Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Current methods in structural proteomics and its applications in biological sciences

ABSTRACT: A broad working definition of structural proteomics (SP) is that it is the process of the high-throughput characterization of the three-dimensional structures of biological macromolecules. Recently, the process for protein structure determination has become highly automated and SP platforms have been established around the globe, utilizing X-ray crystallography as a tool. Although protein structures often provide clues about the biological function of a target, once the three-dimensional structures have been determined, bioinformatics and proteomics-driven strategies can be employed to derive their biological activities and physiological roles. This article reviews the current status of SP methods for the structure determination pipeline, including target selection, isolation, expression, purification, crystallization, diffraction data collection, structure solution, refinement and functional annotation.

SUBMITTER: Manjasetty B

PROVIDER: S-EPMC3376864 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Biological Properties, Current Applications and Potential Therapeautic Applications of Brevinin Peptide Superfamily.

Project description:The Brevinin peptides are antimicrobial agents obtained from frog skin secretions. Brevinin-2R has attracted many attentions due to its very low hemolytic activity, cationic property, and high affinity to cancer cells. Moreover, it has shown little toxicity against normal mammalian cells, while having killed several tumor cell lines by activation of lysosome-mitochondrial death pathway. In this review, we introduced the Brevinin superfamily with a focus on its therapeutic applications. Next, some unique properties of Brevinins were briefly discussed, including their ability to stimulate insulin secretion, dendritic cell maturation, and wound healing. In this context, we also provide information about the decoration of nanoparticles, such as cerium nano-oxide, by Brevinins. Finally, we addressed their potential for anti-tumor and drug design applications.

| S-EPMC7087712 | biostudies-literature

The Scottish Structural Proteomics Facility: targets, methods and outputs.

Project description:The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.

| S-EPMC2883930 | biostudies-literature

Overview of Virus Metagenomic Classification Methods and Their Biological Applications.

Project description:Metagenomics poses opportunities for clinical and public health virology applications by offering a way to assess complete taxonomic composition of a clinical sample in an unbiased way. However, the techniques required are complicated and analysis standards have yet to develop. This, together with the wealth of different tools and workflows that have been proposed, poses a barrier for new users. We evaluated 49 published computational classification workflows for virus metagenomics in a literature review. To this end, we described the methods of existing workflows by breaking them up into five general steps and assessed their ease-of-use and validation experiments. Performance scores of previous benchmarks were summarized and correlations between methods and performance were investigated. We indicate the potential suitability of the different workflows for (1) time-constrained diagnostics, (2) surveillance and outbreak source tracing, (3) detection of remote homologies (discovery), and (4) biodiversity studies. We provide two decision trees for virologists to help select a workflow for medical or biodiversity studies, as well as directions for future developments in clinical viral metagenomics.

| S-EPMC5924777 | biostudies-literature

Uncertainty Visualization: Concepts, Methods, and Applications in Biological Data Visualization.

Project description:This paper provides an overview of uncertainty visualization in general, along with specific examples of applications in bioinformatics. Starting from a processing and interaction pipeline of visualization, components are discussed that are relevant for handling and visualizing uncertainty introduced with the original data and at later stages in the pipeline, which shows the importance of making the stages of the pipeline aware of uncertainty and allowing them to propagate uncertainty. We detail concepts and methods for visual mappings of uncertainty, distinguishing between explicit and implict representations of distributions, different ways to show summary statistics, and combined or hybrid visualizations. The basic concepts are illustrated for several examples of graph visualization under uncertainty. Finally, this review paper discusses implications for the visualization of biological data and future research directions.

| S-EPMC9580861 | biostudies-literature

Systematic review of current natural language processing methods and applications in cardiology.

Project description:Natural language processing (NLP) is a set of automated methods to organise and evaluate the information contained in unstructured clinical notes, which are a rich source of real-world data from clinical care that may be used to improve outcomes and understanding of disease in cardiology. The purpose of this systematic review is to provide an understanding of NLP, review how it has been used to date within cardiology and illustrate the opportunities that this approach provides for both research and clinical care. We systematically searched six scholarly databases (ACM Digital Library, Arxiv, Embase, IEEE Explore, PubMed and Scopus) for studies published in 2015-2020 describing the development or application of NLP methods for clinical text focused on cardiac disease. Studies not published in English, lacking a description of NLP methods, non-cardiac focused and duplicates were excluded. Two independent reviewers extracted general study information, clinical details and NLP details and appraised quality using a checklist of quality indicators for NLP studies. We identified 37 studies developing and applying NLP in heart failure, imaging, coronary artery disease, electrophysiology, general cardiology and valvular heart disease. Most studies used NLP to identify patients with a specific diagnosis and extract disease severity using rule-based NLP methods. Some used NLP algorithms to predict clinical outcomes. A major limitation is the inability to aggregate findings across studies due to vastly different NLP methods, evaluation and reporting. This review reveals numerous opportunities for future NLP work in cardiology with more diverse patient samples, cardiac diseases, datasets, methods and applications.

| S-EPMC9046466 | biostudies-literature

Hydroxy- and Amino-Phosphonates and -Bisphosphonates: Synthetic Methods and Their Biological Applications.

Project description:Phosphonates and bisphosphonates are stable analogs of phosphates and pyrophosphates that are characterized by one and two carbon-phosphorus bonds, respectively. Among the various phosphonates and bisphosphonates, hydroxy and amino substitutes are of interest as effective in medicinal and industrial chemistry. For example, hydroxy bisphosphonates have proven to be effective for the prevention of bone loss, especially in osteoporotic disease. On the other hand, different substitutions on the carbon atom connected to phosphorus have led to the synthesis of many different hydroxy- and amino-phosphonates and -bisphosphonates, each with its distinct physical, chemical, biological, therapeutic, and toxicological characteristics. Dialkyl or aryl esters of phosphonate and bisphosphonate compounds undergo the hydrolysis process readily and gave valuable materials with wide applications in pharmaceutical and agriculture. This review aims to demonstrate the ongoing preparation of various classes of hydroxy- and amino-phosphonates and -bisphosphonates. Furthermore, the current review summarizes and comprehensively describes articles on the biological applications of hydroxyl- and amino-phosphonates and -bisphosphonates from 2015 until today.

| S-EPMC9200139 | biostudies-literature

Methods of Model Reduction for Large-Scale Biological Systems: A Survey of Current Methods and Trends.

Project description:Complex models of biochemical reaction systems have become increasingly common in the systems biology literature. The complexity of such models can present a number of obstacles for their practical use, often making problems difficult to intuit or computationally intractable. Methods of model reduction can be employed to alleviate the issue of complexity by seeking to eliminate those portions of a reaction network that have little or no effect upon the outcomes of interest, hence yielding simplified systems that retain an accurate predictive capacity. This review paper seeks to provide a brief overview of a range of such methods and their application in the context of biochemical reaction network models. To achieve this, we provide a brief mathematical account of the main methods including timescale exploitation approaches, reduction via sensitivity analysis, optimisation methods, lumping, and singular value decomposition-based approaches. Methods are reviewed in the context of large-scale systems biology type models, and future areas of research are briefly discussed.

| S-EPMC5498684 | biostudies-other

Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers.

Project description:Post-translational modifications (PTMs) add a layer of complexity to the proteome through the addition of biochemical moieties to specific residues of proteins, altering their structure, function and/or localization. Mass spectrometry (MS)-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with a high level of sensitivity and specificity. The low stoichiometry of modified peptides means fractionation and enrichment techniques are often performed prior to MS to improve detection yields. Immuno-based techniques remain popular, with improvements in the quality of commercially available modification-specific antibodies facilitating the detection of modified proteins with high affinity. PTM-focused studies on blood cancers have provided information on altered cellular processes, including cell signaling, apoptosis and transcriptional regulation, that contribute to the malignant phenotype. Furthermore, the mechanism of action of many blood cancer therapies, such as kinase inhibitors, involves inhibiting or modulating protein modifications. Continued optimization of protocols and techniques for PTM analysis in blood cancer will undoubtedly lead to novel insights into mechanisms of malignant transformation, proliferation, and survival, in addition to the identification of novel biomarkers and therapeutic targets. This review discusses techniques used for PTM analysis and their applications in blood cancer research.

| S-EPMC8072572 | biostudies-literature

Editorial: Genomic and epigenomic applications in animal and veterinary sciences.

Project description: Not available

| S-EPMC10069669 | biostudies-literature

SARS-CoV-2 Production, Purification Methods and UV Inactivation for Proteomics and Structural Studies.

Project description:Severe acute respiratory syndrome coronavirus-2 is the causative agent of COVID-19. During the pandemic of 2019-2022, at least 500 million have been infected and over 6.3 million people have died from COVID-19. The virus is pleomorphic, and due to its pathogenicity is often handled in very restrictive biosafety containments laboratories. We developed two effective and rapid purification methods followed by UV inactivation that allow easy downstream handling of the virus. We monitored the purification through titering, sequencing, mass spectrometry and electron cryogenic microscopy. Although pelleting through a sucrose cushion, followed by gentle resuspension overnight gave the best particle recovery, infectivity decreased, and the purity was significantly worse than if using the size exclusion resin Capto Core. Capto Core can be used in batch mode, and was seven times faster than the pelleting method, obviating the need for ultracentrifugation in the containment laboratory, but resulting in a dilute virus. UV inactivation was readily optimized to allow handling of the inactivated samples under standard operating conditions. When containment laboratory space is limited, we recommend the use of Capto Core for purification and UV for inactivation as a simple, rapid workflow prior, for instance, to electron cryogenic microscopy or cell activation experiments.

| S-EPMC9505060 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data