scholarly journals QSIdb: quorum sensing interference molecules

2020 ◽  
Author(s):  
Shengbo Wu ◽  
Chunjiang Liu ◽  
Jie Feng ◽  
Aidong Yang ◽  
Fei Guo ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Broad Spectrum ◽  
Dynamic Control ◽  
Data Retrieval ◽  
Molecular Structures ◽  
Genetic Circuits ◽  
Short Supply ◽  
Pubchem Database ◽  
Protein Pockets ◽  
User Friendly

Abstract Quorum sensing interference (QSI), the disruption and manipulation of quorum sensing (QS) in the dynamic control of bacteria populations could be widely applied in synthetic biology to realize dynamic metabolic control and develop potential clinical therapies. Conventionally, limited QSI molecules (QSIMs) were developed based on molecular structures or for specific QS receptors, which are in short supply for various interferences and manipulations of QS systems. In this study, we developed QSIdb (http://qsidb.lbci.net/), a specialized repository of 633 reported QSIMs and 73 073 expanded QSIMs including both QS agonists and antagonists. We have collected all reported QSIMs in literatures focused on the modifications of N-acyl homoserine lactones, natural QSIMs and synthetic QS analogues. Moreover, we developed a pipeline with SMILES-based similarity assessment algorithms and docking-based validations to mine potential QSIMs from existing 138 805 608 compounds in the PubChem database. In addition, we proposed a new measure, pocketedit, for assessing the similarities of active protein pockets or QSIMs crosstalk, and obtained 273 possible potential broad-spectrum QSIMs. We provided user-friendly browsing and searching facilities for easy data retrieval and comparison. QSIdb could assist the scientific community in understanding QS-related therapeutics, manipulating QS-based genetic circuits in metabolic engineering, developing potential broad-spectrum QSIMs and expanding new ligands for other receptors.

scholarly journals In silico Analysis of Plant Based Quorum Sensing Inhibitor against Chromobacterium violaceum CviR

2021 ◽  
pp. 272-277
Author(s):  
P. Nandini ◽  
P. Sankar Ganesh ◽  
A. S. Smiline Girija ◽  
J. Vijayashree Priyadharshini
Keyword(s):  
Quorum Sensing ◽  
Bacterial Resistance ◽  
In Silico Analysis ◽  
Chromobacterium Violaceum ◽  
Receptor Protein ◽  
Homologous Gene ◽  
Binding Interaction ◽  
Ligand Interaction ◽  
Data Set ◽  
Pubchem Database

Background: Chromobacterium violaceum (C. violaceum), a Gram-negative, facultative anaerobic, non-sporing coccobacillus has a quorum-sensing system consisting of CviI/CviR, a homologous gene. Quorum sensing (QS) is a mechanism of intercellular communication in bacteria that received substantial attention as an alternate strategy for combating bacterial resistance and the development of new anti-infective agents. Methods: DATA SET Information of photochemical from the natural source deposited as a machine readable format in PubChem database was utilized to retrieve the compound for the study. To study ligand - receptor interactions, docking paves way to accomplish the protein ligand interaction was docked through rigid docking CviR protein (PDB ID: 3QP5) was prepared and energy minimized to evaluate the best affinity among the complex. Results: The results showed that the Alpha.,2.Alpha.- Epoxy-1.Beta.- Methyl Cholesta-4,6- Dien-3-One had high affinity for CviR receptor protein and Alpha.,2.Alpha.- Epoxy-1.Beta.- Methyl Cholesta-4,6- Dien-3-One binds to the active site of CviR with binding energy of -9.6 kcal/mol. Conclusion: Overall study concluded that 1. Alpha., 2. Alpha.- Epoxy-1.Beta.-Methyl Cholesta-4,6-Dien-3-One with highest binding affinity for the CviR protein possessing strong inhibitory binding interaction. Hence, we concluded that 1.Alpha.,2.Alpha.-Epoxy-1.Beta.- Methyl Cholesta-4, 6-Dien-3-One good serves as potential an anti-quorum sensing molecule for treating C. violaceum infection.

scholarly journals From Broad-Spectrum Biocides to Quorum Sensing Disruptors and Mussel Repellents: Antifouling Profile of Alkyl Triphenylphosphonium Salts

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0123652 ◽  
Author(s):  
Alberto J. Martín-Rodríguez ◽  
Jose M. F. Babarro ◽  
Fernando Lahoz ◽  
Marta Sansón ◽  
Víctor S. Martín ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Broad Spectrum

Retrieval-Oriented Design of Clinical Research Forms

2001 ◽  
Vol 40 (03) ◽  
pp. 253-258 ◽  
Author(s):  
E. Eigenbauer ◽  
S. Rasoul-Rockenschaub ◽  
W. Gall
Keyword(s):  
Clinical Research ◽  
Data Linkage ◽  
State Of The Art ◽  
Data Retrieval ◽  
Complex Data ◽  
Clinical Documentation ◽  
Clinical Forms ◽  
User Friendly ◽  
Intended Use

Abstract:Computerized clinical forms are subject to a wide variety of different requirements. They have to allow detailed documentation and must be user-friendly. State-of-the-art applications for design permit clinicians themselves to create their own forms as needed, with the various variables presented in different ways depending on their intended use. Often, however, only aspects of clinical documentation are considered, with no thought being given to subsequent data retrieval. This article presents guidelines for the retrieval-oriented design of clinical forms. It discusses where anticipatory measures for structuring forms are easier to accomplish than complex data linkage at the time of retrieval and analysis.

Providing a user-friendly outlier analysis service implemented as open REST API

2020 ◽  
Author(s):  
Doron Goldfarb ◽  
Johannes Kobler ◽  
Johannes Peterseil
Keyword(s):  
Web Service ◽  
Data Retrieval ◽  
Environmental Data ◽  
Data Repository ◽  
Outlier Analysis ◽  
Data Set ◽  
Access Methods ◽  
Rest Api ◽  
Definition Of ◽  
User Friendly

<p>As outliers in any data set may have detrimental effects on further scientific analysis, the measurement of any environmental parameter and the detection of outliers within these data are closely linked. However, outlier analysis is complicated, as the definition of an outlier is controversially discussed and thus - until now - vague. Nonetheless, multiple methods have been implemented to detect outliers in data sets. The application of these methods often requires some statistical know-how.</p><p>The present use case, developed as proof-of-concept implementation within the EOSC-Hub project, is dedicated to providing a user-friendly outlier analysis web-service via an open REST API processing environmental data either provided via Sensor Observation Service (SOS) or stored as data files in a cloud-based data repository. It is driven by an R-script performing the different operation steps consisting of data retrieval,  outlier analysis and final data export. To cope with the vague definition of an outlier, the outlier analysis step applies numerous statistical methods implemented in various R-packages.</p><p>The web-service encapsulates the R-script behind a REST API which is decribed by a dedicated OpenAPI specification defining two distinct access methods (i.e. SOS- and file-based) and the required parameters to run the R-script. This formal specification is subsequently used to automatically generate a server stub based on the Python FLASK framework which is customized to execute the R-script on the server whenever an appropriate web request arrives. The output is currently collected in a ZIP file which is returned after each successful web request. The service prototype is designed to be operated using generic resources provided by the European Open Science Cloud (EOSC) and the European Grid Initiative (EGI) in order to ensure sustainability and scalability.</p><p>Due to its user-friendliness and open availability, the presented web-service will facilitate access to standardized and scientifically-based outlier analysis methods not only for individual scientists but also for networks and research infrastructures like eLTER. It will thus contribute to the standardization of quality control procedures for data provision in distributed networks of data providers.</p><p> </p><p>Keywords: quality assessment, outlier detection, web service, REST-API, eLTER, EOSC, EGI, EOSC-Hub</p>

scholarly journals picCASO: A Cellular Automaton for Spatial Organisation

2021 ◽  
Author(s):  
Sankalpa Venkatraghavan ◽  
Sathvik Anantakrishnan ◽  
Karthik Raman
Keyword(s):  
Quorum Sensing ◽  
Cellular Automaton ◽  
Computational Models ◽  
Spatial Organization ◽  
Effective Means ◽  
Microbial Consortia ◽  
Attractive Alternative ◽  
Genetic Circuits ◽  
Natural Systems ◽  
Circuit Components

AbstractMicrobial consortia exhibit spatial patterning in several environments. However, the study of such patterning is limited by the inherent complexity of natural systems. An attractive alternative to study such systems involves the use of model synthetic microbial communities, which are convenient frameworks that allow the reuse of circuit components by eliminating cross-talk through compartmentalization of modules in genetic circuits. Computational models facilitate the understanding of how spatial organization can be harnessed as a tunable parameter in 2D cultures. We propose a Quorum Sensing-Mediated Model to engineer communication between strains in a consortium. This is implemented using a cellular automaton. We further analyze the properties of this model and compare them with those of the traditionally used Metabolite Mediated Model. Our studies indicate that modulating the rate of secretion of quorum sensing molecules is the most effective means of regulating community behavior. The models and codes are available from https://github.com/RamanLab/picCASO.

scholarly journals Stk: An Extendable Python Framework for Automated Molecular and Supramolecular Structure Assembly and Discovery

2021 ◽  
Author(s):  
Lukas Turcani ◽  
Andrew Tarzia ◽  
Filip Szczypiński ◽  
Kim Jelfs
Keyword(s):  
Chemical Space ◽  
General Structure ◽  
Molecular Structures ◽  
Structure Generation ◽  
Supramolecular Materials ◽  
Existing Structures ◽  
Potential Applications ◽  
Speed Up ◽  
User Friendly ◽  
Structure Assembly

<div>Computational software workflows are emerging as all-in-one solutions to speed up the discovery of new materials.</div><div>Many computational approaches require the generation of realistic structural models for property prediction and candidate screening. However, molecular and supramolecular materials represent classes of materials with many potential applications for which there is no go-to database of existing structures or general protocol for generating structures. Here, we report a new version of the supramolecular toolkit, <i>stk</i>, an open-source, extendable and modular Python framework for general structure generation of (supra)molecular structures. Our construction approach follows a bottom-up process and minimises the input required from the user, making <i>stk</i> user-friendly and applicable to many material classes. This version of <i>stk</i> includes metal-containing structures and rotaxanes as well as general implementation and interface improvements. Additionally, this version includes built-in tools for exploring chemical space with an evolutionary algorithm and tools for database generation and visualisation. The latest version of <i>stk</i> is freely available at github.com/lukasturcani/stk</div>

scholarly journals AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Mario S. Valdés-Tresanco ◽  
Mario E. Valdés-Tresanco ◽  
Pedro A. Valiente ◽  
Ernesto Moreno
Keyword(s):  
Molecular Docking ◽  
Search Space ◽  
Docking Studies ◽  
Molecular Structures ◽  
Autodock Vina ◽  
Ligand Selectivity ◽  
Input Structure ◽  
Graphical Tool ◽  
Selectivity Studies ◽  
User Friendly

Abstract AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force field for metalloproteins. AMDock integrates several external programs (Open Babel, PDB2PQR, AutoLigand, ADT scripts) to accurately prepare the input structure files and to optimally define the search space, offering several alternatives and different degrees of user supervision. For visualization of molecular structures, AMDock uses PyMOL, starting it automatically with several predefined visualization schemes to aid in setting up the box defining the search space and to visualize and analyze the docking results. One particularly useful feature implemented in AMDock is the off-target docking procedure that allows to conduct ligand selectivity studies easily. In summary, AMDock’s functional versatility makes it a very useful tool to conduct different docking studies, especially for beginners. The program is available, either for Windows or Linux, at https://github.com/Valdes-Tresanco-MS. Reviewers This article was reviewed by Alexander Krah and Thomas Gaillard.

Broad-spectrum inhibition of AHL-regulated virulence factors and biofilms by sub-inhibitory concentrations of ceftazidime

RSC Advances ◽  
2016 ◽  
Vol 6 (33) ◽  
pp. 27952-27962 ◽  
Author(s):  
Fohad Mabood Husain ◽  
Iqbal Ahmad ◽  
Mohammad Hassan Baig ◽  
Mohammad Shavez Khan ◽  
Mohd Shahnawaz Khan ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Virulence Factors ◽  
Broad Spectrum ◽  
Communication System ◽  
Bacterial Pathogens ◽  
Inhibiting Activity ◽  
Density Dependent ◽  
Expression Of Genes

Quorum sensing in bacteria is a density dependent communication system that regulates the expression of genes. In this study we have shown the broad spectrum anti-quorum sensing and biofilm inhibiting activity of ceftazidime against 3 different bacterial pathogens.

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