IAMPDB Help

1. IAMPDB Text Search Facility

This is a generelized search facility. This search facility is case insensitive. Here one can search with followings.

1. IAMPDB ID (e.g., IAMPDB10)

2. Peptide Name (e.g., Cecropin)

3. Source Organism [Insect only] (e.g., Drosophila melanogaster)

4. Taxonomy [Order] (e.g., Diptera)

5. Peptide Existence (e.g., Evidence at protein level)

6. Sequence (e.g., MNFYNIFVFVALILAITIGQSEAGWLKKIGKKIERVGQHTRDATIQGLGIAQQAANVAATARG) [Note: This is not a BLAST search]

7. Molecular Formula (e.g., C306H621N87O146S1)

8. Structural Class of the Peptide (e.g., alpha OR alpha_beta)

9. Antimicrobial Activities (e.g., Anti-gram-negative)

10. Enzymatic Activities (e.g., Hydrolase)

11. Inhibitory Activities (e.g., Enzyme inhibitor)

12. Other Biological Activities (e.g., Tumor suppressor)

13. Target Organism (Gram Positive Bacteria) (e.g., Staphylococcus aureus)

14. Target Organism (Gram Negative Bacteria) (e.g., Escherichia coli)

15. Target Organism (Fungi) (e.g., Candida)

16. Target Organism (Protozoa) (e.g., Plasmodium vivax)

17. Exception Target Organism (e.g., Serratia marcescens)

18. Binding Target (e.g., Cell membrane)

19. Related Assays Info (e.g., Inhibition Zone assay)

20. PubMed ID (e.g., 2104802)

21. UniProt ID (e.g., C0HKQ7)

22. PDB ID (e.g., 1D9O)

2. IAMPDB Advanced Search Facility

This is a generelized search facility. This search facility is case insensitive. Click on 'Add Field' to add a search field. In case of 'Range Attributes' integer and float values are expected in search fields. An image of a build search query attached below.

3. Understand Text Format of IAMPDB database

The text format of IAMPDB starts with two-character code followed by 4 blank space characters followed by the data. Each line is kept 90 characters long for better readability of the data. The description of the two-character code is given below.

ID => IAMPDB Accession

PN => Peptide Name

GN => Gene Name

SO => Source Organism

TX => Taxonomy (Order)

PE => Peptide Existence Level/Validation

PL => Peptide Length

AC => Counts of Amino Acids

AF => Frequencies of Amino Acids

MA => Missing Amino Acid(s)

MO => Most Occurring Amino Acid(s)

LO => Less Occurring Amino Acid(s)

BA => Hydrophobic Amino Acid(s) Count

LA => Hydrophilic Amino Acid(s) Count

AA => Acidic Amino Acid(s) Count

BC => Basic Amino Acid(s) Count

MC => Modified Amino Acid(s) Count

MF => Modified Amino Acid(s) Frequencies

MM => Molecular Mass

AI => Aliphatic Index

II => Instability Index (Half Life)

HP => Hydrophobicity (GRAVY)

HM => Hydrophobic Moment

IP => Isoelectric Point

NC => Net Charge

SF => Secondary Structure Fraction

AR => Aromaticity

ME => Molar Extinction Coefficient (cysteine|cysteine)

MS => Mass Shift

SC => Structural Class of the Peptide

AM => Antimicrobial Activities

EA => Enzymatic Activities

IA => Inhibitory Activities

OB => Other Biological Activities

TP => Target Organisms (Gram Positive Bacteria)

TN => Target Organisms (Gram Negative Bacteria)

TF => Target Organisms (Fungi)

TV => Target Organisms (Virus)

TZ => Target Organisms (Protozoa)

ET => Exception Target Organisms

BT => Binding Target

MN => Mechanism of Action

HA => Hemolytic Aactivity

CA => Cytolytic Activity

OL => Other Lytic Info

TC => Toxicity

AY => Related Assays Info

XR => Database Cross-reference

SQ => Sequence

XX => Blank Line

// => End of an entry

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