Subject: SUMMARY:Algorithms for variable orthogonalization and PLS

From: Dominique Gorse <[email-masked]>
Date: Mon, 25 Jan 1999 08:41:02 +0100

Dear CCLers,

A lot of thanks to those who replied to my questions about variable
orthogonalization and source code about Partial Least Squares.

Dr. Peter Bladon  : [email-masked]
Paul Davis : [email-masked]
Christian Pilger : [email-masked] 
                  (Organische Chemie - Uni-GH Paderborn)
Dr David B. Turner : [email-masked] 
                  (Dept. of Information Studies University of Sheffield)

I made the summary in 3 parts : References, WWW links and where to get
source code.

**********************
       SUMMARY
**********************

References about PLS:
---------------------

  Paul Geladi and Bruce R. Kowalski (1986), "Partial least-squares
  regression: a tutorial", Analytica Chimica Acta, vol 18, pg 1-17.

  Paul Geladi and Bruce R. Kowalski (1986), "An example of 2-block
  predictive partial least-squares regression with simulated data",
  Analytica Chimica Acta, vol 185, p19-32.

  W.J. Dunn, S. Wold, U. Edlund, S. Hellberg, J. Gasteiger (1984),
  "Multivariate Structure-Activity Relationships Between Data from
  a Battery of Biological Tests and an Ensemble of Structure
  Descriptors: The PLS Method", Quant. Struct.-Act Relat. Vol 3
  p131-137.

  Bush, BL and Nachbar Jr, RB J. Comput.-Aided Mol. Design,7, (1993)
587-619.

  EXTENDING THE TREND VECTOR - THE TREND MATRIX AND SAMPLE-BASED PARTIAL
LEAST-SQUARES SHERIDAN_RP, NACHBAR_RB, BUSH_BL JOURNAL OF COMPUTER-AIDED
MOLECULAR DESIGN, 1994, 8, 3, pp.323-340.

Web links
_________

QSAR-Server of Alex Tropsha at the Univeristy of North Carolina, Chapel
Hill/NC, USA
http://mmlin1.pha.unc.edu/~jin/QSAR/

Svante Wold, the fouder of UMETRI company, has been one of the major
developers of PLS through the last years.
http://www.umetri.se/

Source codes
___________

Peter Bladon has a program which handles QSAR data in the form of a
spreadsheet, and it caters for Principal Component Analysis.  This can
be done in two ways: either by a full diagonalization method (Jacobi) or
by Non-Iterative-Partial-Least-Squares (NIPALS).  The results of PCA can
be subjected to Varimax rotation and then Orthogonalization.
The package is distributed in the form of Fortran-77 source code, which
could be adapted for other programs.  The program itself (CHEMSPREAD)
will only work on Silicon Graphics machines (because the spreadsheet
facilities rely on the SGI GL library).
http://interchem.chem.strath.ac.uk/inter/interprobe.html

PCA and PLS (NIPALS and SIMPLS) source code (Fortran) at the Jay Ponder
Lab page: http://dasher/wustl.edu

SAMPLS can also be purchased from QCPE:
http://www.ccl.net/ccl/qcpe/QCPE/section12.html

Orthogonalisation:
http://www.ccl.net/ccl/qcpe/QCPE/section01.html 

-- 
****************************************************************
Dominique Gorse                                          Synt:em
                                       Parc Scientifique G.Besse
Computational Drug Discovery                         30000 Nimes
email: [email-masked]                             France
Tel: +33 (0)4 66 04 86 65              Fax: +33 (0)4 66 04 86 67
****************************************************************
          Discover New Drugs, Discover Synt:em
                 http://www.syntem.com
****************************************************************