scholarly journals Towards reproducible computational drug discovery

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Nalini Schaduangrat ◽  
Samuel Lampa ◽  
Saw Simeon ◽  
Matthew Paul Gleeson ◽  
Ola Spjuth ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Model Development ◽  
Scientific Progress ◽  
Reproducible Research ◽  
Open Approach ◽  
Laboratory Notebook ◽  
Current State ◽  
Share Data ◽  
New Ideas ◽  
Computational Drug Discovery

AbstractThe reproducibility of experiments has been a long standing impediment for further scientific progress. Computational methods have been instrumental in drug discovery efforts owing to its multifaceted utilization for data collection, pre-processing, analysis and inference. This article provides an in-depth coverage on the reproducibility of computational drug discovery. This review explores the following topics: (1) the current state-of-the-art on reproducible research, (2) research documentation (e.g. electronic laboratory notebook, Jupyter notebook, etc.), (3) science of reproducible research (i.e. comparison and contrast with related concepts as replicability, reusability and reliability), (4) model development in computational drug discovery, (5) computational issues on model development and deployment, (6) use case scenarios for streamlining the computational drug discovery protocol. In computational disciplines, it has become common practice to share data and programming codes used for numerical calculations as to not only facilitate reproducibility, but also to foster collaborations (i.e. to drive the project further by introducing new ideas, growing the data, augmenting the code, etc.). It is therefore inevitable that the field of computational drug design would adopt an open approach towards the collection, curation and sharing of data/code.

scholarly journals J-CO: A Platform-Independent Framework for Managing Geo-Referenced JSON Data Sets

Electronics ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 621
Author(s):  
Giuseppe Psaila ◽  
Paolo Fosci
Keyword(s):  
Query Language ◽  
Open Data ◽  
Internet Technology ◽  
Data Sets ◽  
Specific Storage ◽  
Current State ◽  
Execution Engine ◽  
Share Data ◽  
Cloud Servers ◽  
Computational Resources

Internet technology and mobile technology have enabled producing and diffusing massive data sets concerning almost every aspect of day-by-day life. Remarkable examples are social media and apps for volunteered information production, as well as Open Data portals on which public administrations publish authoritative and (often) geo-referenced data sets. In this context, JSON has become the most popular standard for representing and exchanging possibly geo-referenced data sets over the Internet.Analysts, wishing to manage, integrate and cross-analyze such data sets, need a framework that allows them to access possibly remote storage systems for JSON data sets, to retrieve and query data sets by means of a unique query language (independent of the specific storage technology), by exploiting possibly-remote computational resources (such as cloud servers), comfortably working on their PC in their office, more or less unaware of real location of resources. In this paper, we present the current state of the J-CO Framework, a platform-independent and analyst-oriented software framework to manipulate and cross-analyze possibly geo-tagged JSON data sets. The paper presents the general approach behind the J-CO Framework, by illustrating the query language by means of a simple, yet non-trivial, example of geographical cross-analysis. The paper also presents the novel features introduced by the re-engineered version of the execution engine and the most recent components, i.e., the storage service for large single JSON documents and the user interface that allows analysts to comfortably share data sets and computational resources with other analysts possibly working in different places of the Earth globe. Finally, the paper reports the results of an experimental campaign, which show that the execution engine actually performs in a more than satisfactory way, proving that our framework can be actually used by analysts to process JSON data sets.

A unified approach to computational drug discovery

2015 ◽  
Vol 20 (11) ◽  
pp. 1328-1336 ◽  
Author(s):  
Chih-Yuan Tseng ◽  
Jack Tuszynski
Keyword(s):  
Drug Discovery ◽  
Unified Approach ◽  
Computational Drug Discovery

scholarly journals Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations

2020 ◽  
Vol 26 (42) ◽  
pp. 7598-7622 ◽  
Author(s):  
Xiao Hu ◽  
Irene Maffucci ◽  
Alessandro Contini
Keyword(s):  
Drug Discovery ◽  
Binding Free Energy ◽  
Docking Studies ◽  
Free Energy Calculations ◽  
Binding Energies ◽  
New Drugs ◽  
Water Molecules ◽  
Open Questions ◽  
Dynamics Simulations ◽  
Computational Drug Discovery

Background: The inclusion of direct effects mediated by water during the ligandreceptor recognition is a hot-topic of modern computational chemistry applied to drug discovery and development. Docking or virtual screening with explicit hydration is still debatable, despite the successful cases that have been presented in the last years. Indeed, how to select the water molecules that will be included in the docking process or how the included waters should be treated remain open questions. Objective: In this review, we will discuss some of the most recent methods that can be used in computational drug discovery and drug development when the effect of a single water, or of a small network of interacting waters, needs to be explicitly considered. Results: Here, we analyse the software to aid the selection, or to predict the position, of water molecules that are going to be explicitly considered in later docking studies. We also present software and protocols able to efficiently treat flexible water molecules during docking, including examples of applications. Finally, we discuss methods based on molecular dynamics simulations that can be used to integrate docking studies or to reliably and efficiently compute binding energies of ligands in presence of interfacial or bridging water molecules. Conclusions: Software applications aiding the design of new drugs that exploit water molecules, either as displaceable residues or as bridges to the receptor, are constantly being developed. Although further validation is needed, workflows that explicitly consider water will probably become a standard for computational drug discovery soon.

scholarly journals Re-Designing Hazardous Chemicals with Target-Specific Toxicities by Learning from Structure-Based Drug Design

2018 ◽  
Author(s):  
Traci Clymer ◽  
Vanessa Vargas ◽  
Eric Corcoran ◽  
Robin Kleinberg ◽  
Jakub Kostal
Keyword(s):  
Drug Discovery ◽  
Drug Design ◽  
Adverse Effects ◽  
Environmental Health ◽  
In Silico ◽  
Adverse Outcomes ◽  
Design Stage ◽  
Hazardous Chemicals ◽  
Structure Based Drug Design ◽  
Computational Drug Discovery

Chemicals are the basis of our society and economy, yet many existing chemicals are known to have unintended adverse effects on human and environmental health. Testing all existing and new chemicals on animals is both economically and ethically unfeasible. In this paper, a new in silico framework is presented that affords redesign of existing hazardous chemicals in commerce based on specific molecular initiating events in their adverse outcomes pathways. Our approach is based on a successful methodology implemented in computational drug discovery, and promises to dramatically lower costs associated with new chemical development by synergistically addressing chemical function and safety at the design stage. <br>

FINANCIAL STATUS AND PROSPECTS OF ECONOMIC DEVELOPMENT OF THE OUTSOURCING ENTERPRISE

2018 ◽  
Author(s):  
Olga Batrak ◽  
◽  
Nataliia Flentei ◽  
Keyword(s):  
Economic Development ◽  
National Economy ◽  
External Environment ◽  
External Factors ◽  
Financial Status ◽  
Financial Condition ◽  
Current State ◽  
New Ideas ◽  
Internal And External Factors ◽  
Comprehensive Study

The current state of the national economy means that businesses need to constantly look for ways to improve their efficiency and find new ideas to address their shortcomings. The problem of improving the financial condition of the enterprise and finding ways to improve the financial condition of the enterprise is primarily related to the mechanism for assessing the financial condition of the enterprise. The study of the financial condition of the enterprise gives an advantage to the business entity among competitors, allows to identify shortcomings in the activities of the enterprise and to form methods to improve its activities. Both internal and external factors have a significant impact on the financial condition of the enterprise. Since the internal and external environment is constantly changing, so business is characterized by uncertainty. The article considers the specifics of the analysis of the financial condition and prospects of economic development of the outsourcing company. The author generalizes the concept of "financial condition of the enterprise" and substantiates the importance of a comprehensive study of its evaluation indicators. Based on the analysis of the financial condition of Corplex LLC identified promising ways of economic development of the studied outsourcing company.

An Ideation Framework for Service Process Improvement

2010 ◽  
Vol 1 (3) ◽  
pp. 17-49 ◽  
Author(s):  
Maya Kaner ◽  
Reuven Karni
Keyword(s):  
Best Practices ◽  
Process Improvement ◽  
Case Based Reasoning ◽  
Process Redesign ◽  
Road Map ◽  
Current State ◽  
Successful Design ◽  
New Ideas ◽  
Effectiveness And Efficiency ◽  
Improvement Methodologies

Service delivery processes play a key role in the competitiveness of modern organizations. Their effectiveness and efficiency are a consequence of successful design of new processes and improvement of existing processes. Improvement methodologies commonly focus on generic steps serving as a road map for moving a process from its current state along a guided path to better performance. However, these methodologies ignore the crucial step of methods for modifying processes, which often necessitate the generation of new improvement alternatives; generally based on “randomized” brainstorming rather than on systematic triggering of new ideas and reusing past improvements. The authors’ framework comprises and integrates 21 goal determinants to be achieved through process redesign, 32 best practices describing possible process modifications, 40 TRIZ inventive principles for generating new improvement ideas, and case-based reasoning (CBR) for retaining and reusing past improvements. This paper illustrates the application of the proposed methodology using an example of an inbound telesales process.

Sign in / Sign up

Export Citation Format

Share Document