Subject: Protein Secondary structure prediction

From: [email-masked] (Mark Dalton)
Date: Fri, 8 Apr 1994 17:41:05 -0500 (CDT)

Hi!

	In reference to the request for information about what software
is available for secondary structure prediction of proteins.

1.  MacProt - is a set of programs for analyzing protein sequences for
          secondary structure, chain flexibility, hydropathy, helical
          wheels, homology and amphipathic regions.
2.  NCBI package.
         GREASE, TGREASE - a Kyte-Doolittle hydropathicity plotting
         Garnier - Protein secondary structure prediction.

3. SeqSee - Science( 258:p1369): canopus.biochem.ualberta.ca
        A suite of programs for protein sequence analysis
	
4. Email server:
  Name       : PredictProtein
  Organism   : Protein Design Group
             European Biology Molecular Laboratory (EMBL)
             Heidelberg / Germany
  Type       : ANALYSIS
  Description: Analyze a protein  sequence and  sends  back a multiple
            sequence alignment performed by a  weighted  dynamic
            programming  method (MaxHom) and  a  secondary structure
	    prediction  produced  by a profile network method (PHD).
  Address    : [email-masked]
  Contact    : To report problems: [email-masked]

I have listings of other software for 3D prediction from primary
and secondary structure prediction also.  I am sure there is much
more, but this is a place to start.  I have references for papers
on neural net predictions also.

Thanks!

Mark

OTHER Related software of posible interest:
  Part of the MBCRR and GDE packages: mbcrr.harvard.edu
  PIMA is a multiple sequence alignment program that uses a dynamic
  programming-based   pattern  construction  method to align a  set
  of  homologous protein  sequences  (Smith,   RF  and  Smith,  TF,
  1992, Protein Engineering vol 5, num 1 (should be in US libraries
  this week; see also Smith and Smith, 1990, PNAS 87:118-122).
  The multiple alignment algorithm:
          (1)  is  based  on   a   local  (Smith-Waterman)   rather
  than   global  (Needleman-Wunch-Sellars) dynamic programing algo-
  rithm;
        (2) aligns sequences based on the  pattern  of  conserved
  sequence  elements/domains common to the homologous sequences be-
  ing aligned;
        (3)  represents gaps  within  a  multiple alignment in  a
  simple and consistent manner;
        (4) can employ secondary structure-dependent gap   penal-
  ties  for  use  in  structural modelling of new protein sequences
  when the 3D-structure of one or more members of  the  se-  quence
  family is known.

-- 
Mark Dalton                   AUG-GCU-AGA-AAG                  H      
Cray Research, Inc.           M   A   R   K                    |     
Eagan, MN 55121                                  CH3-S-CH2-CH2-C-COOH
Internet: [email-masked]                                         |   
(612)683-3035                                                  NH2