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SEARCH |
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| BASIC SEARCH |
| This is a very simple and easy search option. User can search any query in any of the fields (e.g. Sequence ILGTILGLLKGL). Results will be displayed according to the selected fields to be dispalyed. e.g. Sequence, PMID, N-terminal modification, C-terminal modification etc. |
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| After clicking on Submit button above, the results will be displayed as shown in the figure below |
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| The Detailed information of each ID of the search result can be retrieved by clicking on that ID as shown in next figure |
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| CONDITIONAL SEARCH |
It is quite helpful when user has predefined query in mind. For instance, User come up with the following questions in mind and wants to SEARCH
- peptides which are CYCLIC only
- among the above selected cyclic peptides; select those having MIX(both L & D amino acids) stereochemistry
- among the above selected cyclic + Mix peptides; select only those having atleast VKLK residues in the sequences
- among the above selection criteria; show peptides with LENGTH less than 14 only
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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The Detailed information of each ID of the search result can be retrieved by clicking on that ID |
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| PEPTIDE SEARCH |
| User can search the query sequence against peptide sequences in the CancerDP database. Search result will provide user either with exactly identical peptide or matching peptides with the given query sequence. |
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| Following Figure displays the result of peptide search using example sequence as query |
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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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| Following Figure displays the result of SMILE search using given example as query |
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CATEGORIZATION |
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| SOURCE |
| This interface allows user to browse the source field in the CancerDP database. Peptides in CancerDP database are collected from different sources like human, sheep, rat, rabbit, mouse etc. User can get the list of all the peptides from a source by clicking on the respective link |
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| PEPTIDE TYPE |
| User can access the information about the type of peptide based upon their stereo-chemistry and configuration. By clicking on the respective link, users can access all the peptides having D amino acids or peptides which are cyclic in nature |
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| FUNCTION |
| User can access information about the peptide based upon their function like all the peptides having Antimicrobial activity or Anticancer, Antibacterial activity |
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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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SIMILARITY |
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| BLAST |
| This page provides the facility to BLAST search user's query peptide sequence against peptide sequence of CancerDP 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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| Following Figure displays the result of BLAST search using given example sequence as query and default parameters |
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| SMITH-WATERMAN |
| This page assist's a user to do local alignment search against peptide sequences of CancerDP database using smith-waterman algorithm. |
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| Following Figure displays the result of local alignment search using smith-waterman algorithm with given example sequence as query |
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| MAPPING |
A user can map his/her peptide/protein sequence against peptides of CancerDP database using (a) Sub-search and (b) Super-search algorithm.
(a) Sub-search: User's query peptide is searched against peptides of CancerDP database to identify peptides having identical segments to query peptide.
(b) Super-search: User can give a protein sequence to search against peptides of CancerDP database to identify peptides which match within user's protein sequence.
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Following Figure displays the result of (a) Sub-search algorithm with given example sequence as query
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Following Figure displays the result of (b) Super-search algorithm with given example sequence as query
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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 CancerDP database by providing IDs of peptides of CancerDP database.
(b) Structure Alignment: A user can input a PDB file of a peptide and can structurally align with peptide of CancerDP 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 CancerDP database
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The result of Sequence alignment is displayed in a graphical manner as shown below
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Structure alignment result is displayed in 3D view as shown in the figure below
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DOWNLOAD |
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| SEQUENCES |
This page provides facility for Downloading Sequences of peptides from CancerDP 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
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| STRUCTURES |
This page provides facility for Downloading predicted 3D structures of peptides of CancerDP database.
A user can download all the predicted peptide structures in pdb format.
Downloading Option for Structures is
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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
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| DATASETS |
This page provids provision to download different type of datasets which will be useful for analysis of hemolytic and non-hemolytic peptides and their prediction
Downloading Option for DATASETS is
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IMPORTANT |
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| SUBMIT FORM |
Using submit form, a user can submit his/her peptide sequence with annotations like hemolytic assay, PMID, end modifications etc in our CancerDP database.
To maintain quality of CancerDP database our team will cross verify the entries manually and then enter it into CancerDP database.
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| STATISTICS |
| A graphical representation of percentage of peptides based on function, source, length, end modifications etc is provided in this page as shown in the figure below |
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Q1. What is CancerDP?
Ans . CancerDP is a manually curated repository of experimentally validated hemolytic peptides.
Q2. What are hemolytic peptides?
Ans . Peptides, which causes lysis of RBCs.
Q3. Why CancerDP Database is created?
Ans.
One of the parameters of safety and toxicity measurements of therapeutic peptides is to determine the capability of peptides to cause hemolysis. The peptides showing high hemolysis are not suitable as therapeutics and thus cannot be used further. Therefore, in order to understand the properties of peptides, which make them hemolytic, cataloging of hemolytic potencies of experimentally validated therapeutic peptides is much needed. Since, to date, there is not a single repository exists, which provide information about the hemolytic potencies of peptides, CancerDP database is created.
Q4. What is unique about CancerDP?
Ans.
CancerDP is a first and unique database of its kind, which provides comprehensive information about hemolytic 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, CancerDP database also provides 3D structures of hemolytic peptides.
Q5. Does this database represent all experimentally validated hemolytic peptides?
Ans.
No. This database is the result of first round curation and we shall update CancerDP database on a rolling basis, regularly adding Hemolytic peptides from literature.
Q6. Why search CancerDP?
Ans.
CancerDP provides all experimental information of experimentally validated hemolytic peptides such as hemolytic activity, nature of peptide, origin of peptide, chirality, amino acid sequence, N- and C- terminal modifications, RBC source etc. This information may be very useful for researchers working in the area of therapeutic peptides. Apart from this, user can search peptides having high/low hemolytic potencies or 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 CancerDP database?
Ans.
User can search a peptide by name, peptide sequence, RBC source, year and PMID etc.
Q8. Is this database useful if users have their own query sequence?
Ans.
Yes, user can use tools like BLAST, SMITH-WATERMAN, peptide mapping, they can also get information regarding amino acid composition, frequency and other physiochemical properties.
Q9. Can User submit their own data?
Ans.
Yes, users can submit their experimentally validated hemolytic peptide sequences on the submission page available on the database, which will be verified by our team.
Q10. To whom can I report a discrepancy?
Ans.
Please refer to the "Contact Us" page.
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