Let Me Explain

  Here's a simple table outlining the differences between a Database Management System (DBMS) and a File Processing System (FPS): Feature Database Management System (DBMS) File Processing System (FPS) Data Redundancy Minimizes redundancy through normalization High redundancy due to isolated data files Data Consistency Ensures data consistency through integrity constraints Difficult to maintain consistency Data Access Provides multiple views and flexible querying Limited and rigid access methods Data Security Strong security features and access control Limited security, often managed by the OS Data Integrity Enforces integrity constraints automatically Requires manual enforcement Concurrent Access Supports concurrent access and transactions Limited support for concurrent access Backup and Recovery Automated backup and recovery features Manual and often complex backup and recovery Data Independence Logical and physical data independence No data independence; changes affect applicatio...

  Preparation   Ensure the structural data (coordinates, experimental data, etc.) is complete and validated. Prepare metadata such as authors, sample information, experimental conditions and methods.  Registration   Create an account on the PDB website.  Data Submission  Use the PDB deposition system (OneDep) to upload the structural data files (PDB/mmCIF format). Submit associated experimental data (NMR, X-Ray diffraction, etc) Annotations   Provide detailed information about the structure, including biological function, related literature and any other relevant details.  Validation   The PDB system runs validation checks on the submitted data. Review and address any validation issue reported by the system.  Review and Approval  Receive a unique PDB ID code for the submitted structure. The data becomes publicly available after the chosen release conditions are met.

Here are brief explanations for SCOP, MMDB, and NDB: SCOP (Structural Classification of Proteins): SCOP is a database that classifies protein structures based on their evolutionary and structural relationships. It organizes proteins into a hierarchy of classes, folds, superfamilies, and families. MMDB (Molecular Modeling Database): MMDB is a database managed by NCBI that contains 3D macromolecular structures, including proteins and nucleic acids. It integrates structural data with functional information and provides tools for visualization and analysis. NDB (Nucleic Acid Database): NDB is a database that specializes in the 3D structures of nucleic acids like DNA and RNA. It stores information on their conformations and interactions, supporting research in structural biology and bioinformatics. 

  Introduction: CATH stands for the Class, Architecture, Topology/fold, Homology Protein Structure Classification Database.  It's a bit of a mouthful, but it basically helps scientists understand how different proteins are built and how they might be related. Let’s understand this in very simple Language: Imagine proteins as intricate Lego structures.  CATH helps classify these structures based on their building blocks and how they're put together.  Here's a breakdown of what CATH looks at: Class (C): This is like the basic material of the Legos - all alpha helices, all beta sheets, a mix of both, or hardly any. Architecture (A): Here, they consider how these basic pieces are arranged in 3D space, like a long strand or a fold-y sheet. Topology/fold (T): This gets more detailed, looking at how the individual pieces connect and fold into more complex shapes. Homology (H): Finally, CATH checks if these similarly built structures are likely from the same "Lego ancesto...

NCBI and its role in solving biological problems: Started in 1988, in Maryland, Bethesda, USA. Part of US National Library of Medicine ( NLM ) AND (NIH) National Institute of Health. Sponsored by the US Government.  Act as a warehouse of data.  https://www.ncbi.nlm.nih.gov/ Resources Available Under NCBI Nucleotide Repository for nucleotide sequences. GenBank Comprehensive database of DNA sequences. Proteins Repository for protein sequences. GenPept Translations of GenBank sequences into proteins. Gene Detailed information on gene sequences and functions. OMIM Online Mendelian Inheritance in Man. Database of human genes and genetic disorders. PubMed Literature database with ~36 million research papers. Paid access for full articles. BLAST Basic Local Alignment Search Tool. Finds sequence similarities. SRA Sequence Read Archive. Repository for raw sequence data. Books Free access to a variety of books, distinct from research papers. BioSample Metadata for biological samples. Sa...