logo        ParaPep -A Database of Anti-parasitic peptides


HELP PAGE OF ParaPep

Parasite types and diseases they are causing

Parasite TypeDiseaseDescription
PlasmodiumMalariaDisease transmitted by female Anopheles mosquito. P.falciparum has biphasic life cycle- Mosquito and Human (Exoerythrocytic and Erythrocytic). Five species infect humans, P.falciparum most deadly. Artemisinin Combination Therapy(ACT) used for treatment.
LeishmaniaLeishmaniasisFemale sandly transmit parasite. Obligate intra-macrophage single-celled protozoan. 20 species of Leishmania infect humans. Possible medications are liposomal amphotericin B, paromomycin, fluconazole.
TrypanosomaTrypanosomiasisParasite transmitted to host by Tsetse fly (Sleeping Sickness).T.brucei, T.cruzi mainly infect humans. Diminazene, homidium, isometadium, suramin, and melarsomine used to treat infections.
ToxoplasmaToxoplasmosiEating undercooked, contaminated food and water mainly causes infection. Parasites mainly form cysts in skeletal muscle, myocardium, brain. Medications include-Pyrimethamine, Clindamycin, Spiramycin, Sulfadiazine
EntamoebaAmoebiasiTransmitted by the fecal-oral route. Ingestion of cyst form of parasite causes infection. Symptoms range from mild diarrhea to severe dysentery. Metronidazole used for treatment. Boiled water used for drinking.
BabesiaBabesiosiUsually transmitted by ticks. Parasite reproduce in red blood cells. Parasite require two host stick and mammal Oral atovaquone with oral azithromycin recommended for treatment.
SchistosomaSchistosomiasiTransmission of disease occurs through contamination of fresh water sources by excreta. It has trematode vertebrate-invertebrate lifecycle. People are infected by larval form of parasite. Drug  praziquantel is used for treatment.
Caryospora Pyrogranulomatous dermatiti In dogs, pyogranulomatous skin lesions appear as papules, nodules. Treatment includes surgical excision of solitary nodules. Tetracycline and niacinamide used.
NeosporaNeosporosiNeuromuscular disease of domestic dogs. It cycles between canine definitive hosts and herbivore intermediate hosts. Clindamycin (12.5-25 mg/kg PO or IM every 12 hours for 4 weeks) Trimethoprim sulfadiazine in combination with pyrimethamine is also used.
Besnoitia BesnoitiosiTransmission is through direct contact with animals with wounds. Life cycle complex with various intermediate hosts. Pedunculated lesions in the skin, nasal cavity and larynx of domestic animal are the major signs.
EimeriaHemorrhagic cecal coccidiosi Acquired via fecal contamination of food and water. Monoxeous life cycle with the definitive (only) host as chickens. Morbidity is 10-40% and mortality up to 50%. Toltrazuril, Sulphonamides, Amprolium, Vitamins A and K in feed or water.
CryptosporidiumCryptosporidiosiSpread through the fecal-oral route, often through contaminated water. Self-limiting diarrhea , stomach pains or cramps, low fever, nausea are the major symptoms. Nitazoxanide (FDA) is used for cure. paromomycin, atovaquone and azithromycin are also sometimes used.

How to use ParaPep

This page provides help to the users and explains the working of each tool integrated in this database.Click on the links below to go to the help section of the respective tool.
Search Browse Similarity Downloads Important

SEARCH

SIMPLE SEARCH
This is a very simple and easy search option. User can search any query in any of the fields (e.g. Sequence GRFKRFRKKFKKLFKKLS). Results will be displayed according to the selected fields to be displayed. e.g. Sequence, PMID, N-terminal modification, C-terminal modification, Assay type, Parasite type etc.


Explore more information by clicking on peptide ID as well as on peptide Structure.


COMPLEX SEARCH
Conditional Search is a quite helpful tool specially when user has predefined queries in mind. For instance, user can come up with the following questions in mind and wants to search:
  1. peptides which are only LINEAR
  2. among the above selected Linear peptides; select those having D amino acids stereochemistry
  3. among the above selection criteria, show peptides with LENGTH greater than 8 only
  4. among the above selected peptides, select only those having atleast RIG residues in the sequences

By clicking Submit; user can get desired output.
In a similar way, query can be extended using "+" button and reduced using "-" button.

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PEPTIDE SEARCH
User can search the query sequence against peptide sequences in the ParaPep database. Search result will provide user either with exactly identical peptide or matching peptides with the given query sequence.

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SMILES SEARCH
User can search the query in the SMILES format against whole peptide database stored in SMILES format. In this way user can search peptides with similar SMILES notation as that of their query molecule.

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BROWSE

DISEASE
This interface allows user to browse the different Disease type in the parapep database.

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CHIRALITY
User can access the information about the type of peptide based upon their stereo-chemistry (L/D/Mix) and configuration (Linear/Cyclic). User can also access peptides which are chemically modified by clicking on the respective link.

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NATURE
User can access information about the peptide based upon their nature like peptides having Antimicrobial, Antimalarial, Antibacterial activity etc.

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LENGTH
User can access information about the peptide based upon their length like all the peptides with 5 to 10 residues or with 11 to 15 residues.

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PARASITE TYPE
User can access information about the peptide based upon parasite type like Plasmodium falciparum, Trypanasoma brucei etc. .

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SIMILARITY

BLAST
This page provides the facility to BLAST search user's query peptide sequence against peptide sequence of ParaPep database to identify similar sequences. By default all parameters of blast like word size, matrix etc are set for peptide blast. User can change parameters as per his/her use.

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SMITH-WATERMAN
This page assist's a user to do local alignment search against peptide sequences of parapep database using smith-waterman algorithm.

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MAPPING
A user can map his/her peptide/protein sequence against peptides of ParaPep database using (a) Sub-search and (b) Super-search algorithm.
(a) Sub-search: User's query peptide is searched against peptides of ParaPep database to identify peptides having identical segments to query peptide.
(b) Super-search: User can give a protein sequence to search against peptides of ParaPep database to identify peptides which match within user's protein sequence.

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ALIGNMENT
This page provides facility for Sequence or Structure alignment. A user has 2 options for aligning

(a) Sequence Alignment: A user can input multiple sequences in fasta format and can align their sequences against peptide sequences of ParaPep database by providing IDs of peptides of ParaPep database.
(b) Structure Alignment: A user can input a PDB file of a peptide and can structurally align with peptide of ParaPep database by providing ID of that peptide.

Following figure shows an example of how to proceed for sequence alignment between user sequences and peptide sequences of ParaPep database.

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DOWNLOAD

SEQUENCES
This page provides facility for Downloading Sequences of peptides from ParaPep database.
A user can download all the peptide sequences with D-amino acids or with cyclic configuration or having non-natural residues.

Downloading Option for Sequences is COMING SOON !!

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STRUCTURES
This page provides facility for Downloading predicted 3D structures of peptides of ParaPep database.
A user can download all the predicted peptide structures in pdb format.

Downloading Option for Structures is COMING SOON !!

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REFERENCES
This page provides facility for downloading articles related to hemolytic peptides in the PDF file format. These articles are freely accessible in Pubmed Central. For other articles which are not open access, user can download its abstract.

Downloading Option for REFERENCES is COMING SOON !!

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DATASETS
This page provides provision to download different type of datasets which will be useful for analysis of antiparasitic and non-antiparasitic peptides and their prediction.

Downloading Option for DATASETS is COMING SOON !!

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IMPORTANT

SUBMIT FORM
Using submit form, a user can submit his/her peptide sequence with annotations like assay type, disease, PMID, end modifications etc in our ParaPep database.
To maintain quality of ParaPep database our team will cross verify the entries manually and then enter it into ParaPep.

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Frequently Asked Questions (FAQs)


Q1. What is parasite and parasitic disease?
Ans . A parasite is an organism that lives in another organism, called the host, and often harms it. It is dependent on its host for survival - it has to be in the host to live, grow and multiply. A parasite cannot live independently. A parasitic disease is an infectious disease caused or transmitted by a parasite. Many parasites do not cause diseases. Parasitic diseases can affect practically all living organisms, including plants and mammals.

Q2. What the need of anti-parasitic peptide?
Ans. The most important parasitic diseases, malaria, leishmaniasis, trypanosomiasis, and schistosomiasis, are a great burden to mankind, threatening the life of millions of people worldwide and mostly affecting the poorest. Because drug resistance is increasing and vaccines are rarely available, novel chemotherapeutic compounds are necessary in order to treat these devastating diseases. Insects serve as vectors of many human parasitic diseases and have been shown to express a huge variety of antimicrobial peptides (AMPs). Therefore, research activity on insect-derived AMPs has been increasing in the last 40 years.

Q3. Why we created ParaPep?
Ans. ParaPep is experimentally validated peptides that target parasites have been created with an objective to provide a useful resource, to understand the properties of peptides, which make them susceptible to parasite, cataloging of anti-parasitic potencies of experimentally validated therapeutic peptides is much needed. These peptides were collected and compiled from published papers, patents and databases. Since, to date, there is not a single repository exist, which provide information about the anti-parasitic peptides, that’s why ParaPep is created.

Q4. What is unique about ParaPep?
Ans. ParaPep is a first and unique database of its kind, which provides comprehensive information about anti-parasitic peptides and it has many online tools. One of the powerful tools is peptide mapping and similarity search, which allows user to search similar peptides/motifs in a query sequence. In addition, ParaPep also provides 3D structures of anti-parasitic peptides.

Q5. Does this database represent all experimentally validated anti-parasitic peptide?
Ans. No, This database is the result of first round curation and we shall update ParaPep on a rolling basis, regularly adding anti-parasitic peptides from literature.

Q6. Why search ParaPep?
Ans. ParaPep provides all information of experimentally validated anti-parasitic peptides such as anti-parasitic activity, target and mode of action, hemolytic activity, nature of peptide, origin of peptide, chirality, amino acid sequence, N- and C- terminal modifications, etc. This information may be very useful for researchers working in the area of therapeutic peptides. Apart from this, user can use various tools available to calculate physicochemical properties like amino acid frequency, amino acid composition and hydrophobicity of a query sequence.

Q7. How do I process a text search with ParaPep?
Ans.User can search a peptide by name, peptide sequence, parasite type, assay type, mode of action, year and PMID etc.

Q8. Is this database useful if users have their own query sequences?
Ans. We appreciate user input. The easiest way is to users can submit their experimentally validated antiparasitic peptide sequence on the submission page available on the database, which will be verified by our group. In particular, we encourage you to include complete information. This will minimize potential errors during data registration

Q9. To whom can I report a discrepancy?
Ans. Please refer to the "Contact Us" page.