menu also at the end of this page protic:fast server Overview links search www.protic.com/toolbox.html browser setup help contact us about Help and reference lists Correlation with function Tour and tutorial Evolutionary trees Substrate and inhibitor catalogs Mutations Structure analyzer Sequence analyzer Structure index Family and sequence index horiz_blue.gif
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What's next ?

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The current release of this web site is still a beta version. This version will be full (1.0) at the end of August or beginning of September 1999.

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About databases ...horiz_blue.gif

Sequences

Now Swiss-Prot, soon EMBL and Genbank, then sequenced genomes
This first version released the 07/09/99 works with the list of proteases included in the Swiss-Prot database. We are extending this list to serine proteases from EMBL and Genbank database: the date of the database extention of this release would be about the middle of August. The next step will be the extension in September of the database to serine proteases from the released sequenced genomes.

 
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Structures

Predicted 3D-structures with a quality label of the used threading methods
The Brookhaven Protein Database is our source of serine protease structures. We are currently threading some sequences to the structure of their close relatives. We will shortly add them to the structure index with a non-confusing description. The threading of several sequences of known structure were and will be done with the same methods and the deviation with the crystalographic data will be displayed in "quality graphs".

  More description of Proteases in the structure analysis module
The database of the structure analysis programs is currently based on 10 serine proteases. We expect to extend to all serine proteases from the PDB in September.
 
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Trees Now Fitch, soon Kitch and PileUp with 89 S1-sequences, later with 700 sequences
  A Fitch-tree is accessible. A Kitch and a PileUp will be soon available from the same selection of 89 S1-sequences. A pile-up tree of the 700 sequences listed in SwissProt could be released in September.
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 Bibliography

Weekly review of articles about serine proteases
A review of articles is done every week. Only the NML-links (NIH) to papers about serine proteases are selected and displayed. You can customize the review and get a sorted list according to the estimated impact in your field (available end of august).

  A paper alert will be available in september. You may register your email and your specified keywords and you get by email a review of 20 articles with the estimated highest impact in your field. You will have to reniew your subscription every month.
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About sequences analysishoriz_blue.gif

  Family/Clan Identify: Identify if a sequence could be a serine protease
Still a project until we have something good and fast enough to propose. Until this time try Prosite at the Expasy web site.
  Sequence set maker: Select a set of sequences close to a reference sequence, first half of August!
  Sequence set maker: Select a set of sequences close to a sequence motif, first half of August !
  Sequence set maker: Perform logical operations on sets, first half of August !
  Sequence set maker: Save and read sets localy, first half of August !
   
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About structures analysishoriz_blue.gif

 

AC Identify: Identify if a sequence accession number is linked to a PDB file, first half of August!

  Structure Identify: Identify if a sequence is described by a PDB file, middle of August.
  PDB code identify: Identify the name of a protease from its PDB accession number , first half of August!
  Structure viewer: all cgi-tools are ready to link, , first half of August!
  Structure superimposition: end of August
  Structure analysis: all cgi-tools are ready to link, first half of August!
  Residue set maker: all cgi-tools are ready to link, first half of August!
  Analysis of mutation effect: September.
  Analysis of domain-domain interaction: September.
  Docking: middle of August
  Prediction of metal ion binding sites: first half of August!
   
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About mutation catalogs and analysishoriz_blue.gif

 

Thrombin catalog: in progress!

  tPA catalog: in progress!
  Trypsin catalog: in progress!
  Chymotrypsin catalog: in progress!
  Factor X catalog: in progress!
  For other catalogs, it will depend on the help we will get (see contact us)
  Mutation catalog by position: September.
  Mutation analyzer: Position tolerance analyzer, middle of August!
  Mutation analyzer: Correlation between functions and substitution effects, middle of August!
  Mutation analyzer: Correlation between functions and addition or deletion, still a project.
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About evolutionary tree analysishoriz_blue.gif

 

see in databases.

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About ligand catalog and analysishoriz_blue.gif

 

The thrombin catalogs are openned and still in progress!
tPA catalog in progress !

  Docking: End of August
  Prediction of metal ion binding sites: first half of August!
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About correlation with functionshoriz_blue.gif

 

Knock out gene references: in August.

  Sequence-Function: works for qualitative functions. Others in August.
  Structure-Function correlation: August.
  Evolution-function correlation: August.
  Sequence/Evolution/Structure-Function: September
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Knock out gene and mutations references: End of August.

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Go to the Washington University in St Louis
Go to the School of MedicineGo to the Department of Biochemistry and Molecular Biophysics


Thierry Rose, PhD and Enrico Di Cera, MD
Department of Biochemistry and Molecular Biophysics
Washington University School of Medicine
Saint Louis, MO, U.S.A.

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