries

2022 ◽  
Author(s):  
Sarah Crunkhorn
Keyword(s):  
Virtual Libraries

Permeability Through Bacterial Porins Dictates Whole Cell Compound Accumulation

2020 ◽  
Author(s):  
Silvia Acosta Gutiérrez ◽  
Igor Bodrenko ◽  
Matteo Ceccarelli
Keyword(s):  
Cell Envelope ◽  
Scoring Function ◽  
Modern Medicine ◽  
New Drugs ◽  
Prediction Ability ◽  
Whole Cell ◽  
Virtual Libraries ◽  
Major Bottleneck ◽  
Global Threat ◽  
Bacterial Porins

The lack of new drugs for Gram-negative pathogens is a global threat to modern medicine. The complexity of their cell envelope, with an additional outer membrane, hinders internal accumulation and thus, the access of molecules to targets. Our limited understanding of the molecular basis for compound influx and efflux from these pathogens is a major bottleneck for the discovery of effective antibacterial compounds. Here we analyse the correlation between the whole-cell compound accumulation of ~200 molecules and their predicted porin permeability coefficient (influx), using a recently developed scoring function. We found a strong linear relationship (75%) between the two, confirming porins key role in compound penetration. Further, the remarkable prediction ability of the scoring function demonstrates its potentiality to guide the optimization of hits to leads as well as the possibility of screening ultra-large virtual libraries. Eventually, the analysis of false positives, molecules with high-predicted influx but low accumulation, provides new hints on the molecular properties behind efflux.<br>

Herramientas digitales para recolección, procesamiento y presentación de datos de campo como instrumento para afrontar la contingencia COVID-19

2021 ◽  
Vol 5 ◽  
pp. 96-104
Author(s):  
Didier Haid Alvarado Acosta
Keyword(s):  
Learning Curve ◽  
Training Programs ◽  
Communication Technologies ◽  
Field Work ◽  
Web Based ◽  
Face To Face ◽  
The Past ◽  
Online Platforms ◽  
Virtual Libraries ◽  
Different Types

In March of 2020, the COVID-19 outbreak forced people to lock themselves inside their homes and begin the process of transitioning from face-to-face activities at work, schools and universities to a 100 % virtual method. Even when Communication Technologies (ICT) and online platforms have seen growth over the past two decades, including various virtual libraries developed by database publishers or web-based training programs that appear to shorten the learning curve (Lee, Hong y Nian, 2002), many people were unprepared for this transition and all of them are now dedicated to entering the new reality. In this order of ideas, the activities that have traditionally required the assistance of the staff have had to adapt with the use of new tools, which meet daily needs. A clear example is the field work collection tasks. In this group, there are different types such as surveys, photographs, reviews or on-site inspections. The current work presents the use of tools for collecting, validating, analysing and presenting data remotely and in real time. All of them based on the ArcGIS Online platform.

Synthon-based ligand discovery in virtual libraries of over 11 billion compounds

Nature ◽  
2021 ◽  
Author(s):  
Arman A. Sadybekov ◽  
Anastasiia V. Sadybekov ◽  
Yongfeng Liu ◽  
Christos Iliopoulos-Tsoutsouvas ◽  
Xi-Ping Huang ◽  
...  
Keyword(s):  
Virtual Libraries ◽  
Ligand Discovery

Book museums or virtual libraries

1994 ◽  
Vol 19 (4) ◽  
pp. 4-9 ◽  
Author(s):  
Clive Phillpot
Keyword(s):  
Electronic Publishing ◽  
Public Access ◽  
Access To Information ◽  
Verbal Information ◽  
Foreseeable Future ◽  
Virtual Library ◽  
Short Term ◽  
Virtual Libraries

Although its replacement has not yet been fully developed, the traditional book is likely to be largely superseded in the foreseeable future by electronic publishing. Libraries will become book museums; with librarians as curators; many other librarians will find themselves dealing with unlimited and unpackaged information rather than with pre-packaged artefacts, in a role which will include facilitating and championing public access to information. The electronic ‘virtual library’ will encompass visual as well as verbal information; it will subsume art libraries except insofar as art libraries will become museums, but both the ‘virtual library’ and art libraries will continue to require the skills and vision of art librarians. Finally, in the short term, and perhaps indefinitely, the ‘virtual library’ and the ‘book library’ may not diverge to the extent of parting company altogether: the latter may continue to function as one gateway providing access to the latter.

scholarly journals CONTRIBUTIONS OF FIGURES NUMBERS IN THE DEVELOPMENT OF GEOMETRIC THOUGHT

2019 ◽  
Vol 7 (1) ◽  
pp. 16-30
Author(s):  
Maria José Costa dos Santos ◽  
Arnaldo Lopes Bezerra
Keyword(s):  
Mathematics Teaching ◽  
Teaching And Learning ◽  
Basic Education ◽  
Mathematical Thinking ◽  
Algebraic Thinking ◽  
Ethical Awareness ◽  
Pedagogical Tools ◽  
Geometric Thinking ◽  
Virtual Libraries ◽  
Abstract Content

This study was constituted with the purpose of promoting reflections on Mathematics of basic education, from a transdisciplinary view of teaching and learning processes. To do so, we aim to analyze the contributions of figures in the development of geometric thinking. We characterize this research in empirical-exploratory, because for Lakatos and Marconi (2017), this type of research distinguishes itself as a scientific process of investigation that allows the researcher to formulate questions, with three purposes: to raise hypotheses, to increase the familiarization of the researcher in order to research, modify or clarify concepts, based on a qualitative and quantitative approach, according to the depth of the discussion about the object in question. For this, we look for information in other researches, databases of universities and virtual libraries, periodicals.  We hope that the results contribute to the critical and ethical awareness from views of the importance of the development of mathematical thinking, but specifically of geometric thinking, aiming at non-rupture with arithmetic thinking, in order to interweave with algebraic thinking . We consider this research relevant because mathematics teaching is based on abstract content that often makes no sense to the student, and here we show a part of mathematics that is formal but can be fun when well crafted in the classroom. Finally, we present pedagogical tools of innovation, aimed at contributing to the emancipation of the knowledge of this science, without ruptures. Keywords: Geometric thinking. Figurative numbers. Mathematics Teaching.

scholarly journals VLVS: A Knime Based Virtual Library Generation and Screening Workflow

2021 ◽  
pp. 16-30
Author(s):  
Ismail Hakki Akgün
Keyword(s):  
Open Source Software ◽  
Screening Method ◽  
Virtual Library ◽  
Design Development ◽  
Autodock Vina ◽  
Computer Aided Drug Design ◽  
Drug Molecules ◽  
Virtual Libraries ◽  
Computer Aided ◽  
Short Time

Objective: Tocreate an easy-to-use structure-based screening workflow using KNIME and open source software to prepare and screen virtual libraries in order to discover novel bioactive or drug molecules. Materials and Methods: In the preparation of the workflow we mentioned in the article KNIME version 4, AutoDock Vina, Pymol were used. KNIME plugins used in this study are RDKit KNIME Integration, ChemAxon/Infocom Marvin Extensions Feature, KNIME Python Integration, Lhasa Metabolism Feature, KNIME Ploty and KNIME JavaScript View. We have used Python3 and libraries in the python scripts through Anaconda installation. Results: A workflow that can work with a single click after making required adjustments which uses docking as structure-based screening method was created and tested. Conclusion: With the workflow we have created, it will be possible for researchers especially those who are working in the field of computer-aided drug design/development to create personalized molecule libraries, perform virtual screening, reporting the results in a short time with the least effort.

scholarly journals Importância da assistência de enfermagem no cuidado ao paciente transplantado renal

2018 ◽  
Vol 12 (12) ◽  
pp. 3436 ◽  
Author(s):  
Rafaella Vezzoli da Silva Marques ◽  
Vera Lucia Freitas
Keyword(s):  
Renal Transplant ◽  
Nursing Care ◽  
Renal Transplant Patient ◽  
Transplant Patient ◽  
Kidney Diseases ◽  
Calidad De Vida ◽  
Virtual Libraries ◽  
Study Type ◽  
Nursing Diagnoses

RESUMOObjetivo: descrever a importância da assistência de Enfermagem ao paciente transplantado renal. Método: trata-se de um estudo bibliográfico, tipo revisão integrativa, na base de dados LILACS e bibliotecas virtuais SciELO e BVS, incluindo artigos completos, em português, inglês ou espanhol. Estabeleceu-se, um período de 15 anos para a inclusão dos estudos, e os resultados apresentam-se em figuras. Resultados: encontraram-se 1114 artigos, dos quais, após a leitura dos títulos e dos resumos e a aplicação dos critérios de inclusão e exclusão, foram selecionados dez, sendo dois na SciELO, três na BVS e quatro na LILACS. Verifica-se que os artigos abordam, de forma significativa, a relação dos diagnósticos de Enfermagem na elaboração de intervenções adequadas ao paciente. Conclusão: conclui-se que a Enfermagem possui um papel fundamental no sucesso, na recuperação e na melhoria da qualidade de vida do paciente transplantado renal. Descritores: Assistência ao Paciente; Cuidados de Enfermagem; Nefropatias; Pacientes; Sobrevida; Transplante de Rim.ABSTRACT Objective: to describe the importance of nursing care to the renal transplant patient. Method: this is a bibliographical study, type integrative, in the LILACS database and virtual libraries SciELO and VHL, including complete articles, in Portuguese, English or Spanish. A period of 15 years for the inclusion of the studies was established, and the results are presented in figures. Results: 1114 articles were found, of which, after reading titles and abstracts and applying the inclusion and exclusion criteria, ten were selected, two in SciELO, three in VHL and four in LILACS. It is verified that the articles approach, in a significant way, the relation of Nursing diagnoses in the elaboration of adequate interventions to the patient. Conclusion: it is concluded that Nursing plays a fundamental role in the success, recovery and improvement of the quality of life of the renal transplant patient. Descriptors: Patient Care; Nursing Care; Kidney Diseases; Patients; Survival; Kidney Transplantation.RESUMEN Objetivo: describir la importancia de la asistencia de enfermería al paciente trasplantado renal. Método: se trata de un estudio bibliográfico, revisión integrada de tipo, la base de datos LILACS y SciELO bibliotecas virtuales y BVS, incluyendo los artículos completos en portugués, inglés o español. Se estableció, un período de 15 años para la inclusión de los estudios, y los resultados se presentan en figuras. Resultados: se encontraron 1114 artículos, de los cuales, después de la lectura de los títulos y de los resúmenes y la aplicación de los criterios de inclusión y exclusión, fueron seleccionados diez, siendo dos en la SciELO, tres en la BVS y cuatro en la LILACS. Se verifica que los artículos abordan de forma significativa la relación de los diagnósticos de Enfermería en la elaboración de intervenciones adecuadas al paciente. Conclusión: se concluye que la Enfermería tiene un papel fundamental en el éxito, la recuperación y la mejora de la calidad de vida del paciente trasplantado renal. Descriptores: Atención al Paciente; Atención de Enfermería;  Enfermedades Renales; Pacientes; Supervivencia; Trasplante de Riñón.

scholarly journals Datasets and Their Influence on the Development of Computer Assisted Synthesis Planning Tools in the Pharmaceutical Domain

2019 ◽  
Author(s):  
Amol Thakkar ◽  
Thierry Kogej ◽  
Jean-Louis Reymond ◽  
Ola Engkvist ◽  
Esben Jannik Bjerrum
Keyword(s):  
Model Performance ◽  
Computer Assisted ◽  
Patent Office ◽  
United States Patent ◽  
Planning Tool ◽  
Virtual Libraries ◽  
Synthesis Planning ◽  
Synthetic Routes ◽  
The Cost ◽  
States Patent

<p>Computer Assisted Synthesis Planning (CASP) has gained considerable interest as of late. Herein we investigate a template-based retrosynthetic planning tool, trained on a variety of datasets consisting of up to 17.5 million reactions. We demonstrate that models trained on datasets such as internal Electronic Laboratory Notebooks (ELN), and the publicly available United States Patent Office (USPTO) extracts, are sufficient for the prediction of full synthetic routes to compounds of interest in medicinal chemistry. As such we have assessed the models on 1,731 compounds from 41 virtual libraries for which experimental results were known. Furthermore, we show that accuracy is a misleading metric for assessment of the ‘filter network’, and propose that the number of successfully applied templates, in conjunction with the overall ability to generate full synthetic routes be examined instead. To this end we found that the specificity of the templates comes at the cost of generalizability, and overall model performance. This is supplemented by a comparison of the underlying datasets and their corresponding models.</p>

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