Last modified : November 24, 2000
Go to Japanese page

  1. Summary of retrieval system of PMD The protein mutant database (PMD) at the moment complies over 81,000 mutants, including artificial as well as natural mutants of various proteins extracted from about 10,000 articles. We recently developed a powerful viewing and retrieving system, which is integrated with the sequence and tertiary structure databases. The system has the following features :
    1. Mutated sequences are displayed after being automatically generated from the information described in the entry together with the sequence data of wild-type proteins integrated. This is convenient to see the position of altered amino acids (shown in a different color) in the entire sequence of a wild-type protein.
    2. For those proteins whose 3D structures have been experimentally determined, a 3D structure is displayed to show mutation sites in a different color.
    3. A sequence homology search against PMD can be carried out with any query sequence.
    4. A summary of mutations of homologous sequences can be displayed, which shows all the mutations at a certain site of a protein, recorded throughout the PMD.

  2. How to search ?

    1. Keyword Search
      A simple strict-match keyword search is available against PMD database. The users can choose the target item in the menu form, such as "AUTHORS", "TITLE",and "PROTEIN". The search starts by filling query words and clicking the "SUBMIT" button. If "**ALL ITEM**" in the menu is selected, a search against all the text of PMD is carriied out. The "AND" or "OR" searches with the two or three conditions are available by filling the column of the 2nd and 3rd condition. The search program does not distinguish upper and lower letters, if the [Upper/Lower] radio button is in the "ignore" position. For example, "Hemoglobin" matches either "HEMOGLOBIN" and "hemoglobin". And it recognize an asterisk "*" as any one letter: "A*P" matches either "ATP" and "ADP".

    2. Sequence Homology Search
      A sequence homology search against the PMD database can be carried out with any query sequence, pasted on the input area of our web page. Using this function, it is easy to find entries that have related sequences. The search is performed against the wild-type, but not against mutated sequences. The program for sequence homology search was written by one of the authors (T.K.). The algorithm was based on the standard alignment technique and the ktup filtering. The user can choose a threshold value of sequence identity between the range from 30 to 100 %. A result of the search is displayed as a multiple alignment of wild-type sequences, whose mutated sites are differently colored.

      By clicking a site of the sequence homology search result, a summary of mutants at the site can be generated from all related PMD entries. This function is convenient because it allows the user to find active sites or structurally important sites.

    * Sample results of the search

Comments and questions to : pmd-admin@pmd.ddbj.nig.ac.jp

Go to Title page