Frequently Asked Questions

The general PoPS programs:

Proteome predictions:

  • I wanted to hide buried predictions, but no homologues were listed.
  • PoPS will only display homologues with an expect value of 0.001 or less. Therefore, if no proteins are listed, it means that there is no protein of known three-dimensional structure that is similar enough to your protein to be useful in predicting buried/accessible residues.

  • I tried to hide buried predictions, but nothing happened.
  • Make sure that you have clicked on/selected a structure before clicking "OK" (the structure will be highlighted when it is selected). If you click "OK" without selecting a structure, then no accessible data will be applied to the substrate.

  • I created a protease model file in Word, but PoPS won't load it.
  • The format of any file that is loaded in to PoPS must be text format. If the file is created with a program such as Word, you must ensure that you save the file as text, and not another format such as Word format (*.doc) or Rich Text Format (*.rtf), because these files are not readable by PoPS.

  • Where has the old PoPS Applet gone?
  • Due to changes in the Java programming language, and the way that Java is supported by web browsers, the PoPS Applet is no longer about to be maintained, and has been retired from service. It has been replaced by the JNLP version (the main PoPS program), available from the

  • How and why are the reasoning tables in the proteome output limited?
  • Because the proteomes are so large, the processing time and the disk space consumed when trying to predict new targets quickly increases. For example, a request to search the human proteome with a threshold set at the minimum score for an average model will take over 24 hours to process, and use over 1Gb of the server's available processing power. Clearly, when multiple job are running, this cannot be supported. As a consequence, reasoning tables in the output are now limited to a maximum of the top five sites in a given protein.

    Complete reasoning tables can be obtained by using the main PoPS program.