|Visitors To Date:|
|Welcome to the 3D-PSSM Web Server V 2.6.0|
A Fast, Web-based Method for Protein Fold Recognition using 1D and 3D Sequence Profiles coupled with Secondary Structure and Solvation Potential Information.
|3D-PSSM frozen - new system shortly||Jun 18 2004|
I have today frozen the updates for 3D-PSSM. New pdb structures will
no longer be added to the fold database.
I intend to release our new server to the public in September. Benchmarking has shown the new system to be a substantial improvement over 3D-PSSM.
|Completely new protein structure prediction system||Apr 5 2004|
A brand new fold recognition system is on its way. The new system is
nearing completion. Benchmarking suggests it is far superior to
3D-PSSM. However, it requires substantially more CPU power. As a
result I will probably have to shut down 3D-PSSM once the new system
is up and running. More details to follow.
|Temporary removal of d3btaa3||Mar 26 2002|
The domain d3btaa3 is problematic and its sequence profile has drifted
out of control. I have temporarily removed this template from the
library until I can fix it. It can give strong false positive hits
because its profile has become very flat (generic) matching many
different and unrelated sequences.
|Move to Imperial College of Science, Technology and Medicine||Mar 4 2002|
The 3DPSSM service has moved to Imperial College, London. There may be
a few teething troubles with the new system at first, so please let me
know of any problems you experience with the system. E-mail me,
Lawrence Kelley at
|3D-Genomics||Nov 13 2001|
Protein structure and domain assignments for fully sequenced genomes
are available from our 3D-GENOMICS database
|Fold Library Now SCOP 1.53||Aug 1 2001|
The fold library is now 'up-to-date' with SCOP 1.53. As I was updating
the library SCOP decided to move to version 1.55 with a whole bunch of
format changes. So for the time being 1.53 will have to do.
Many people's results may be different now compared to the older 1.50
library. Everything is currently in a beta phase, and I would like to
hear from anyone who gets strikingly different results now compared to
a few days ago, or whether there are any problems with the new library.
|Fold Library SCOP 1.53 Update and Browser Downtime||Jun 19 2001|
I have begun the monumental task of updating the fold library to be in
sync with SCOP 1.53. Most things should work fine (famous last words)
while the update is in progress EXCEPT FOR THE FOLD LIBRARY BROWSER.
The library browser will be unavailable until the update is complete,
which could be for the next several days. I will make an announcement
when it's back up.
If you have any difficulties or the system appears to be behaving strangely please let me know (Lawrence Kelley)
|Biotext (and a bugfix)||May 9 2001|
I have incorporated some work going on in the lab by Ben Stapley called
Biotext. This is an enhanced version of the SAWTED textual annotation
In the experimental version I have incorporated into the server, your
query protein is represented by a set of SwissProt Keywords taken from
Swissprot homologues to your query. In addition, similarly to SAWTED,
a cosine similarity between said keywords and corresponding keywords
in each of the top 20 structural hits is presented. Contrary to SAWTED,
scores closer to 1 are good, and 0 is bad. This will probably change
in the near future.
Also a slight bug fix: The text e-mail e-values were wrong and did not correspond to the HTML web pages. This unfortunately has been the case for a few weeks without me noticing! However, this is now fixed.
|Server Problem (Fixed)||Apr 19 2001|
Apologies to users who have submitted sequences this morning. There
was a problem with the automatic library updating, which I have now
fixed. However, I'm still testing the update script and there may be a
few more problems on Wednesday night/Thursday morning next week when
it updates again.
|A variety of small changes||Apr 14 2001|
Just a bunch of small changes made over the last couple of weeks:
P.S. Oh, you'll also notice the little status bar near the top of the page to keep you up-to-date with when the fold library was updated, and how many entries there are. The library is updated weekly in synch with the PDB.
Server Version 2.5.6
|New sidechain modelling with SCWRL||Mar 25 2001|
I've incorporated a new experimental feature into the server. For the
top 5 high
confident (>95% / red hits) side chains will be modelled for your
sequence using Roland Dunbrack's
SCWRL program. This may increase the time required for some jobs, but
very soon I will be also incorporating a speed-up in 3d-pssm which
should easily compensate for any increased processing time caused by
When sidechains have been added to your model, an extra link will appear below the gif image of your structure. Clicking on this will either download the coordinates or launch rasmol, depending on how your browser/system is set up.
Please remember this is experimental.If anything starts going wrong that worked before, please Let Me know. Also, if you find it useful (or not) I'm keen to hear your comments.
Server Version 2.5.5
|New PSI-Blast Version 2.1.2||Mar 22 2001|
I've upgraded our PSI-Blast version to 2.1.2. This version is supposed
to have better statistics than earlier PSI-Blast versions. As a result, some people's
results may change if re-run with the new version. As usual, if you get radically
different results now compared to previously, please let me know. |
Server Version 2.5.4
|Experimental New PSI-Blast Parameters||Feb 8 2001|
I have altered the parameters for the PSI-Blast run that is initially
performed on your sequence in the 3D-PSSM server. I've increased the
number of iterations performed (to 5) and slightly loosened the
h-value (which determines when a sequence is included in the profile
for the next iteration [from 0.001 to 0.002]).|
This means that if your sequence looked like an orphan (had no homologous sequences) in previous 3D-PSSM runs, this may no longer be the case. That is, the server may now find homologues it missed before, and as a result generate a better secondary structure prediction, and have a higher probability of finding a good structural match in our library.
I'm not sure if I will keep these parameters as it adds extra load to our server, and may bring in false positives due to PSI-Blast drift. I'll see how it goes. Please let me know if you get radically different (good or bad) answers as a result of this change.
|More Hardware = Faster Turnaround||Jan 11 2001|
We have approximately 8 new processors for web jobs now, so the queue
should clear much more quickly from now on. As usual, there may be
some hiccups along the way, so please E-mail me if things seem
to be breaking/not working like they used to. Happy submitting...
|Improved Secondary Structure Prediction - PSIpred2||Dec 13 2000|
I have integrated version 2 of PSIpred from David Jones (http://insulin.brunel.ac.uk/psipred/)
into the server. The improved secondary structure prediction accuracy
(approx 80%) should lead to improved recognition of folds and possibly
improved alignment accuracy (although this will be dealt with
separately in the near future).
This has warranted a server version number change.
We are now at Server Version 2.5.3.
|Simplified submission page and default global-local||Dec 9 2000|
I have simplified the submission page. There is a link at the top of the
submission page to the advanced page where you can still do things like upload
your file, submit multiple sequences, switch between global and global-local
By default, your submission will now use the global-local option. Tests and the results from CASP4 meeting have indicated that this method is by and large superior to the previous default method - global. This has warranted a server version number change. We are now at Server Version 2.5.2.
|Searchable Fold Library and Renewable Results||Aug 8 2000|
The fold library (see menu to the left) now has a simple search
facility permitting you to find folds, superfamilies, families,
etc. in our library containing a search term or terms. It is not a
full boolean search and order of terms is important, but it should
help you find things a bit quicker.
It is now possible to renew your results on the server so they are not automatically deleted after four days. On the HTML results page near the top next to "Download your results" is "Renew your results". Clicking this option will ensure your results are kept on the server for 4 more days from the current date.
The server can now accept a multiple sequence alignment in
format. This can be useful in cases where you may have homologous
sequences that cannot be found by our 3 iterations of PSI-Blast. For
example, you may have searched various DNA databases. Having multiple
homologous sequences can radically improve Secondary Structure
prediction, and create a more powerful sequence profile (or 1D-PSSM),
both of which can improve the likelihood of useful fold recognition results.
|Browse and Explore the Fold Library||June 6 2000|
I'm opening up a major new aspect to the 3D-PSSM server
today. Finally, the link in the menubar to the left for "Fold Library"
actually goes somewhere! You may browse through a hierarchical
tree-structured representation of the library which is essentially a
cut-down version of SCOP.
When you find the protein you want, you will be presented by a representation of the sequence,accessibility,secondary structure, and core residues as well as a variety of links. These links permit visualisation of the multiple sequence and multiple structure alignments, in a variety of views (secondary structure,accesibility,etc). In addition, you may view the actual sequence profiles (PSSMs) used by the server. You can also bring up 3D superpositions of structural homologues (using Rasmol).
It is hoped that these facilities will enable users (and myself) to better appreciate the nature of the diversity and similarity on both the sequence and structural levels of potential hits produced by the server. It may also highlight advantages/shortcomings in our library, which may help us improve it in the future. Your feedback is very welcome.
As an example you can jump straight to a Globin protein d3sdha_
|JMB Paper reference||May 19 2000|
The 3D-PSSM paper in the Journal of Molecular Biology describing the
method will be published on 2 June 2000. The full reference is:|
Kelley LA, MacCallum RM & Sternberg MJE (2000). Enhanced Genome Annotation using Structural Profiles in the Program 3D-PSSM. J. Mol. Biol. 299(2), 501-522
|New Fold Library - approx. 5000 templates - automatic updating||May 10 2000|
The new, bigger, and hopefully better fold library is now in place.
VersionsI have included in both the html and e-mail results output, some version information for the sequence and template libraries, the server, and the 3dpssm binary.
Regular Automatic UpdatesAs new structures appear in the PDB, they are checked against the library, and added if necessary. This, along with a system to keep current with SCOP, should mean the system will always be up-to-date. (fingers crossed).
As this is its first release, it has not yet been extensively tested. So any feedback from you, the users, would be most appreciated. Comments/Complaints/Suggestions to me (Lawrence Kelley).
|New Fold Library very soon||Apr 26 2000|
Within a few days (probably this week) the new improved fold library
will be incorporated into the 3D-PSSM server. This will increase the
number of representative structures from approximately 3000 to
5000. In addition, the library will be automagically updated (every
few days or every day - not sure yet) as new PDB structures are
released. This, along with a variety of bug-fixes, and possibly a new
post-filtering technique, will amount to a new version of 3D-PSSM
(Version 2.5). Also, version information will be returned with each
and the versions will change with each update of the library
In the slightly more distant future, the fold library and its accompanying derived information will be browsable through the web (finally).
|Paper in Journal of Molecular Biology||Apr 6 2000|
A paper describing the 3D-PSSM methodology is in press and will be available shortly.
This paper will be the primary citation in the future.
Kelley LA, MacCallum RM & Sternberg MJE (2000). Enhanced Genome Annotation using Structural Profiles in the Program 3D-PSSM. J. Mol. Biol. in press
|Multiple Sequence View||Mar 28 2000|
I have altered the viewing mechanism (i.e. the mview output parameters) for the multiple sequence alignment of your query. The previous system, although looking nice, could not be properly handled by MS Internet Explorer, but could be handled fine by Netscape Navigator. I have opted for the lowest common denominator so everyone can easily view their multiple sequence alignments.
|Orphan Rescued||Mar 2000|
Managed to fix the orphan problem. Wish someone had alerted me to this earlier :(. Nevertheless, all is now right in the world of 3D-PSSM and its orphans.
|Orphan Problems||Mar 2000|
The server is currently not processing orphan sequences at the moment. When PSI-Blast is run on an orphan (i.e. a sequence with no sequence homologues) no PSSM is generated and the fold recognition process dies. I will fix this a.s.a.p. Apologies for any inconvenience caused. I will make an announcement when it is fixed.
|PROSITE Added||Feb 25 2000|
I've added a PROSITE search to the server. This is run on your sequence and results are displayed in the HTML output.
If anything is found, you can click on the PS accession number to get more details (from www.expasy.ch). Although it will probably be rare to get a PROSITE match, I thought it would be useful just in case something obvious is missed by the server. In the future I intend to mark up the locations of prosite motifs in the library structures in the alignment view.
|Help page Added||Feb 24 2000|
After a very long wait I have finally done version 1 of the help page. Click on the help option in the menu bar on the left to have a look. Hopefully this will address some of the questions people have had. If I have missed something out which you want to know, or something is not clear in the help, then please let me know and I can do something about it.
|Bug fixes and optional Seg||Feb 16 2000|
Found a bug in the global-local option (oops) which is now fixed. It probably wasn't working until now. Also, I managed to fix some bugs which crop up with long sequences. Apologies to anyone who this affected.
Finally, I've added an "Advanced Options" box to the bottom of the submission page. I've placed the Global-local option there along with a facility to turn off the low-complexity filter which by default marks with "X"s, regions of your sequence deemed to be low-complexity or coiled coil by the program "seg". If your results show your query sequence to contain "X"s, and you are certain the region in question is not low complexity, you can switch off the low-complexity filter and resubmit your sequence.
|Global Local Alignment||Feb 04 2000|
I've placed an experimental new option on the fold recognition page. By default submissions will be treated as always - using a Global End gap penalisation dynamic programming algorithm. However, you may now choose Global-Local as an alternative technique. If your sequence is over 300 or 400 residues long I would recommend using this Global-Local option. Also, if a first attempt using the default does not make a confident assignment, it may be worth trying the Global-Local option.
As I have said this is experimental, so any feedback would be greatly appreciated. Many people are using the server, and if users can tell me when they get a confident, sensible hit with one method as opposed to another, we can achieve some real-world benchmarking - and maybe learn something. Good Luck!
|E-mail Address Accuracy||Jan 17 2000|
For some weeks now I have been receiving results for 3D-PSSM submissions that have bounced back to me because of problems with people's E-mail addresses.
PLEASE ENSURE YOUR E-MAIL ADDRESS IS CORRECT.
I have no way of getting these "lost" results to the submitter, as my only route to you is your E-mail address. If you do not receive any reply from the server when you have submitted your results, it is almost certainly because the E-mail address supplied is not valid. I would place these results in a "lost" section on the website, but I do not want to violate anyone's privacy of submission.
If you do not receive your results within an hour and you know the descriptor you used, feel free to ask me (L.Kelley@icrf.icnet.uk) if I have the results.
|Downloadable Results||Oct 15 1999|
It is now possible to download your html results in the form of a gzipped tar file. This contains all the models, multiple sequence alignments, etc. You can click either near the top of the html results page, or on your E-mail results. I know some people have wanted this functionality for some time. Its here at last.|
Also, I've fixed some submission problems. The server now tells you as soon as you click submit whether your sequence contains characters the server can't cope with. This is in contrast to having to wait 10 minutes only to receive an E-mail saying there's something wrong with the submission. I hope this is useful.
|Apologies for Broken Jobs     ||Sep 2, 1999|
|Apologies to anyone who has had jobs killed since the re-opening of the server. Due to the extra functionality of the server, greater load is being placed on the machines. As a result, even relatively short sequences (300 residues) can sometimes cause our machines to grind to a halt. Work on fixing this is in progress. Please be patient, and in the meantime try to submit fragments of your sequence (100-200 residue chunks). Once again, apologies for the inconvenience. We will have this fixed a.s.a.p.|
|New Server, New address, New functionality     ||Aug 25, 1999|
Please Note: I've just this moment released this to the community. It could fall over in any number of glorious ways. Use it at your own risk. I'm sure there are still some problems hiding in there, and I'll try to get everything smooth again a.s.a.p.. On another note, I have removed the facility for submitting PhD predictions. Its too much hassle trying to keep up with changes made to PhD output, and the secondary structure prediction here is now far better. It is currently NOT possible to submit a multiple sequence alignment in fasta format, but this will soon(ish) be remedied. |
Finally, I've just noticed some problems with our caching facilities. It looks as though the server is not working at top speed at the moment...a job for tomorrow.
|Old News     ||Aug 25, 1999|
Previous News items for 3D-PSSM Version 1 can be found here