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ANTIMIC: A database of Antimicrobial peptides

What are Antimicrobial peptides (AMPs)?. Important components of the innate immune system of many speciesAMPs are found in eukaryotes and prokaryotesAMPs are mostly gene encoded peptidesThere are more than 50 known families. What are characteristics of AMPs?. AMPs have the following properties: pathogen-lytic activity, anti-tumor activity, mitogen activity, activity of signaling molecules effective action against pathogens resistant to conventional antibioticscan serve as natural templates for design of novel synthetic antimicrobial drugs.

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ANTIMIC: A database of Antimicrobial peptides

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    1. ANTIMIC: A database of Antimicrobial peptides A master’s thesis project by Manisha Brahmachary Supervisors: Prof. Vladimir Bajic,Dr. Vladimir Brusic, Prof. Tan Tin Wee

    2. What are Antimicrobial peptides (AMPs)? Important components of the innate immune system of many species AMPs are found in eukaryotes and prokaryotes AMPs are mostly gene encoded peptides There are more than 50 known families

    3. What are characteristics of AMPs? AMPs have the following properties: pathogen-lytic activity, anti-tumor activity, mitogen activity, activity of signaling molecules effective action against pathogens resistant to conventional antibiotics can serve as natural templates for design of novel synthetic antimicrobial drugs

    4. Why do we need the ANTIMIC database? Data about AMPs is scattered across various databases like NCBI, SwissProt, AMSdb. No common platform or resource exists which: enables easy access to systematized information about AMPs provides analytical tools to facilitate analysis of AMPS and search for new members of AMP classes

    5. Datamining for AMPs Building a user-friendly and comprehensive database of AMPs Integrating relevant tools useful to biologists for data extraction and analysis Performing analysis of abilities to search for new AMPs by the integrated tools

    6. Datamining for AMP

    7. What the ANTIMIC database contains? Currently: ~1700 sequences covers eukaryotic and prokaryotic sequences contains sequences with known families and ones with unknown families Contains data extraction tools: Search using keywords BLAST Contains structure viewer ANTIMIC database http://www.research.i2r.org.sg/Templar/DB/ANTIMIC

    8. Data analysis tools (1) Antimic profile tool: Consists of three modules: Building profiles Querying profiles Querying other databases using profiles Uses HMMER package in the background

    9. Data analysis tools (2)

    10. Data analysis tools (3) Query profiles: helps a user to predict to which family a query sequence most likely belongs to and the critical (conserved) residues for the analyzed domain which maybe important for functioning of antimicrobial sequences

    11. A result of Query profile

    12. Data analysis tools (4) Query db: allows users to search for homologous sequences in the GenBank’s ‘nr’ database and the ANTIMIC database

    13. Conclusion ANTIMIC database is the most comprehensive database of natural AMPs to date It allows users different types of searches (keyword, BLAST) It allows users to perform several type of peptide analysis and viewing (BLAST similarity and Antimic profile matching, Structure viewing) Users can query external database resources Users can tentatively classify the query peptide sequence into several available AMP families

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