Bioinformatics and Amino Acids

Bioinformatics

• Bioinformatics is a crucial field that combines computational tools and biological data to analyze and understand biological systems.

History of Bioinformatics

• The term "bioinformatics" was first coined by Paulien Hogeweg and Ben Hesper in 1960.

Special Cases of Amino Acids

• Proline (Pro): Has a unique ring structure that can impact protein folding and stability.
• Glycine (Gly): Is a crucial component of protein structures due to its simplicity and flexibility.
• Cysteine (Cys): Forms disulfide bonds that are essential for protein structure stabilization.
• Histidine: Has an amphoteric nature and can switch between protonation states, making it crucial for enzyme catalysis and protein function.

Importance of Amino Acids

• Amino acids play diverse and essential roles in protein structure, function, and overall biological processes.

Data and Information

• Data is raw, unorganized facts that need to be processed.
• Information is processed, organized, structured, or presented in a given context to make it useful.

Biological Databases

• Classified into two types based on the nature of data and source.

Primary Databases

• Contain biomolecular data in its original form.
• Experimental results are submitted directly into the database by researchers.
• Data is essentially archival in nature and cannot be changed further once a database accession number is assigned.
• Examples: GenBank, EMBL, DDBJ for DNA/RNA sequences, and SWISS-PROT and PIR for protein sequences.

GenBank

• A database from NCBI that includes sequences from publicly available resources.
• A genetic sequence database, an annotated collection of all publicly available DNA sequences.
• Part of the International Nucleotide Sequence Database Collaboration.

EMBL

• European Molecular Biological Laboratory, a nucleic acid database that comes under EBI (European Bioinformatics Institute).
• Established in collaboration with DDBJ and GenBank.
• EBI's Sequence Retrieval System (SRS) is a network browser for databanks in molecular biology.

DDBJ

• The DNA Data Bank of Japan, a biological database that collects DNA sequences.
• Located at the National Institute of Genetics in Japan.
• A member of the International Nucleotide Sequence Database Collaboration or INSDC.

SWISS-PROT

• A curated protein sequence database that provides high-level annotation.
• Annotations include description of protein function, domains, post-translational modifications, variants, etc.
• Created in 1986 by Amos Bairoch with Swiss Institute of Bioinformatics.

PIR

• The Protein Information Resources (PIR) is an integrated public resource of protein informatics.
• Supports genomic and proteomic research and scientific discovery.
• Maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283,000 sequences.

Secondary Database

• Contains data derived from analyzed primary data.
• Data is either manually created or generated automatically.
• Contains valuable information such as about mutations or evolutionary relationships.
• Examples: PROSITE, Pfam.

PROSITE

• A protein database that consists of entries describing protein families, domains, and functional sites.
• Manually curated by a team of the Swiss Institute of Bioinformatics.
• Tightly integrated into Swiss-Prot protein annotation.

Pfam

• A database of protein families that includes their annotations and multiple alignments generated using hidden Markov models.
• Provides a complete and accurate classification of protein families and domains.

Structural Database

• PDB (Protein Data Bank): comprises of PDBe (PDB of Europe), PDBj (PDB of Japan), SCOPE, and CATH.
• Contains information generated from X-Crystallgraphy and NMR Experiments.