What's New about PAPIA System

Last Updated Apr. 15, 2009

Announcement

Apr. 15, 2010

PDB-REPRDB for Membrane Protein Chains Version 2009_05_08 ( based on PDB Rel.#2009_05_08, 1747 chains) came out.

This is based on SCOP version 1.75 June 2009 ( Membrane Protein 1747 chains).
PDB-REPRDB Version 2009_05_08 ( based on PDB Rel.#2009_05_08, 124212 chains), which is based on SCOP version 1.75, came out.

Oct. 14, 2009

PDB-REPRDB Version 2009_05_08 ( based on PDB Rel.#2009_05_08, 124212 chains) came out.

This is based on SCOP versi on 1.73 Nov. 2007 ( Membrane Protein 1506 chains).

Apr. 15, 2009

PDB-REPRDB Version 2007_11_14 ( based on PDB Rel.#2007_11_14, 99469 chains) came out.

This is based on SCOP version 1.73 Nov. 2007 ( Membrane Protein 1506 chains).

Feb. 14, 2007

PDB-REPRDB Version 2007_01_21 ( based on PDB Rel.#2007_01_21, 84719 chains) came out.

This is based on SCOP versi on 1.71 Oct. 2006 ( Membrane Protein 1125 chains).

Note that thease 14 chains replaced after the release of SCOP are included in the membrane proteins as previous data.
2OARA, 2OARB, 2OARC, 2OARD, 2OARE (previous versions:1MSL)
2OAUA, 2OAUB, 2OAUC, 2OAUD, 2OAUE, 2OAUF, 2OAUG (previous versions:1MXM)
2BS2C, 2BS2F (previous versions:1QLA)

Sep. 19, 2006

Fixed the problems that ID%, RMSD and Dmax were treated as integral numbers in PDB-REPRDB.
The distaces of each pairs are calculated to decimal the first place (cut off second place) now.

Sep. 13, 2006

PDB-REPRDB Version 2006_08_20 ( based on PDB Rel.#2006_08_20, 77911 chains) came out.

Changed the default settings of "Apply constraints" selection in PDB-REPRDB.
"Apply constraints" selection of "number of chain break" and "ratio of non-standard residues" were changed from "yes" to "no".
Using this default settings, the chains whitch include selenomethionine or other non-standard residues are no longer eliminated now.
Note that the sample data are not affected this change and used all chains (no elimination) as before.

Apr.28, 2006

Selenomethionine residues are treated as "non-standard residues" in PDB-REPRDB now.

Apr. 27, 2006

There were some errors in the data of PDB-REPRDB Version 2006_02_26 used from 21st Apr to 23rd Apr.

If you'd used the system from 21st Apr. to 23rd Apr., please retry and get the correct results.

Sorry for the inconvenience.

Apr.25, 2006

Fixed the problems that selenomethionine residues were treated as "chain break" in PDB-REPRDB.
Even now, some other modified residues are still treated as "chain break", sorry.

Apr. 5, 2006

PDB-REPRDB Version 2006_02_26 ( based on PDB Rel.#2006_02_26, 71597 chains) came out.

Mar. 27, 2006

PDB-REPRDB ( based on PDB Rel.#2005_12_04, I=95%,Dmax=10A, 16560 chains) was rivised.
(The database of Protein Structure Similar ity Search, Protein Sequence Homology Search)

Mar. 22, 2006

There were some errors in the data of PDB-REPRDB Version 2005_12_04.

If you'd used the system from 11th Jan. to 20th Mar., please retry and get the correct results.

Sorry for the inconvenience.

Mar. 14, 2006

Change Protein Structure Similarity Search, Protein Sequence Homology Search, Protein Sequence Multiple Alignment service machine from PAPIA Cluster to COMPAQ Cluster, (1.4GHz Pentium III Dual, 1GB / 18GB x2) x 16nodes .
PDB-REPRDB Version 2005_12_04 ( based on PDB Rel.#2005_12_04 ) came out. ( Protein Structure Similarity Search, Protein Sequence Homology Search )

Jan. 11, 2006

Change PDB-REPRDB service machine from COMPAQ Cluster, (1.4GHz Pentium III Dual, 1GB / 18GB x2) x 16nodes with DSA system to HP Integrity rx4640, (1.5GHz Itanium2, 32GB / 300GB).
PDB-REPRDB Version 2005_12_04 came out.
This is based on SCOP version 1.69 Jul. 2005 ( Membrane Protein 1111 chains).

Jun. 10, 2005

PDB-REPRDB Version 2005_05_29 came out.

Mar. 23, 2005

PDB-REPRDB Version 2005_03_06 came out.
This is based on SCOP version 1.67 Feb. 2005 ( Membrane Protein 973 chains).

Jan. 6, 2005

PDB-REPRDB Version 2004_12_12 came out.

Oct. 6, 2004

There were errors in the data of PDB-REPRDB Version 2004_09_05.

If you'd used the system from 16th Sep. to 6th Oct., please retry and get the correct results.

Sorry for the inconvenience.

Sep. 21, 2004

PDB-REPRDB Version 2004_09_05 came out.

This version runs by DSA system.
New function of fragment option is added.

Aug. 20, 2004

Complex option is improved -> PDB-REPRDB

Jul. 22, 2004

PDB-REPRDB for membrane protein chains is available. (based on PDB Rel.#2004_06_20, SCOP Rel. 1.65)

Jul. 9, 2004

PDB-REPRDB Version 2004_06_20 came out.
There are three new categories of protein chains:

1.high resolution (<=3.0 angstrom)
2.low resolution (>3.0 angstrom)
3.membrane protein

Mar. 17, 2004

PDB-REPRDB Version 2004_02_22 came out.
Chains classified into coiled coil proteins or peptides, according to SCOP, are removed from the database.

Dec. 18, 2003

New version SCOP ( Membrane Protein 752 chains) came out. ( version 1.65 Dec. 2003 )
--> PDB-REPRDB

Dec. 15, 2003

PDB-REPRDB Version 2003_12_08 came out.

Nov. 13, 2003

We got new address:

PAPIA http://mbs.cbrc.jp/papia/
TFSEARCH http://mbs.cbrc.jp/research/db/TFSEARCH.html
PDB-REPRDB http://mbs.cbrc.jp/pdbreprdb/

Please update your bookmarks.

Oct. 10, 2003

PDB-REPRDB Version 2003_10_01 came out.

Aug. 7, 2003

PDB-REPRDB Version 2003_07_27 came out.

Jun. 11, 2003

New function - download of the PDB-REPRDB result, is available.

Jun. 9, 2003

PDB-REPRDB Version 2003_05_25 came out.

Jun. 2, 2003

New version SCOP (Membrane Protein 684 chains) came out. ( version 1.63 May 2003 )
--> PDB-REPRDB

Apr. 14, 2003

PDB-REPRDB Version 2003_03_23 came out.

Feb. 13, 2003

PDB-REPRDB Version 2003_01_26 came out.

Dec. 26, 2002

PDB-REPRDB Version 2002_12_08 ( based on PDB Rel.#2002_12_08 ) came out. ( Protein Structure Similarity Search, Protein Sequence Homology Search )

Dec. 20, 2002

SCOP concise classification strings(sccs) are added in PDB-REPRDB result.
New version SCOP (Membrane Protein 644 chains) came out. ( version 1.61 Nov 2002 )

Dec. 18, 2002

PDB-REPRDB Version 2002_12_08 came out.

Oct. 29, 2002

PDB-REPRDB Version 2002_10_20 came out.

Sep. 6, 2002

PDB-REPRDB Version 2002_09_01 came out.
A new elimination factor, which excludes membrane protein chains, is introduced in the PDB-REPRDB system.
The PDB-REPRDB for membrane protein chains based on SCOP ( version 1.59 Membrane Protein 551 chains ) is available.

Aug. 13, 2002

PDB-REPRDB Version 2002_08_04 came out.

Jul. 22, 2002

PDB-REPRDB Version 2002_07_14 came out.

Jul. 11, 2002

PDB-REPRDB Version 2002_06_16 came out.

May 21, 2002

PDB-REPRDB Version 2002_05_12 came out.

May 2, 2002

PDB-REPRDB Version 2002_04_07 ( based on PDB Rel.#2002_04_07 ) came out. ( Protein Structure Similarity Search, Protein Sequence Homology Search, Protein Sequence Multiple Alignment, Protein Secondary Structure Prediction )

April 18, 2002

Change PDB-REPRDB service machine from EnterPrise 450, (480MHz UltraSPARC II 4cpu, 4GB / 144GB)SunOS 5.8(Solaris 2.8) to Sun Blade 1000, (900MHz UltraSPARC III 2pu, 8GB / 109GB)SunOS 5.8(Solaris 2.8).
PDB-REPRDB Version 2002_04_07 came out.

February 20, 2002

PDB-REPRDB Version 2001_12_02 came out.

August 16, 2001

PDB-REPRDB Version 2001_08_10 came out.

July 10, 2001

Change PDB-PEPRDB service machine from SPARCcenter 2000E, (85MHz SuperSPARC II 20cpu, 5GB / 160GB) SunOS 5.4(Solaris 2.4) to EnterPrise 450, (480MHz UltraSPARC II 4cpu, 4GB / 144GB) SunOS 5.8(Solaris 2.8).
PDB-REPRDB Version 2001_05_16 ( based on PDB Rel.#2001_05_16 ) came out. ( Protein Structure Similarity Search, Protein Sequence Homology Search, Protein Sequence Multiple Alignment )

July 3, 2001

PDB-REPRDB Version 2001_05_16 came out.

March 29, 2001

PDB-REPRDB Version 2001_01_07 ( based on PDB Rel.#2001_01_07 ) came out. ( Protein Structure Similarity Search, Protein Sequence Homology Search, Protein Sequence Multiple Alignment )

March 13, 2001

PDB-REPRDB Version 2001_01_07 ( based on PDB Rel.#2001_01_07 ) came out.

October 25, 2000

PDB-REPRDB Version 2000_09_24 ( based on PDB Rel.#2000_09_24 ) came out.

September 26, 2000

PDB-REPRDB Version 2000_08_06 ( based on PDB Rel.#2000_08_06 ) came out.

June 29, 2000

PDB-REPRDB Version 2000_06_11 ( based on PDB Rel.#2000_06_11 ) came out.

September 20, 1999

The structure viewer in Protein Structure Similarity Search become to have some new function.
1. Residue Labels
2. Residue Numbering
3. Ball and Stick Mappings
4. Color Mappings
5. Font Control
6. C&N Terminals

September 16, 1999

PDB-REPRDB Dynamic 1.0 based on PDB Rel.#89.

June 18, 1999

Now you can see the sequence of the identified structures obtained by Protein Structure Similarity Search -Search Protein Structures similar to given 3-D coordinates.

Mar 30, 1999

PDB-REPRDB Dynamic 1.0 ( based on PDB Rel.#86 ) came out.

Feb 5, 1999

Now A* Algorithm is available as a searching method for Protein Sequence Multiple Alignment.

Jan 8, 1999

PDB-REPRDB Version 8.0 ( based on PDB Rel.#85 ) came out.

Dec 25, 1998

Protein Secondary Structure Prediction now accepts FASTA format.

Nov 18, 1998

Now five popular score matrices are available for Protein Sequence Homology Search and Protein Sequence Multiple Alignment.

Nov 7 - 13, 1998

We gave a live demonstration of PAPIA system at SC98 : HIGH PERFORMANCE NETWORKING AND COMPUTING CONFERENCE in Florida, USA. ( Booth R230 )
Brochure [MS Word]

Oct 8, 1998

Protein Structure Similarity Search for 3D coordinates now accepts so-called PDB ATOM lines.

Aug 21, 1998

PDB-REPRDB Version 7.0 ( based on PDB Rel.#84 ) came out.

July 14, 1998

Protein Sequence Homology Search now accepts FASTA format.

July 8, 1998

The result of Protein Sequence Homology Search is now shown as pairwise alignment.
Now you can send the results from Protein Sequence Homology Search directly to the input form of Protein Sequence Multiple Alignment via GUI.

June 26, 1998

Regarding the result of Protein Structure Similarity Search - for a protein fragment in PDB-REPRDB, now that structure viewer shows the query structure fragment together with the fragments found.
Two remarkable changes were made to Protein Sequence Homology Search.
1. Both the maximum and minimum threshold is configurable.
2. The two different score matrix BLOSUM80 and PAM250 are available.

June 25, 1998

The data set for Protein Structure Similarity Search and Protein Sequence Homology Search was enlarged to PDB-REPRDB( ID = 95%, MAXD = 10A ).

June 1, 1998

Japanese version of PDB-REPRDB came out.

May 25, 1998

We made a press release. PAPIA system was opened to public.

May 22, 1998

Japanese version of PAPIA system came out.

May 7, 1998

PDB-REPRDB Version 6.0 ( based on PDB Rel.#83 ) came out.

April 20, 1998

PAPIA sytem WWW service tentatively started.
'SWISS-PROT' is available for Protein Sequence Homology Search.
Descriptions of protein entries were attached to the Protein Sequence Homology Search's results.

April 17, 1998

Protein Secondary Structure Prediction service came out.

March 27, 1998

PDB-REPRDB Version 5.0 ( based on PDB Rel.#82 ) came out.

March 13, 1998

Protein Structure Similarity Search - for a protein fragment in PDB-REPRDB service came out.

March, 1998

'Service status' page came out.

February, 1998

Protein Structure Similarity Search - for amino acid sequence exact match service came out.

January, 1998

Java pages were replaced with HTML pages.

November 15 - 21, 1997

PAPIA system was demonstrated on RWC PC Cluster II in SC'97 : High Performance Networkingand Computing conference exhibition (US San Jose).