Full Guidance on Amino Acid/Protein Databases for Beginners

This Bioinformatics course is going to game changer for you. Currently, there is an explosion of biological data. Bioinformatics is at the intersection of biology and computer science.

What is Bioinformatics ?

In biology, bioinformatics is defined as, “the use of computer to store, retrieve, analyze or predict the composition or structure of bio-molecules” . Bioinformatics is the application of computational techniques and information technology to the organization and management of biological data. Classical bioinformatics deals primarily with sequence analysis.

Aims of Bioinformatics

• Development of database containing all biological information.
• Development of better tools for data designing, annotation and mining.
• Design and development of drugs by using simulation software.
• Design and development of software tools for protein structure prediction function, annotation and docking analysis.
• Creation and development of software to improve tools for analyzing sequences for their function and similarity with other sequences

Biological Databases

Biological data are complex, exception-ridden, vast, and incomplete. Therefore several databases have been created and interpreted to ensure unambiguous results. A collection of biological data arranged in a computer-readable form that enhances the speed of search and retrieval and convenient to use is called a biological database. A good database must have updated information.

Importance of Biological Database

A range of information like biological sequences, structures, binding sites, metabolic interactions, molecular action, functional relationships, protein families, motifs and homologous can be retrieved by using biological databases. The main purpose of a biological database is to store and manage biological data and information in computer readable forms.

In this course we learned about the different biological databases that are being used in bioinformatics and get to know a little bit about their details. Mainly these databases are divided into four categories and we learned about them base by base. And explained the difference among the primary and secondary database and explained their utilization in bioinformatics.

Amino acid / protein databases

Several publicly available data repositories and resources have been developed to support and manage protein related information, biological knowledge discovery and data-driven hypothesis generation. The databases in the table below are selected from the databases listed in the Nucleic Acids Research (NAR) databases issues and database collection and the databases cross-referenced in the UniProtKB. Most of these databases are cross-referenced with UniProt / UniProtKB so that identifiers can be mapped to each other.

                        Sequence databases

CCDS                       The Consensus CDS protein set database

DDB                         JDNA Data Bank of Japan

ENA                         European Nucleotide Archive

GenBank                GenBank nucleotide sequence database

Refseq                    NCBI Reference Sequence Database

UniGene                 Database of computationally identifies transcripts from the same locus

UniProtKB              Universal Protein Resource (UniProt)

               3D structure protein databases

DisProt                                 Database of Protein Disorder

MobiDB                                Database of intrinsically disordered and mobile proteins

ModBase                             Database of Comparative Protein Structure Models

PDBsum                               Pictorial database of 3D structures in the Protein Data Bank

ProteinModelPortal           Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

SMR                                     Database of annotated 3D protein structure models

This course will be extremely helpful to students of data analyst and bioinformaticians because they use the databases a lot in their work.

If you guys have any questions or suggestions please let me know in instructor inbox I’ll try to answer all of your questions within 12 hours.