Subject: Software/Databases for Review

From: "STEPHEN R. HELLER" <[email-masked]>
Date: 25 Jul 94 14:30:00 EDT

25 July, 1994

Subject:  Computer Software for Review

     As the Software Review Editor for the ACS Journal of
Chemical Information and Computer Science (JCICS) I often get
software for review in the journal.  I now have twelve packages
in hand (see below) and I am looking for someone who is willing
to review these software/databases products.  In return for the
review you get to keep the software.  The review should be
completed in 1-3 months.  The length of the review is 4-10 double
spaced typed pages.  Sample reviews can be found in most of the
recent issues of JCICS.

     Please try to give me some (short) reason to choose you over
another person. DO NOT SAY YOU WILL REVIEW ANYTHING I HAVE
AVAILABLE. Messages with such replies are trashed!

     I have tried this approach for about the past three years
and it is working reasonably well. (REMINDER: For those who
haven't finished your reviews of software sent months and months
ago, this last sentence does not apply to you!)  As a result, I
am continuing this new method to find reviewers using this e-
mail/user group system.  I reserve the right to abandon this if
it is a problem, or inappropriate.  I will not notify people if I
have found a reviewer.  If you don't hear from me within a few
days I have chosen someone else to review the particular package.

     As I get many, many, (too many) replies to this message,
please do not respond after 27 July, 1994 (Wednesday), as I am
sure the software will be gone by then.

     I can be reached on Internet ([email-masked]).

     PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX
NUMBER!!!  (I send the software by Federal Express.)  Without
this information I WILL NOT consider your request.

     Steve Heller

The packages I now have are:

1. Accord for Excel (4.0 and 5.0) from Synopsys Ltd (Leeds, UK)
allows one to manage chemistry and associated data within Excel. 
For the IBM PC.  Does NOT include the Microsoft Excel software!

(The following softwre packages are from SYRACUSE RESEARCH).

2. LOGKOW  This program estimates the log octanol-water partition
coefficient (log P) of organic chemicals using an atom/fragment
contribution method developed at SRC (Group Contribution Method
for Estimating Octanol/Water Partition Coefficients, SETAC
Meeting in Cincinnati, OH, Nov 1992;updated manuscript submitted
to J. Pharmac. Sci.).  Chemical structures are entered using
SMILES notation [butanol = CCCCO, J Chem Inf Comput Sci 28: 31-36
(1988).  Using a training set of 2351 chemicals with 125 groups
and 230 correction factors, a correlation coefficient (r2) of
0.98 was found between the experimental and estimate log Kow's. 
The method was evaluated using a validation set of experimental
values for 6055 chemicals other than those included in the
training set with a resulting r2 of 0.94 and a mean error of
0.31.  Both PC compatable DOS and Windows 3.1 or higher versions
are available for this and all of the following programs.  

3. DERMAL  This program estimates the dermal permeability
coefficient (Kp) and the dermally absorbed dose per event
(DAevent) of organic compounds using chemical structure input and
the above program to estimate the octanol/water partition
coefficient.  The estimation methodology was taken from the U.S.
EPA document Dermal Exposure Assessment: Principles and
Applications (EPA/600/8-91-011B, January 1992).  The program uses
one general estimation equation and three specific class
estimation equations to predict Kp.  DAevent is predicted by two
separate methods (an adapted equation of Fick's first law and
another method both of which are indicated in the EPA report) and
requires (1) input of the duration of the event, and (2)
concentration of the chemical in water (a default water
solubility is calculated for the user if no value is entered).   

4. Atmospheric Oxidation Rate Program  This program estimates the
gas-phase reaction rate between organic chemicals and hydroxyl
radicals using the estimation methods developed by Dr. Roger
Atkinson and co-workers [Internat J Chem Kinetics 19: 799-828
(1987); Chem Rev 85: 69-201 (1985); Environ Toxicol Chem 7:
435-442 (1988)].  Ozone reaction rates are also estimated for
olefinic and acetylenic compounds [Chem Rev 84: 437-470 (1984)]. 
Chemical structures are entered using SMILES notation and
available experimental values for reaction rates with hydroxyl
radicals, ozone, and nitrate radicals are presented.  The
hydroxyl radical and ozone rate constants are calculated using
the Atkinson method and the atmospheric half-life is also
estimated using an average hydroxyl radical concentration and an
average ozone concentration.  See Chemosphere 26:2293-2299 (1993)

5. Henry's Law Constant Program  
This program calculates the Henry's Law constant (air/water
partition coefficient) from SMILES notation structure using both
the group contribution and the bond contribution method of Hine
and Mookerjee [J Org Chem 40: 292-8 (1975)].  SRC has recently
published a paper describing the correlations [Environ Toxicol
Chem 10:1283-93 (1991)] and has updated the group contribution
coefficients with new experimental data.

6. Biodegradation Probability Program.
This program calculates the probability that a chemical under
aerobic conditions with mixed cultures of microorganisms will
biodegrade rapidly or slowly.  It uses fragment constants
developed using multiple linear and non-linear regressions and
data from SRC's data base of evaluation biodegradation data
(BIODEG file).  The results have been published [Environ Toxic
Chem 11:593-603 (1992)].  A new version of the program is now
available that uses the previous experimental data and some new
expert survey data.  The model uses a slight revision of the
previous fragments and molecular weight to (a) calculate the
probability of rapid biodegradation from the experimental data,
and (b) to estimate the primary and ultimate biodegradation times
for complete degradation (days, weeks, months, longer) using the
evaluations of 200 chemicals by 17 biodegradation experts
[Environ. Sci. & Technol 28: 459-465 (1994)].                 

7.  PC-HYDRO.

This program calculates the hydrolysis rate constant
for esters, carbamates, halomethanes, alkyl halides, and epoxides
using a method developed by the U.S. EPA's Office of Pollution
Prevention and Toxics.  It uses SMILES notation structural input
to calculate a second-order acid- or base-catalyzed hydrolysis
rate constant at 25o C.  Acid- and base-catalyzed half-lives are
calculated for pH 7 and/or pH 8.                                 

8. PC-KOC   This program calculates the soil or sediment
adsorption coefficient (Koc) (ratio of the chemical adsorbed per
unit weight of organic carbon (oc) in the soil or sediment to the
concentration of the chemical in solution at equilibrium). 
SMILES notation structural input are used to calculate the Koc
from a correlation to the molecular connectivity indices and
correction factors for certain chemical classes.  The method was
developed with the U.S. EPA's Office of Pollution Prevention and
Toxics using a training set of 189 chemicals and evaluated with a
validation set of 131 chemicals.  R2 for the validation set was
0.92.  The results have been published [Environ Sci. Technol.
26:1560-67 (1992)].                                              

9. ChemBase  Physical Properties Data Base   Contains chemical
structures and names (approximately 7,000) and physical
properties (melting point, boiling point, water solubility, vapor
pressure, dissociation constant, octanol/water partition
coefficient, and Henry's Law constant) for over most of the
chemicals.  With this Physical Properties Data Base  and the
ChemBase  software, one can substructure search, name fragment
search, or search by physical properties.  This is an excellent
starter data base for new ChemBase , ISIS Base , or MACCS   users
who need a base set of chemical structures and physical
properties.                                   

10. PC Environmental Fate Data Bases   SRC's Environmental Fate
Data Bases  is available in a PC version for IBM compatibles with
similar software to that available on the VAX version.  Each of
the four major files (DATALOG , CHEMFATE , BIOLOG , and BIODEG )
are available separately and include the corresponding full
references from the 23,000 references in the full citation file,
XREF  (requires 14 Mb for support files and software).  These are
each briefly discussed below.

     DATALOG   This file is the largest, containing about 218,000
records on about 13,800 chemicals.  This file indicates where
environmental fate and exposure data can be found by using 18
different indexing terms (e.g., water solubility, Henry's Law
constant, hydrolysis, and ambient monitoring).  Requires
additional  13 Mb.
     CHEMFATE   This file contains actual physical property
values, rate constants, and monitoring concentrations for
approximately 1700 commercially significant chemicals.  Recently,
recommended physical property values were collected for the SARA
Section 313 TRI chemicals. Requires additional  26 Mb.
     BIOLOG    This file, which contains about 45,000 records,
indicates sources of microbial toxicity and biodegradation data
on approximately 6500 chemicals. Indexing and searching is
allowed on toxicity or biodegradation data; aerobic or anaerobic
conditions; pure enzyme, cell free extract, pure culture, or
mixed culture; source of microorganisms (e.g., soil, sewage,
etc.); and whether the metabolism pathway has been studied. (2.6
Mb).
     BIODEG    This file contains actual experimental results on
biodegradation studies for approximately 700 chemicals.
Experimental details, such as chemical concentration and rate of
degradation, are included.  This file was used to develop the
Biodegradation Probability Program.  (13 Mb).                    

11.    Chapman & Hall CD-ROM of the Dictionary of Drugs.

12.    Chapman & Hall CD-ROM of the Dictionary of Analytical
Reagents.