Influence of Genomic and Other Biological Data Sets in the Understanding of Protein Structures, Functions and Interactions

2011 ◽  
Vol 2 (1) ◽  
pp. 24-44
Author(s):  
N. Srinivasan ◽  
G. Agarwal ◽  
R. M. Bhaskara ◽  
R. Gadkari ◽  
O. Krishnadev ◽  
...  
Keyword(s):  
Protein Structures ◽  
Biological Properties ◽  
Biological Data ◽  
Biological Information ◽  
Biological Databases ◽  
Homology Detection ◽  
Putative Gene ◽  
Remote Homology ◽  
Strategic Integration ◽  
Remote Homology Detection

In the post-genomic era, biological databases are growing at a tremendous rate. Despite rapid accumulation of biological information, functions and other biological properties of many putative gene products of various organisms remain either unknown or obscure. This paper examines how strategic integration of large biological databases and combinations of various biological information helps address some of the fundamental questions on protein structure, function and interactions. New developments in function recognition by remote homology detection and strategic use of sequence databases aid recognition of functions of newly discovered proteins. Knowledge of 3-D structures and combined use of sequences and 3-D structures of homologous protein domains expands the ability of remote homology detection enormously. The authors also demonstrate how combined consideration of functions of individual domains of multi-domain proteins helps in recognizing gross biological attributes. This paper also discusses a few cases of combining disparate biological datasets or combination of disparate biological information in obtaining new insights about protein-protein interactions across a host and a pathogen. Finally, the authors discuss how combinations of low resolution structural data, obtained using cryoEM studies, of gigantic multi-component assemblies, and atomic level 3-D structures of the components is effective in inferring finer features in the assembly.

scholarly journals Structural Bioinformatics: Computational Software and Databases for the Evaluation of Protein Structure

2018 ◽  
Vol 9 (2) ◽  
pp. 94-101
Author(s):  
Ayisha Amanullah ◽  
Suad Naheed
Keyword(s):  
Protein Structure ◽  
Protein Structures ◽  
Similarity Index ◽  
Biological Data ◽  
Biological Information ◽  
Biological Databases ◽  
Protein Structure Analysis ◽  
Clinical Consequences ◽  
Structural Databases ◽  
Types Of Information

Databases are the computerized platform where information is stored and can be retrieved easily by public users. Biological databases are the repositories of biological data. These biological data libraries contain facts and figures related to various disciplines of research including genomics, proteomics, microarray technology, metabolomics and phylogenetics. By using biological databases, a broad collection of essential biological information can be exploited ranging from function, structure and localization of gene, clinical consequences of mutation to similarity index among biological sequences and structures. Nowadays, different kinds of biological databases are available on the web. The present write up focuses on biological databases and bioinformatics tools for protein structure analysis. This review also aims to elaborate the searching schemes, available in different structural databases. The wide variety of different levels and types of information content related to 3D protein structures are available on web-based databases. Regarding the biological functions and 3D structures of various proteins, these databases provide a huge range of useful links, schematic diagrams as well as strategies for detailed analysis of proteins and other macromolecules structures. 3D structural illustration of proteins stored in structural databases is determined and visualized by X-ray crystallography, electron microscopy and NMR spectroscopy. On regular basis, a large number of protein structures are submitted by structural biologists, updated and curated by subject experts. Most familiar biological databases that store 3D protein and other macromolecules structures include, PDB, 3D Genomics, CATH, & SCOP. These databases contain valuable information of overall protein structures, domains and motif structures, protein-protein complex systems and complex of protein with other biomolecules.

scholarly journals R3D Prediction Model: Remote Homology Prediction using Protein Contact Map with Dimensionality Reduction

2019 ◽  
Vol 9 (1) ◽  
pp. 3829-3841
Keyword(s):  
3D Structure ◽  
3D Models ◽  
Biological Data ◽  
Vector Representation ◽  
Homology Detection ◽  
Contact Map ◽  
Remote Homology ◽  
Sequence Homologies ◽  
Genomics And Proteomics ◽  
Remote Homology Detection

Bioinformatics is one of a developing field that utilizations evaluation to extort information from Biological Data. Bioinformatics approaches are regularly utilized for significant activities that create expansive informational collections. Two basic tremendous scale practices that use bioinformatics are genomics and proteomics. Proteins are the far reaching, complex atoms that are essential for normal working of cells. 20% of the human body is involved proteins. Proteins are involved smaller units called amino acids, which are building squares of proteins. Protein remote homology identification and recognition are focal issues in bioinformatics. Sequence homologies are a vital source of data about proteins. In this research, the framework propose different strategy that diminishes the high dimensionality of the vector representation in remote homology detection by utilizing models that are characterized at the 3D level and consequently are very structurally and practically related. Subsequently, the 3D models are mapped from the protein primary sequence. The framework proposes to address the issue of remote homology identification by reducing 3D structure models. The new technique, called remote homology identification by the Reduction of 3D models (remote-R3D), is introduced and tested on various protein families.

THE TYPES OF BIOLOGICAL DATABASES (BIOBANKS)

2021 ◽  
pp. 136-148
Author(s):  
Elena S. Boltanova ◽  
◽  
Maria P. Imekova ◽  
Keyword(s):  
Biological Samples ◽  
Local Level ◽  
Legal Regulation ◽  
Biological Data ◽  
Biological Information ◽  
Biological Databases ◽  
Legal Regime ◽  
Eu Countries ◽  
Legal Method ◽  
The Eu

In the world, it is customary to create biological databases of different species. And initially, the databases for the investigation of crimes were widespread. However, later, when their potential and benefits, including for medicine, were assessed, the databases for other areas appeared. Russia was no exception in this regard. Although, in our country, unlike foreign states, the activities of biological databases based on purposes other than the disclosure of crimes are practically not regulated in any way. This article deals with the analysis of legal regulation of biobanks in the Russian Federation and abroad. Special attention is paid to the classification of biobanks. The purpose of the study is to determine the feasibility in the legislative regulation of their activities, as well as the patterns in such a regulation. To achieve this goal, the authors studied extensive regulatory material, which included EU directives and national regulations of the EU member states. The methodological basis of the study was the general scientific and private scientific meth-ods of research. Of course, such private scientific research methods as the comparative-legal method and the formal legal method have been widely used. Due to the comparative legal analysis, it is established that the EU countries have a high level of legislative activity in terms of determining the legal regime of biological databases. All countries recognize the specifics of such a legal regime, which can largely be explained by a special legal nature of biological samples and biological data. In this regard, the following issues related to the activities of biological databases are reflected everywhere in the EU countries at the level of law: the procedure for their creation; the procedure for receiving, processing, storing and transmitting biological samples and the data obtained on their basis; the rights and obligations of database creators and persons who have provided their biological samples and biological data about themselves; a set of measures aimed at protecting the rights and interests of donors and third parties, etc. As it seems, a similar approach to the regulation of the activities of biological bases estab-lished not for the investigation of crimes should be implemented by Russia. At the same time, special attention should be paid to the research of biological databases. In the Russian Federa-tion, they are created, as a rule, at the local level. Their main drawback is that they are sepa-rate sources of limited biological information, functioning independently of each other while comprehensive (concentrated in one place) information can bring invaluable benefits and advantages for Russian science and medicine as a whole. However, this requires the estab-lishment of an appropriate legal framework.

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