Subject: Summary THREADING PROGRAMS

From: "schoonman Account" <[email-masked]>
Date: Mon, 26 May 1997 12:32:17 +0000

Summary THREADING PROGRAMS
______________________________________________________________________

* Threader 2 (released May 14th 1997) (downloadable):
  http://globin.bio.warwick.ac.uk/~jones/threader.html

* 123D (server):
  http://www-lmmb.ncifcrf.gov/~nicka/run123D.html

* Match-Box Web Server (server):
  http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.html

* ProFIT - Protein Fold Identification Tool:
  (threading based on an empirical "energy" function)
  For information:
  http://lore.came.sbg.ac.at/Extern/software/Profit/profit.html
  For the program:
  ftp: "gundi.came.sbg.ac.at"

* Threading by Recursive Dynamic Programming [RDP]and
  Easy ToPLign Fold Prediction (servers):
  http://cartan.gmd.de/ToPLign.html

* 123D TopLign : threading tool based on secondary structure prediction
  and residue-residue contact potential (part of the GMD-SCAI server),
  Zimmer group

  http://cartan.gmd.de/123D-test.html

  REF: N.N. Alexandrov, R. Nussinov and R.M. Zimmer
       Fast protein fold recognition via sequence to
       structure alignment and contact capacity potentials
       Pacific Symposium on Biocomputing '96
       (Lawrence Hunter & Teri E. Klein, Eds)
       World Scientific Publishing Co., Singapore, pp. 53-72

* Gon+predss / Gon+predss+MULT : (part of the UCLA-DOE frsvr server)
  Fischer threading approach, considers predicted secondary
  structure in addition to fold recognition, Eisenberg group

  http://www.mbi.ucla.edu/people/frsvr/frsvr.html

  REF: D. Fischer and D. Eisenberg
       Fold recognition using sequence-derived predictions.
       Protein Science 5:947-955 (1996)

* H3P2 : Rice threading approach (part of the UCLA-DOE frsvr server),
  considers predicted secondary structure, Eisenberg group

  http://www.mbi.ucla.edu/people/frsvr/frsvr.html

  REF: D. Rice and D. Eisenberg
       A 3D-1D substitution matrix for protein fold recognition that
       includes predicted secondary structure of the sequence
       J.Mol.Biol. submitted (1996)

* RDP : threading by recursive dynamic programming (part of the
  GMD-SCAI server), Lengauer group

  http://cartan.gmd.de/cgi-bin/ToPLignLogin?/home/protal/WWW+/home/protal/
         WWW/fast+FastLogin.rc+FastRDP

  REF: R. Thiele, R. Zimmer and T. Lengauer
       Recursive dynamic programming for adaptive
       sequence and structure alignment
       Ismb 3:384-92 (1995)

* TOPITS (called PHDthreader as part of the PredictProtein server) :
  threading based on secondary structure prediction and solvent
  accessibility prediction, Burkhard Rost

  http://www.embl-heidelberg.de/predictprotein/

  REF: B. Rost
       TOPITS: threading one-dimensional predictions into
       three-dimensional structures
       Ismb 3:314-321 (1995)

* The PSCAN server Page:
  http://www.biokemi.su.se/~threader_server/pscan/

* Swiss-Model (M.Peitsch) (server):
  http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html

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-- 

___________________________________________________________________
Marten J.L. Schoonman			Organon N.V. RK2340
[email-masked]	P.O.Box 20
tel 0412-661469 daytime			5340 BH OSS
0317-423088(4) evening			The Netherlands
___________________________________________________________________
Summary THREADING PROGRAMS
______________________________________________________________________

* Threader 2 (released May 14th 1997) (downloadable):
  http://globin.bio.warwick.ac.uk/~jones/threader.html 

* 123D (server):
  http://www-lmmb.ncifcrf.gov/~nicka/run123D.html

* Match-Box Web Server (server):
  http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.html

* ProFIT - Protein Fold Identification Tool: 
  (threading based on an empirical "energy" function)
  For information:
  http://lore.came.sbg.ac.at/Extern/software/Profit/profit.html 
  For the program:
  ftp: "gundi.came.sbg.ac.at" 

* Threading by Recursive Dynamic Programming [RDP]and 
  Easy ToPLign Fold Prediction (servers):
  http://cartan.gmd.de/ToPLign.html

* 123D TopLign : threading tool based on secondary structure prediction
  and residue-residue contact potential (part of the GMD-SCAI server), 
  Zimmer group

  http://cartan.gmd.de/123D-test.html

  REF: N.N. Alexandrov, R. Nussinov and R.M. Zimmer 
       Fast protein fold recognition via sequence to 
       structure alignment and contact capacity potentials
       Pacific Symposium on Biocomputing '96 
       (Lawrence Hunter & Teri E. Klein, Eds) 
       World Scientific Publishing Co., Singapore, pp. 53-72 

* Gon+predss / Gon+predss+MULT : (part of the UCLA-DOE frsvr server) 
  Fischer threading approach, considers predicted secondary 
  structure in addition to fold recognition, Eisenberg group

  http://www.mbi.ucla.edu/people/frsvr/frsvr.html

  REF: D. Fischer and D. Eisenberg 
       Fold recognition using sequence-derived predictions.  
       Protein Science 5:947-955 (1996)
  
* H3P2 : Rice threading approach (part of the UCLA-DOE frsvr server), 
  considers predicted secondary structure, Eisenberg group

  http://www.mbi.ucla.edu/people/frsvr/frsvr.html

  REF: D. Rice and D. Eisenberg 
       A 3D-1D substitution matrix for protein fold recognition that
       includes predicted secondary structure of the sequence
       J.Mol.Biol. submitted (1996)

* RDP : threading by recursive dynamic programming (part of the 
  GMD-SCAI server), Lengauer group

  http://cartan.gmd.de/cgi-bin/ToPLignLogin?/home/protal/WWW+/home/protal/
         WWW/fast+FastLogin.rc+FastRDP

  REF: R. Thiele, R. Zimmer and T. Lengauer
       Recursive dynamic programming for adaptive 
       sequence and structure alignment
       Ismb 3:384-92 (1995)

* TOPITS (called PHDthreader as part of the PredictProtein server) : 
  threading based on secondary structure prediction and solvent 
  accessibility prediction, Burkhard Rost

  http://www.embl-heidelberg.de/predictprotein/

  REF: B. Rost           
       TOPITS: threading one-dimensional predictions into 
       three-dimensional structures
       Ismb 3:314-321 (1995)

* The PSCAN server Page:
  http://www.biokemi.su.se/~threader_server/pscan/

* Swiss-Model (M.Peitsch) (server):
  http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html

===========================================
Replies from and thanks to:

-> [email-masked]
-> [email-masked]
-> [email-masked]
-> [email-masked]
-> [email-masked]
-> [email-masked]
-> [email-masked]
-> [email-masked]
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===========================================