Literature Databases & Bioinformatics Resources
PubMed • PLOS • BioMed Central • NAR • NCBI • EMBL-EBI • ExPASy • RCSB PDB
Complete Bioinformatics Notes for CSIR-NET, GATE BT, DBT-BET, CUET PG & Life Science Exams
Introduction
Bioinformatics is a field where biology, computer science, mathematics and information technology work together to understand biological information. Modern biological research produces a huge amount of information, including DNA sequences, RNA sequences, protein sequences, protein structures, gene expression data and scientific publications.
Finding, organizing and understanding this information would be extremely difficult without specialized databases and online resources. Literature databases help researchers find scientific papers, while bioinformatics resources provide access to biological databases, analysis tools, structures and other research information.
In this chapter, we will study important Literature Databases and Bioinformatics Resources that are commonly used in biotechnology, microbiology, molecular biology, genetics, biochemistry and life-science research.
📚 Table of Contents
- What are Literature Databases?
- Open Access and Open Sources
- PubMed
- PubMed Central (PMC)
- PLOS
- BioMed Central (BMC)
- Nucleic Acids Research (NAR) Databases
- What are Bioinformatics Resources?
- NCBI
- EMBL-EBI
- ExPASy
- RCSB Protein Data Bank (RCSB PDB)
- Comparison of Major Resources
- How These Resources Are Used in Research
- Important Exam Points
- MCQs
- Frequently Asked Questions
- Important Links
- One-Minute Revision
Literature Databases and Bioinformatics Resources
1. What are Literature Databases?
A literature database is an organized online collection of information about scientific publications. It allows students, researchers and scientists to search for research papers, review articles, clinical studies, conference information and other scientific literature.
Instead of searching through thousands of individual journal websites, researchers can use literature databases to search for relevant information using keywords, authors, journal names, publication dates and other filters.
Examples of Literature Databases
- PubMed
- PubMed Central
- PLOS
- BioMed Central
- NAR Database Issue
"What research has already been published about my topic?"
2. Open Access and Open Sources
Open Access (OA) means that research literature is available online without requiring the reader to pay a subscription fee for access to the article.
Open-access publishing has become very important because it allows researchers, students and the public to access scientific information more easily.
Advantages of Open Access
- Research can be accessed online easily.
- Students can read scientific literature without institutional subscriptions.
- Research findings can reach a wider audience.
- Scientific knowledge can be shared more quickly.
- Researchers can discover previous work more efficiently.
3. PubMed
PubMed is one of the most widely used literature-search resources in biomedical and life-science research.
It is maintained by the U.S. National Library of Medicine (NLM) and is provided through the National Center for Biotechnology Information (NCBI).
What can you search in PubMed?
- Research articles
- Review articles
- Clinical studies
- Biomedical literature
- Authors
- Journal names
- Publication dates
- Topics and keywords
Important PubMed Features
| Feature | Use |
|---|---|
| Keyword Search | Find papers related to a topic |
| Author Search | Find publications by an author |
| Journal Search | Search publications from a journal |
| Filters | Limit results by date, article type and other criteria |
Official website: https://pubmed.ncbi.nlm.nih.gov/
4. PubMed Central (PMC)
PubMed Central (PMC) is a free full-text archive of biomedical and life-science journal literature.
A very important distinction is that PubMed is primarily a literature citation and abstract database, whereas PMC provides access to the full text of articles that are deposited in the archive.
PubMed → Search biomedical literature
PMC → Access full-text articles available in the archive
Official website: https://pmc.ncbi.nlm.nih.gov/
5. PLOS
PLOS stands for Public Library of Science. It is a nonprofit organization associated with open science and open-access publishing.
PLOS publishes journals covering a wide range of scientific disciplines, including biology, medicine, genetics, microbiology and other areas of life science.
Why is PLOS important?
- It promotes open scientific communication.
- It publishes research through open-access journals.
- It covers many areas of biological and medical research.
- Researchers can search and read articles through its journal platforms.
Official website: https://plos.org/
PLOS Journals: https://plos.org/our-journals/
6. BioMed Central (BMC)
BioMed Central (BMC) is a major open-access scientific publishing platform. It publishes journals in biomedical sciences, life sciences, medicine and related fields.
BMC journals cover many research areas such as microbiology, biotechnology, genetics, molecular biology, bioinformatics and medicine.
Important Points
- BMC is strongly associated with open-access publishing.
- It publishes journals covering biomedical and life sciences.
- Individual journals may have their own publication policies.
- Researchers should always check the specific journal's current guidelines.
Official website: https://www.biomedcentral.com/
7. Nucleic Acids Research (NAR) Database Issue
Nucleic Acids Research (NAR) is an important scientific journal in molecular biology and bioinformatics.
One particularly useful resource for bioinformatics students is the NAR Database Issue. It contains papers describing important biological databases and updates to existing databases.
These databases may contain information related to genes, proteins, genomes, molecular pathways, structures and other biological resources.
Official NAR website: https://academic.oup.com/nar
8. What are Bioinformatics Resources?
Bioinformatics resources are online databases, tools, servers and knowledge platforms that help researchers store, retrieve, analyze and interpret biological information.
They can provide information about DNA, RNA, proteins, genomes, protein structures, pathways, molecular functions and many other biological features.
Examples
- NCBI
- EMBL-EBI
- ExPASy
- RCSB Protein Data Bank
9. NCBI
NCBI stands for National Center for Biotechnology Information.
NCBI is one of the most important bioinformatics resources used by researchers and students around the world. It provides access to biological and biomedical databases, literature resources and analysis tools.
Major NCBI Resources
| Resource | Main Use |
|---|---|
| PubMed | Biomedical literature |
| GenBank | Nucleotide sequence data |
| Protein | Protein sequence information |
| BLAST | Sequence similarity searching |
| Gene | Gene-related information |
| Genome | Genome information |
NCBI: https://www.ncbi.nlm.nih.gov/
NCBI Guide: https://www.ncbi.nlm.nih.gov/guide/
BLAST: https://blast.ncbi.nlm.nih.gov/
10. EMBL-EBI
EMBL-EBI stands for the European Molecular Biology Laboratory – European Bioinformatics Institute.
EMBL-EBI provides access to a large collection of biological data resources, analysis tools and services. It is an important resource for researchers working in molecular biology, genomics, proteomics, structural biology and bioinformatics.
Major Areas Covered
- Genomics
- Proteomics
- Structural biology
- Gene expression
- Sequence analysis
- Biological databases
- Bioinformatics tools
Official website: https://www.ebi.ac.uk/
EBI Services: https://www.ebi.ac.uk/services/
Data Resources & Tools: https://www.ebi.ac.uk/services/data-resources-and-tools/
11. ExPASy
ExPASy is the Expert Protein Analysis System associated with the Swiss Institute of Bioinformatics (SIB).
It provides access to a wide range of biological databases, knowledge resources and software tools. It is particularly useful for protein analysis and proteomics, while also covering several other areas of bioinformatics.
Uses of ExPASy
- Protein analysis
- Proteomics research
- Sequence-related analysis
- Access to biological databases
- Structural biology resources
- Systems biology resources
- Other bioinformatics tools
Official website: https://www.expasy.org/
12. RCSB Protein Data Bank (RCSB PDB)
The RCSB Protein Data Bank (RCSB PDB) provides access to three-dimensional structural information from the global Protein Data Bank archive.
The database contains experimentally determined structural information for biological macromolecules such as proteins, DNA and RNA.
What can researchers do with RCSB PDB?
- Search for protein structures.
- Search for DNA and RNA structures.
- View three-dimensional molecular structures.
- Analyze structural information.
- Download structure files.
- Study ligand and macromolecule interactions.
Official website: https://www.rcsb.org/
Search PDB: https://www.rcsb.org/search
Structure Search: https://www.rcsb.org/structure
Which Resource Should You Use?
13. Comparison of Major Resources
| Resource | Main Purpose | Useful For |
|---|---|---|
| PubMed | Biomedical literature search | Research papers and reviews |
| PMC | Full-text archive | Reading available full-text articles |
| PLOS | Open-access publishing | Open scientific literature |
| BioMed Central | Open-access publishing | Biomedical and life sciences |
| NAR Database Issue | Database information | Finding biological databases |
| NCBI | Biological and biomedical data | Sequences, genes, genomes, literature |
| EMBL-EBI | Biological data and tools | Genomics, proteomics and bioinformatics |
| ExPASy | Protein and bioinformatics resources | Protein analysis and databases |
| RCSB PDB | 3D structural data | Protein, DNA and RNA structures |
14. How These Resources Are Used in Real Research
Suppose you are working on a research project involving a particular protein. You can use different resources at different stages.
Step 1 — Literature Search
Start with PubMed to identify previous research papers and understand what is already known.
Step 2 — Sequence Information
Use NCBI resources to find nucleotide or protein sequences and related gene information.
Step 3 — Protein Resources
Use ExPASy and related resources for protein-oriented analysis and database access.
Step 4 — Structural Information
Use RCSB PDB to determine whether a three-dimensional structure is available.
Step 5 — Further Analysis
Use appropriate bioinformatics tools for sequence comparison, annotation, structural analysis or other research questions.
15. Important Exam Points
Important biomedical literature search resource.
Free full-text archive of biomedical literature.
Nonprofit organization associated with open science and open-access publishing.
Important source of information about biological databases.
Major biological and biomedical information resource.
European bioinformatics data resources and analysis services.
Important resource for protein analysis and bioinformatics.
Three-dimensional structures of biological macromolecules.
16. Important MCQs
Q1. Which database is widely used for biomedical literature?
A. RCSB PDB
B. PubMed
C. GenBank
D. ExPASy
Answer: B. PubMed
Q2. PubMed Central is mainly associated with:
A. Protein structures
B. Full-text biomedical literature
C. Genome assembly only
D. Molecular docking only
Answer: B. Full-text biomedical literature
Q3. PLOS is associated with:
A. Open science and publishing
B. Protein crystallization only
C. DNA sequencing only
D. Molecular docking only
Answer: A. Open science and publishing
Q4. Which resource is strongly associated with three-dimensional biological structures?
A. PubMed
B. RCSB PDB
C. PLOS
D. PMC
Answer: B. RCSB PDB
Q5. NCBI stands for:
A. National Center for Biological Information
B. National Center for Biotechnology Information
C. National Council of Bioinformatics Information
D. National Center for Biochemical Investigation
Answer: B. National Center for Biotechnology Information
Q6. Which resource is associated with the European bioinformatics community?
A. EMBL-EBI
B. PubMed
C. PLOS
D. RCSB PDB
Answer: A. EMBL-EBI
Q7. ExPASy is particularly useful for:
A. Protein-related analysis and resources
B. Weather forecasting
C. Geological mapping
D. Financial analysis
Answer: A. Protein-related analysis and resources
Q8. The NAR Database Issue mainly provides information about:
A. Biological databases
B. Hospital management
C. Chemical industries
D. Weather databases
Answer: A. Biological databases
Q9. Which NCBI tool is commonly used for sequence similarity searching?
A. BLAST
B. PubMed
C. PDB
D. PLOS
Answer: A. BLAST
Q10. RCSB PDB provides information mainly related to:
A. Three-dimensional biological structures
B. Scientific journal citations only
C. Weather information
D. Population census
Answer: A. Three-dimensional biological structures
17. Frequently Asked Questions
What is a literature database?
A literature database is an organized collection of scientific publication information that helps users search for research papers and related literature.
What is PubMed used for?
PubMed is mainly used to search biomedical and life-science literature.
What is PubMed Central?
PubMed Central is a free full-text archive of biomedical and life-science journal literature.
What is PLOS?
PLOS is a nonprofit organization focused on open science and open-access publishing.
What is NCBI?
NCBI is a major biological and biomedical information resource providing databases, literature resources and bioinformatics tools.
What is EMBL-EBI?
EMBL-EBI provides biological data resources, bioinformatics tools and analysis services.
What is ExPASy?
ExPASy is a Swiss Institute of Bioinformatics resource providing biological databases, knowledge resources and software tools, with strong relevance to protein analysis.
What is RCSB PDB?
RCSB PDB provides access to three-dimensional structural information for biological macromolecules such as proteins, DNA and RNA.
18. Important Bioinformatics Links
🔹 PubMed: Open PubMed
🔹 PubMed Central: Open PMC
🔹 PLOS: Open PLOS
🔹 BioMed Central: Open BioMed Central
🔹 Nucleic Acids Research: Open NAR
🔹 NCBI: Open NCBI
🔹 NCBI BLAST: Open BLAST
🔹 EMBL-EBI: Open EMBL-EBI
🔹 ExPASy: Open ExPASy
🔹 RCSB PDB: Open RCSB PDB
19. One-Minute Final Revision
- Literature Database → Used to find scientific publications.
- Open Access → Research available online without subscription barriers.
- PubMed → Biomedical literature search.
- PMC → Full-text biomedical literature archive.
- PLOS → Open science and open-access publishing.
- BioMed Central → Open-access biomedical and life-science publishing platform.
- NAR Database Issue → Information about biological databases.
- NCBI → Biological and biomedical databases and tools.
- EMBL-EBI → European biological data resources and analysis tools.
- ExPASy → Protein and bioinformatics resources.
- RCSB PDB → 3D structures of biological macromolecules.
🧠 Easy Memory Trick
“Papers → Sequences → Proteins → Structures”
📚 PubMed → Papers
🧬 NCBI → Biological sequences and genes
🧪 ExPASy → Protein-related resources
🧊 RCSB PDB → 3D structures
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