Protein Secondary Structure Prediction Servers and FTP Sites
Web sites which perform protein secondary structure prediction. Some
implement very new procedures, and some implement older ones. Organized
Parametric and Semiparametric Methods
- (Local) QL server
(Munson, NIH) Quadratic-Logistic prediction method is based on maximum-likelihood
- (Local) QL
with homologs (Munson, NIH) Allows prediction from multiple sequences.
Program Description (Solovyev, Baylor College) for secondary structure
prediction uses linear discriminant analysis. The actual prediction server
for SSP and NNSSP is: pssprediction
- (Local) GOR-IV server
(Garnier, NIH) from the Garnier group
- Download GOR-IV
code from NCBI
- Download GOR-IV
code from Jouy, France
Neural Network Methods
(Rost&Sander, EMBL) Email service for prediction of protein structure.
This is the PHD/MaxHom server of Rost and Sander.
- NNPRED (Fred
Cohen , UCSF) D. G. Kneller, F. E. Cohen and R. Langridge (1990) "Improvements
in Protein Secondary Structure Prediction by an Enhanced Neural Network"
J. Mol. Biol. (214) 171-182.
- Program, NNSSP (Salamov, Baylor), nnssprediction
is an implementation and improvement of a nearest-neighbor/neural network
method by Yi and Lander
- The actual prediction server for SSP and NNSSP is: pssprediction
- Anonymous FTP of program code for the SIMPA96
program from the Garnier group
(Frishman&Argos, EMBL) allows you to submit by email or WWW and receive
a response by email.
Documentation (Prediction by Mehta, Heringa, Argos , EMBL) "Prediction
of protein secondary structure using exchange statistics in multiply aligned
- SOPMA (Geourjon at
IBCP, Lyon, France)
Secondary Structure Content Prediction
OTHER INTERESTING SITES
Documentation, an alternative method to DSSP for secondary structure
- A related, interesting server is search-launcher
by Randal Smith at Baylor College of Med
- ExPASy - Tools
Nice collection of protein sequence analysis tools collected at University
of Geneva. Includes pointers to many local sequence servers and pointers
to many other servers
Next are the ISREC(Swiss Institute for Experimental Cancer Research
in Epalinges/Lausanne, Switzerland sites:ISREC
COILS Server coiled coil prediction search form
Last updated : 1/20/2000