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Full Guidance on Amino Acid/Protein Databases for Beginners

Name: Full Guidance on Amino Acid/Protein Databases for Beginners
Rating: 4.2 (16 reviews)

Complete Beginner's Guide of Top Amino Acid/Protein Databases used in Bioinformatics along with their Utilization

Created byMuhammad Ahsan Riaz

Last updated 8/2022

English

What you'll learn

You will learn 15+ Amino Acid / Protein Different Databases used in Bioinformatics
You will learn the Whole Concept of Databases
You will learn about the Primary Databases in Bioinformatics
You will learn about the Secondary Databases in Bioinformatics
You will learn about the Amino Acid / Protein Databases in Bioinformatics
Complete up-to Date Beginner's Guide of top Amino Acid / Protein Used in Bioinformatics along with their utilization
Tools Used in Amino Acid / Protein Databases

Course content

7 sections • 17 lectures • 1h 3m total length

Introduction of Bioinformatics Databases2:58
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures.
Importance of Biological Database
Databases are important tools in assisting scientists to analyze and explain a host of biological phenomena from the structure of biomolecules and their interaction, to the whole metabolism of organisms and to understanding the evolution of species. This knowledge helps facilitate the fight against diseases, assists in the development of medications, predicting certain genetic diseases and in discovering basic relationships among species in the history of life.
Biological database design, development, and long-term management is a core area of the discipline of bioinformatics
Types of Biological Databases3:13
Types of biological database on the base of biological molecules sequence, structure and functions:
Nucleic acid databases
Amino acid / protein databases
Specialized databases
Types of biological database:
There are three to four main types of biological databases on the base of data it contain;
Primary database
Secondary Databases
Specialized Database
Literature Databases
Difference between Primary & Secondary Databases1:57
Primary Database : Primary databases (also known as data repositories) are highly organized, user-friendly gateways to the huge amount of biological data produced by researchers around the world. Most protein sequences found in databases are the product of conceptual translation of the genes and genomes determined using DNA sequencing.
Examples of these include Swiss-Prot & PIR for protein sequences, GenBank & DDBJ for Genome sequences and the Protein Databank for protein structures.
Secondary Database : Secondary databases comprise data derived from analyzing entries in primary databases. In most cases, they also provide tools to investigate further the genes and proteins.
Secondary databases contain information derived from primary sequence data which are in the form of regular expressions (patterns), Fingerprints, profiles blocks or Hidden Markov Models. The type of information stored in each of the secondary databases is different.
Examples of Secondary databases are as follows.
InterPro
UniProt
RefSeq
1000 Genomes Project

Introduction of Primary Databases0:40
Primary Databases
Are populated with experimentally derived data
Original biological data.
Raw data submitted by researcher
DDBJ EMBL NCBI
Explaining Primary Databases5:14
Explained the different primary databases
DDBJ
EMBL
NCBI
Introduction of Secondary Databases0:56
Secondary Databases
Computationally processed or manually curated information,
based on primary databases
23andMe's
RefSeq
OMIM
1000 genome browser
Explaining Secondary Databases7:36
Explained Secondary Databases
23andMe's
RefSeq
OMIM
1000 genome browser

Introduction of Protein Sequence Databases1:02
Protein sequence databases
PROSITE: database of protein families and domains
Protein Information Resource (Georgetown University Medical Center [GUMC])
Swiss-Prot: protein knowledgebase (Swiss Institute of Bioinformatics)
NCBI: protein sequence and knowledgebase (National Center for Biotechnology Information)
Explaining Protein Sequence Databases8:04
Explained Protein Sequence Databases
PROSITE
NCBI
Swiss-Prot
Protein Information Resource

Introduction of Protein Structure Databases1:02
Protein structure databases
Protein Data Bank (PDB), comprising:
Protein Data Bank in Europe (PDBe)
Protein Data bank in Japan (PDBj)
Research Collaboratory for Structural Bioinformatics (RCSB)
Structural Classification of Proteins (SCOP)
CATH : Protein Structure Classification database
Explaining Protein Structure Databases8:17
Explained Protein Structure Databases
Protein Data Bank
CATH
Structural Classification of Proteins

Introduction of Protein Model Databases2:39
Protein model databases
ModBase
Similarity Matrix of Proteins (SIMAP)
Swiss-model
AAindex
Explaining Protein Model Databases (PMDB)4:03
Protein model databases
ModBase: database of comparative protein structure models
Similarity Matrix of Proteins (SIMAP): database of protein similarities computed using FASTA
Swiss-model: server and repository for protein structure models
AAindex: database of amino acid indices, amino acid mutation matrices, and pair-wise contact potentials

Introduction of Protein-Protein and Other Molecular Interactions3:49
Protein-protein and other molecular interactions
BioGRID
RNA-binding protein database
Database of Interacting Proteins
IntAct
Explaining Protein-Protein and Other Molecular Interactions6:11
Protein-protein and other molecular interactions
BioGRID: general repository for interaction datasets
RNA-binding protein database
Database of Interacting Proteins
IntAct: open-source database for molecular interactions (EMBL-EBI)

Introduction of Protein Expression Databases2:37
Protein production is the biotechnological process of generating a specific protein. It is typically achieved by the manipulation of gene expression in an organism such that it expresses large amounts of a recombinant gene. This includes the transcription of the recombinant DNA to messenger RNA (mRNA), the translation of mRNA into polypeptide chains, which are ultimately folded into functional proteins and may be targeted to specific subcellular or extracellular locations.
Explaining Protein Expression Databases2:58
Protein expression databases
Human Protein Atlas: aims at mapping all the human proteins in cells, tissues and organs

Requirements

Basic Bioinformatics terms
Basic Understanding of Biology and Bioinformatics
Willingness to learn
Good Internet and notebook to note down the lectures

Description

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.

Who this course is for:

Bioinformaticians are Encouraged to take this course.
Data Scientist are Encouraged to take this course
Researchers are also encouraged to take this Course
Anyone who wants to learn something NEW.

Full Guidance on Amino Acid/Protein Databases for Beginners

What you'll learn

Explore related topics

Course content

Introduction to Bioinformatics Databases3 lectures • 8min

Primary & Secondary Databases4 lectures • 14min

Protein Sequence Databases2 lectures • 9min

Protein Structure Databases2 lectures • 9min

Protein Model Databases (PMDB)2 lectures • 7min

Protein-Protein and Other Molecular Interactions2 lectures • 10min

Protein Expression Databases2 lectures • 6min

Requirements

Description

Who this course is for: