Traditional drug discovery approaches are time-consuming, tedious and expensive. Identifying a potential drug-like molecule using high throughput screening (HTS) with high confidence is always a ...challenging task in drug discovery and cheminformatics. A small percentage of molecules that pass the clinical trial phases receives FDA approval. This whole process takes 10-12 years and millions of dollar of investment. The inconsistency in HTS is also a challenge for reproducible results. Reproducible research in computational research is highly desirable as a measure to evaluate scientific claims and published findings. This paper describes the development and availability of a knowledge based predictive model building system using the R Statistical Computing Environment and its ensured reproducibility using Galaxy workflow system.
We describe a web-enabled data mining analysis pipeline which employs reproducible research approaches to confront the issue of availability of tools in high throughput virtual screening. The pipeline, named as "Galaxy for Compound Activity Classification (GCAC)" includes descriptor calculation, feature selection, model building, and screening to extract potent candidates, by leveraging the combined capabilities of R statistical packages and literate programming tools contained within a workflow system environment with automated configuration.
GCAC can serve as a standard for screening drug candidates using predictive model building under galaxy environment, allowing for easy installation and reproducibility. A demo site of the tool is available at http://ccbb.jnu.ac.in/gcac.
Metabolic reactions have been extensively studied and compiled over the last century. These have provided a theoretical base to implement models, simulations of which are used to identify drug ...targets and optimize metabolic throughput at a systemic level. While tools for the perturbation of metabolic networks are available, their applications are limited and restricted as they require varied dependencies and often a commercial platform for full functionality. We have developed MetaNET, an open source user-friendly platform-independent and web-accessible resource consisting of several pre-defined workflows for metabolic network analysis.
MetaNET is a web-accessible platform that incorporates a range of functions which can be combined to produce different simulations related to metabolic networks. These include (i) optimization of an objective function for wild type strain, gene/catalyst/reaction knock-out/knock-down analysis using flux balance analysis. (ii) flux variability analysis (iii) chemical species participation (iv) cycles and extreme paths identification and (v) choke point reaction analysis to facilitate identification of potential drug targets. The platform is built using custom scripts along with the open-source Galaxy workflow and Systems Biology Research Tool as components. Pre-defined workflows are available for common processes, and an exhaustive list of over 50 functions are provided for user defined workflows.
MetaNET, available at http://metanet.osdd.net , provides a user-friendly rich interface allowing the analysis of genome-scale metabolic networks under various genetic and environmental conditions. The framework permits the storage of previous results, the ability to repeat analysis and share results with other users over the internet as well as run different tools simultaneously using pre-defined workflows, and user-created custom workflows.
Molecular Property Diagnostic Suite (
MPDS
TB
) is a web tool (
http://mpds.osdd.net
) designed to assist the in silico drug discovery attempts towards Mycobacterium tuberculosis (Mtb).
MPDS
TB
tool ...has nine modules which are classified into data library (1–3), data processing (4–5) and data analysis (6–9). Module 1 is a repository of literature and related information available on the Mtb. Module 2 deals with the protein target analysis of the chosen disease area. Module 3 is the compound library consisting of 110.31 million unique molecules generated from public domain databases and custom designed search tools. Module 4 contains tools for chemical file format conversions and 2D to 3D coordinate conversions. Module 5 helps in calculating the molecular descriptors. Module 6 specifically handles QSAR model development tools using descriptors generated in the Module 5. Module 7 integrates the AutoDock Vina algorithm for docking, while module 8 provides screening filters. Module 9 provides the necessary visualization tools for both small and large molecules. The workflow-based open source web portal,
MPDS
TB
1.0.1 can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular.
Graphical Abstract
SYNOPSIS: A web-based
MPDS
TB
Galaxy tool is developed for assessing therapeutic potential of molecules.
MPDS
TB
is categorized into Data Library, Data Processing and Data Analysis. It can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular.
Ensembl 2021 Howe, Kevin L; Achuthan, Premanand; Allen, James ...
Nucleic acids research,
01/2021, Letnik:
49, Številka:
D1
Journal Article
Recenzirano
Odprti dostop
Abstract
The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, ...regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.
PDF
