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      Withanolides from Withania somnifera as an immunity booster and their therapeutic options against COVID-19

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          Cytoscape: a software environment for integrated models of biomolecular interaction networks.

          Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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            Is Open Access

            STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

            Abstract Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein–protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein–protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.
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              AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.

              We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique. (c) 2009 Wiley Periodicals, Inc.
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                Author and article information

                Contributors
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                Journal
                Journal of Biomolecular Structure and Dynamics
                Journal of Biomolecular Structure and Dynamics
                Informa UK Limited
                0739-1102
                1538-0254
                January 18 2021
                : 1-14
                Affiliations
                [1 ]Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, India
                [2 ]School of Pharmacy, University of East Anglia, Norwich, UK
                [3 ]School of Pharmaceutical Technology, Adamas University, Kolkata, West Bengal, India
                [4 ]Department of Pharmacology, Orotta College of Medicine and Health Sciences, Asmara University, Asmara, Eritrea
                [5 ]Department of Pharmacy Practice, NGSM Institute of Pharmaceutical Sciences, NITTE (Deemed to be University), Deralakatte, Karnataka, India
                [6 ]PES’s Rajaram and Tarabai Bandekar College of Pharmacy, Ponda, Goa University, Goa, India
                [7 ]Department of Botany, A. Veeriya Vandayar Memorial Sri Pushpam College (Autonomous), Affiliated to Bharathidasan University, Thanjavur, India
                [8 ]Goa College of Pharmacy, Department of Pharmacognosy, Panaji, Goa University, Goa, India
                Article
                10.1080/07391102.2020.1869588
                33459174
                045dac20-9190-420d-b960-04528b134ebe
                © 2021
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