Updates commitment

We are responsible for maintaining the website daily and updating the resources regularly (Last update for the DB: May 2022).

Integrated knowledge

ADAPTABLE intregates knowledge from the following resources:

• ADAM
• ANTISTAPHYBASE
• APD
• AVPdb
• BACTIBASE
• BaAMPs
• CAMP_R3
• CancerPPD
• ConoServer
• CPPsite
• DBAASP
• DADP
• Defensins
• DRAMP
• Hemolytik
• HIPdb
• InverPep
• LAMP
• MilkAMP
• ParaPep
• Peptaibol
• PhytAMP
• ProtParam
• PubChem
• RCSB-PDB
• SATPdb
• The.Microbe.Directory
• YADAMP
• UniProt

How to extract .tar.xz files from DOWNLOAD RESULTS

	If it doesn't extract by itself, you may need to install a file extractor like PeaZip, 7-Zip or WinRAR.
	Supported by default with included graphical extracting tools or you can run tar xvf example.tar.xz
	Supported by default with included graphical extracting tool or you can run tar xvf example.tar.xz
	Supported by default with included graphical extracting tools or you can run tar xvf example.tar.xz

What is DSSP?

DSSP stands for "Define Secondary Structure of Proteins". Wolfgang Kabsch and Chris Sander defined an algorithm to assign secondary structure to the amino acids of a protein.

H

Alpha helix (4-12)

B

Isolated beta-bridge residue

E

Strand

G

3-10 helix

I

Pi helix

T

Turn

S

Bend

-

None

What is 'simple' mode for alignment?

In simple mode hydrophobic residues (A, V, I, L, M) are represented by A, negative residues (D, E) by D, positive residues (K, R) by K, aromatic residues (W, Y, H, F) by F, polar residues (S, T, N, Q) by S, modified amino acids by Ⓜ. Gly, Pro, Cys are treated individually.

What do we mean by SR 'family'?

In ADAPTABLE, the meaning of 'family' fits with 'groups of sequence-related peptides' (i.e 'sequence-related families' or SR families) and is not related with the taxonomic meaning of families.

What do we mean by 'father' of the family?

Based on sequence alignment, ADAPTABLE has classified all peptides of its database in groups of sequence-related peptides (families), each represented by a single sequence chosen among the members of the family (called the father). The father has the highest resemblance to all other peptides. In this terminology, each family is composed by a father and multiple sons (the other members of the family).

I made a mistake, how can I stop my running process?

While a process is running, you can click on the "Kill processes" button. That will forward you to a form asking the calculation label of your running experiment. Simply type the calculation label and "kill" the running process. You will be then able to start a new experiment.

How to fill each field in "FAMILY GENERATOR" form

In general, you will not need to fill each field on first run of ADAPTABLE. The only mandatory fields are the calculation label and the username. When hovering the mouse over any legend you will see a help message, suggesting proper values of each field. Leaving a field unaltered simply means that no filter will be applied with regards to its related property. A closer look to your results will inspire you on further fields you might want to specify in order to refine your search.

How can I help to incorporate a new DATABASE or AMP to ADAPTABLE?

ADAPTABLE manages this kind of file to read entries for each sequence. If you want to add a new peptide, you can use that template as a model trying to fill as many fields as possible and using "_" if not available. For incorporating a new DATABASE to ADAPTABLE, you can provide your script/program that is able to download the sources, parse them and provide an output analogous to the template we use.

Feel free to go to our GitLab repository and file and issue or pull request with your contributions

Browser compatibility

This webpage adheres to HTML Recommendation, hence, browsers following it should work.

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