Family Generator

In this page you can create a family of antimicrobial peptides featuring user-selected properties.

Please take a look at the Frequently Asked Questions (FAQ) and the tutorial.

Note: To know more about each field simply hover your mouse over it. in some fields the following options are available: y="yes; n="no"; or i=ignored.

Calculation label ^(mandatory)Choose a name for the experiment to run
Username ^(mandatory)Choose a key that will be used to group your experiments	Email notification ^(mandatory) Send by mail information about the calculation label and the start and finishing of the experiment
Append User peptidesSpecify one or more user customized sequences to include in the experiments (separated by commas)	Create the family of a specific peptide

Optional selection criteria (a run with unspecified criteria might require long calculation times):

Peptide nameSelect peptide by its common name (e.g. aurein)	A run with unspecified criteria might require long calculation times
Sequence pattern Select peptide by a pattern (e.g. KKV will find all peptides containing such pattern, GL-DIVKKVVGA-GS- with allow - positions to be any residue, but note that last - will need to be dropped to include shorter peptides than that length). Users can also specify residues to be used for substitutions setting them between braces (e.g K-KK{polar}KK{K,P,L}). Groups of residues can also be used if wanted: hydrophobic (A, V, I, L, M), negative (D, E), positive (K, R), aromatic (W, Y, H, F), polar (S, T, N, Q). Please remember that if you set "work in simplified aa space" to "DSSP" you need to pass your sequence in DSSP field instead
Target OrganismSelect by the activity towards one specific organism (e.g. baumannii) or multiple separated by commas (eg. coli,cereus). In order to avoid certain organisms you can add "n_" in front of the name (i.e. "n_coccus" will select all species but coccus). To get peptides against any organism type "X"	Activity (µM) µM concentration for activity against the specified Organism, type X for peptides with any defined activity value and separate values by commas to match is specified Target Organism. By default maximum concentration is used, it is possible to tune it using >,<,>=,<= operators before each quantity. Activity test Type of activity test experimentally used (e.g. MIC, MAC, LD50, IC50, IC100, GI50, HC10, EC50, EC100, HD50, HC50, LC50, MHC, MBC...)

Advanced _{(+) Expand Me}

Peptide properties _{(+) Expand Me}

Simple DSSP Substitution matrix

y n i y n

y n y n

Sequence length rangeSpecify the minimum and maximum length of the peptide you want to select.(e.g. 4-20)
StereoisomerismSelect by the stereoisomerism of the aminoacids (by choosing i both D and L amino acids are retained)
ID Select peptides by their database ID (e.g. satpdb24776, canPPD1290, hemo2586, DRAMP00001, HIP518, PHYT00014, CAMPSQ232)
source Select the source of the peptide (e.g. human, frog, synthetic...)
taxonomy Select by the taxonomy of the source (e.g. Viridiplantae, Animalia, Bacteria...)
Family Select by the traditional name of the family (e.g. Brevinin, defensin...)
gene Select by the name of gene that codes the peptide (e.g. ple4, Defb38...)
N terminus Presence of N terminal modifications (e.g Acetylation, amidation...)
C terminus Presence of C terminal modifications (e.g Amidation, acetylation...)
PTM Specify a type of post-transcriptional modification (e.g. amidation, glycosylated)
target Specify a binding target (e.g. cell_membrane)
pdb Specify the PDB code of the desired peptide (e.g. satpdb21843, 2JMY...). Note that you can select peptides with experimental structure choosing y in the field "experim structure" below)
DSSP Predicted secondary structure by DSSP. You can look for peptide with a certain structure using the DSSP syntax for 8 types of secondary structure: H: alpha-helix; B: isolated beta-bridge; E: extended strand; G: 3/10 helix; I: pi helix; T: Turn; S: Bend and Blank; C: Loop (e.g. HHHHHHHHCCC).
PMID Select by PudMed ID of the work describing desired peptide (e.g. 12969798)

Family generator

In this page you can create a family of antimicrobial peptides featuring user-selected properties.

Please take a look at the Frequently Asked Questions (FAQ) and the tutorial.

Optional selection criteria (a run with unspecified criteria might require long calculation times):

Results will be viewable in the DOWNLOAD RESULTS section. You can extract meaningful information from the experiment using FAMILY ANALYZER tool too.

In this page you can create a family of antimicrobial peptides featuring user-selected properties.

Please take a look at the Frequently Asked Questions (FAQ) and the tutorial.

Optional selection criteria (a run with unspecified criteria might require long calculation times):

Results will be viewable in the DOWNLOAD RESULTS section. You can extract meaningful information from the experiment using FAMILY ANALYZER tool too.

Special characters for modified aminoacids

Special characters for modified aminoacids

Special characters for modified aminoacids