USER MANUAL
Search
Simple search in CAMP allows users to search based on keywords like "brevinin" or string searches like "human defensin". Users can restrict the search to a particular field descriptor.
Searches using Boolean operators are possible using the Advanced search option.
All searches are case insensitive. A complete list of the field descriptors and their description is given below:
DESCRIPTORS |
DESCRIPTION |
| SEQUENCE |
Sequences should be represented as single letter amino acids.
E.g. FLPKI
|
| SEQUENCE LENGTH |
To search for sequences of a defined length.
E.g. 10 |
| SOURCE |
Users should enter genus name only.
E.g. Homo |
| TAXONOMY |
The sequences are classified as Amoebazoa, Animalia, Archae, Bacteria, Fungi, Hetrobolosea, Viridiplantae, Viruses
E.g. Viridiplantae |
| ACTIVITY |
The antimicrobial activity is represented as antibacterial, antifungal, antiviral, antimicrobial, anticancerous.
E.g. antibacterial
|
| GRAM NATURE |
The Gram status of the target bacteria can be mentioned here.
E.g. Gram+
|
| TARGET ORGANISM |
Target organism can be searched as shown in the example.
E.g. E.coli
Sequences with Minimum inhibitory concentration [MIC values] can also be searched. The syntax is as shown below:
E.g. MIC
|
| HEMOLYTIC ACTIVITY |
Sequences with hemolytic activity against human or sheep RBC can be searched using this option.
E.g. RBC or "5 µg/ml"
|
| PUBMED ID |
E.g. 16386333 |
| GI |
This field allows search by GenInfo Identifier of NCBI.
E.g. 108533 |
| PROTEIN NAME |
Users can search for peptides by peptide name.
E.g. brevinin |
| SWISS-PROT ID |
Users can search the database by Swiss-Prot ID.
E.g. P82050 |
| PDB ID |
PDB accession numbers can be used for searching the database
E.g. 1VM5 |
| DATASET |
Users can limit their search to experimental or predicted dataset of CAMP.
E.g. experimental, predicted |
Search sequences with MIC value
DESCRIPTORS |
DESCRIPTION |
SELECT ORGANISM |
Users can search for sequences having antimicrobial activity against a particular organism
E.g. E. coli
|
DATASET |
Users can extract all sequences active against a particular test organism or only those with MIC values
|
Tools
Tools for calculating length, amino acid composition, net charge, aliphatic index, instability index, hydrophobicity and secondary structure propensity are included in CAMP. Users can paste their sequence/s or browse a text file with sequence/s.
Aliphatic index
The aliphatic index of a protein is defined as the relative volume occupied by aliphatic side chains (alanine, valine, isoleucine, and leucine). It may be regarded as a positive factor for the increase of thermostability of globular proteins. The aliphatic index of a protein is calculated according to the following formula.
Aliphatic index = X(Ala) + a * X(Val) + b * ( X(Ile) + X(Leu) ) where X(Ala), X(Val), X(Ile), and X(Leu) are mole percent (100 X mole fraction)
of alanine, valine, isoleucine, and leucine.
The coefficients a and b are the relative volume of valine side chain (a = 2.9)
and of Leu/Ile side chains (b = 3.9) to the side chain of alanine.
Reference:
Ikai, A.J. (1980) Thermostability and aliphatic index of globular proteins. J. Biochem. 88, 1895-1898.
Instability index
The instability index provides an estimate of the stability of your protein in a test tube. The authors of this method have assigned a weight value of instability to each of the 400 different dipeptides (DIWV).
Using these weight values it is possible to compute an instability index (II) which is defined as:
i=L-1
II = (10/L) x Sum {DIWV(x[i]x[i+1])}
i=1
where: L is the length of sequence |
DIWV(x[i]x[i+1]) is the instability weight value for the dipeptide starting in position i.
|
A protein whose instability index is smaller than 40 is predicted as stable, a value above 40 predicts that the protein may be unstable.
Reference:
Guruprasad, K., Reddy, B.V.B. and Pandit, M.W. (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng. 4,155-161.
Hydrophobicity
The Hydrophobicity of a peptide or protein is represented as Grand Average Hydrophobicity Value (GRAVY), calculated as the sum of hydropathy values of all the amino acids, divided by the number of residues in the sequence. Positive value of the score indicates hydrophobic and negative score indicates hydrophilic peptide.
Reference:
Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.
Secondary Structure Propensity
This feature displays reduced alphabets for secondary structure as present in PROFEAT server.
The results are indicated as follows :
Query: G L L S V L G S V A
Results: C H H C S H C C S H
where H: Helix; S: Strand; C: Coil.
Reference:
Dubchak I, Muchink I, Holbrook SR, Kim SH. (1995) Prediction of protein folding class using global description of amino acid sequence. Proc Natl Acad Sci USA . 92, 8700-8704.
BLAST
CAMP has two blast modules:
1) BLAST AGAINST CAMP: Users can search for similar sequences in the CAMP database.
2) BLAST AGAINST NCBI-PROT: Users can search for similar sequences in the non-redundant protein database of NCBI.
Reference:
Altschul, S. F. et al. (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402.
FASTA format
FASTA format for sequences begins with a single-line description, followed by lines of sequence data. The description line is demarked from the sequence data by a greater-than ('>') symbol in the first column.
For example :-
>sp|P18646|10KD_VIGUN 10 kDa protein OS=Vigna unguiculata PE=3 SV=1
MEKKSIAGLCFLFLVLFVAQEVVVQSEAKTCENLVDTYRGPCFTTGSCDDHCKNKEHLLS
GRCRDDVRCWCTRNC
Three prediction algorithms for antimicrobial peptides are incorporated in the database. These are based on Support Vector Machines (SVM), Random Forests (RF) and Discriminant Analysis (DA). The user can select the algorithm required for prediction.
Mature peptide sequence/s in FASTA format can be pasted or uploaded for prediction.
The results for RF (MCC = 0.859), DA (MCC = 0.754) and SVM (MCC = 0.88) are explained below:
AMP: The sequence is predicted to be antimicrobial.
Non-AMP: The sequence is predicted to be not antimicrobial.
RF and SVM also gives a probability score (0 to 1) for the prediction. Higher the probability, greater is the possibility of the prediction being correct.
In case of DA, the discriminant score can be compared with the threshhold
(-0.251) to decide the strength of prediction.
Submit Sequence
Researchers can submit their newly identified sequences using the submit sequence link.
Disclaimer
The authors do not assume any responsibility for losses of any kind incurred by use of this database.
Users can contact us with queries and suggestions at camp@bicnirrh.res.in
Users can contact us with queries and suggestions at biomedinfo@nirrh.res.in |