The PSIPRED Server Help Page

Input Sequence

Type your AMINO ACID sequence here. Please do not try to enter a nucleic acid sequence. We recommend that you enter your sequence as a plain single-letter string like this:
Alternatively, you can enter your sequence in FASTA format, but the description text will be ignored by the server.

Note that there is an upper limit to the length of sequences which can be submitted. For mGenTHREADER that limit is 1000 residues. For the other methods, the limit is 1500 residues. If your sequence is longer than this, try breaking it into likely domains before submitting it. Our DomPred server can help you in doing this.

Choose Prediction Method

Select which method you wish to use. See the PSIPRED home page for more details on the different methods (and references).

Filtering Options

To reduce the false positive rate of fold recognition methods, particularly when applied to long sequences, it is important that biased regions of the target sequence are filtered out before the prediction is carried out. The PSIPRED server uses the PFILT program to perform the masking and has 3 filtering options, which will filter out low complexity regions, likely transmembrane segments and coiled-coil regions. The default setting is for just low-complexity regions of the sequence to be masked out. Regions which are masked out will be replaced with 'X' (unknown) residues.

Obviously, if you filter out transmembrane helices and then try to use MEMSAT2 to predict the transmembrane topology, you will not get sensible results. For GenTHREADER and mGenTHREADER we recommend turning on all filtering if you are expecting matches to globular proteins.

E-mail Address

Enter your e-mail address here. Results will be returned as soon as they are available - usually within 20 minutes, though sometimes longer depending on the server load. Bear in mind that if you enter an incorrect e-mail address, there is no way the server can contact you! Also watch out that your anti-spam software isn't rejecting the messages from our server.


This field should be ignored if you are accessing the server from an academic site (i.e. a University). If you are a commercial user who has a current license to use the PSIPRED server then you should enter your password here. Please contact us if your password does not work for some reason. Note that if your e-mail address is commercial - e.g. ends .com or - then you must enter your PSIPRED password in order to use the server. This applies even if you are an academic user who is using a private e-mail account. PSIPRED passwords are only granted to licensed users or commercial collaborators.

Please note that you cannot use free e-mail addresses such as or to access the PSIPRED server under any circumstances. It is not possible to make exceptions to this, so please do not ask us about it.

Short name for sequence

Use this field to assign a short memorable name to your prediction job. This is useful so that you can identify particular jobs in your mailbox. This is particularly important because PSIPRED will not necessarily return your results in the order you submitted them! Generally speaking, shorter jobs will be returned first. The name you specify will be included in the subject line of the e-mail messages sent to you from the server. For example, here is the message header for a job called "MySeq":
Date: Fri, 14 Jan 2002 14:55:39 GMT
Subject: MySeq PSIPRED Results


... results ...