From:	youkha %! at !% biosym.com (Philippe Youkharibache)
Date:	Thu, 3 Jun 93 17:55:52 -0700
Subject:	summary: shortage of compuational chemists

Dear netters:

In my original posting, I made the following answer/remarks to a question
on the net:

>        >Question for everyone?  Is there really a shortage of computational
>        >chemists/chemists in general?
>
>And my answer is : there is an incredible shortage of computational
>chemists in the chemical industry, all over the world.  In fact, it is
>much worse in Europe and Japan. (So it is not only a green card issue)
>
>Many people even wonder HOW one becomes a computational chemist in the
>pharmaceutical industry. Was one trained for that ? Some experimental
>chemists even wonder: what is computational chemistry ? It certainly would
>be interesting to hear about ways one can become a computational chemist
>today for many young graduate students.  The only way I know is to
>come from a lab that does some sort of molecular modeling or theoretical
>chemistry , but usually the training one will get there will be narrower
>than what will be needed to tackle drug design or protein engineering
>problems for example, from a computation standpoint.  It certainly will
>be a start though.
>
>Maybe a discussion on what should be the necessary training in academia
>or engineering schools for computational chemistry would be of interest;
>and how to make that field more central (should I also say reliable ?) in
>industry.


I have received quite a bit of mail about this posting, mostly questions
from graduate students and young Ph.Ds. who would like to know how
to "break-into" computational chemistry, as they put it (more than one used
that word. It must be significant.).  Questions on how to write a resume
to pass screening when looking for an industrial job, and when you have
a purely theoretical background.  Questions on where are the "job openings"
that I am talking about. Some requested background references for
computational chemistry, to learn about applications.
Most questions came from scientists with a theoretical background either
in theoretical (quantum) chemistry, applied math and computer science
who would like to "switch" to molecular modeling.
 
First of all,  I must apologize to those who might have been mislead by my
remarks, and are looking for a job in the immediate future.  In saying that
there is a "shortage of computational chemists" in the chemical industry, I
did not mean to say that there are a lot of job openings right now.  An
obvious reason is the coming (?) health care system reform and the
uncertainty it creates for pharmaceutical companies.  I just had in mind to
stimulate a discussion on the role that computational chemists and
computational chemistry plays in industry, and what training should be
required for those who would like to "break into" that field.

For those who asked what is industry looking for, just ask yourself what
are these companies products, and you'll have your answer in broad terms.
A drug company hiring a computational chemist will expect him/her to use
state of the art computations to help designing drugs and/or protein
structures (or other biopolymers) and properties. Knowing about SOFTWARE
used in industry will tell you what computational techniques are used.
Stop by these companies booths at shows to learn about them.  Ask them
some litterature on products, look at their references. These programs
are used also in academia (a lot of them come from academia), get access to them.
The knowledge of protein structure should be considered as a must, if
it is not already. For those looking for references, a very good primer
is Dickerson & Geis's book.  It might be old but it's the best.  Have things
changed anyway ?

For those who want their resume to pass screening: it is clear that showing
some knowledge of applications is necessary.  If you do not have any, get it.
You can read textbooks (see hereafter), you can make connections with labs
that do some applied modeling, it will allow you to see if you like that
anyway.  If you want to know about hot topics, read Science and Nature,
Academics and industrials work on the same problems, when you are talking
about biological sciences, an example is AIDS (see the last Science issue !)
They both would publish in these journals the hot stuff.
Also I hate to say that, nothing draws more attention than the lab/university
you come from, it is not really different than academia. If your resume shows
applications, and your lab is known for techniques such as conformational
search, molecular mechanics/dynamics, Poisson-Boltzmann Electrostatics,
Free Energy calculations, Homology modeling, QSAR, Distance Geometry,
molecular graphics,  etc..., there is a good chance you will be perceived
as a good candidate.  For people with QM background, it really depends
more on the specific job offering.  Certainly if your work involved
essentially diatomic/triatomic molecules, chances are very small.  DFT
techniques are certainly becoming more and more important though.  What I
would suggest to people seriously interested in "switching" from a
theoretical field to applications in the pharmaceutical industry, is to
actually get a post-doc experience in a lab with some recognition in the
fields mentioned.  I prefer not to mention any, but these are known.

For those interested in method development, there are few pharmaceutical
companies that will look for that, but the largest ones, or some special
cases that have started on the basis of "rational drug design".
On the other hand, molecular modeling software companies are normally
the most likely to be interested, provided that you can and want to
code (preferably in C). As far as I know, only Biosym performs basic
research and basic method development among them though, as these relate
to applications, usually in collaboration with pharmaceutical companies.

Ben Burke from Agouron Pharmaceuticals (burke-0at0-tbone.agouron.com )
suggested "that graduate students take Medicinal Chemistry
curricula and complement that with additional courses (ugh) in
a strong chemistry department (for areas like QM).
This should help the student have a reasonable chemistry background,
know what it takes to produce (in theory) a successful drug (eg ADME),
and have practice modelling ligands and/or protein systems (in the
"lab").  The additional course work helps them understand reaction
surfaces, transiton states, and geometry-related questions.  They
would even be on their way to generating necessary parameters, etc.
Of course, the quality of the student will depend highly on the mentor
as well as the student.  The ability to succinctly ask the right
question is one that comes from a combination of training (your advisor's
at first) and experience generated while working on your project.
PS Some statistics training is useful for QSAR work."

Gene Fleishman from Cray suggested " If your question really
is:  What training do I get in computational chemistry to maximize my
employmentin the pharmaceutical arena?  Then call up some pharmaceutical
companies andask them about the experience and training of their
computational chemistry staff and while your at it ask about summer
internships and work/study programs".

Frederick Ignatz-Hoover from Monsanto suggested to "Try J. Chem. Ed., Vol
69, No 7, p. 533 (1992) for a start....", an article on a Molecular
modeling teaching course at the Universite de Montreal by Hermann Dugas,
which should give a good overview of common molecular modeling techniques
of use in industry AND gives basic textbook references.

Finally, I would add that apart from the leading companies, who are heavily
committed to molecular modeling and have very talented modelers, there is a
significant number of companies that did not invest fully in getting BOTH
molecular modeling software and molecular modelers.  The efficiency of
modeling is not due to the software alone.  But how many trained molecular
modelers are they ?  When modeling is central and reliable in a company, is
that due to the software, the science behind, or the scientist-user behind ?
and to what extent ?  I'll let you think about it.

For those who asked textbook references (more applications oriented), in addition
to the those cited in the J. Chem Ed., 69(7), 1992 paper, I would add a few.
It is not an exhaustive list but just a selection. There are plenty of
good reviews out there as well (... maybe another time or somebody on the
net could volunteer). Specially as one look in the future,
the knowledge of protein structure and function is necessary. Is it
necessary to say that biology is becoming a branch of chemistry.  So
shouldn't "computational chemistry" include "computational biology" ?

- "Reviews in Computational Chemistry"
   Lipkowitz & Boyd, eds. Vol. I,II,III
   VCH publishers: New York

-  "Computer-Aided Drug Design, Methods and Applications",
   Thomas J Perun and C.L. Propst, Eds,
   Marcel Dekker, New York, 1989

- " A Handbook of Computational Chemistry" - a practical guide to chemical
     structures and energy calculations, Tim Clark, John Wiley and Sons,
     New York, 1985.

- "The structure and action of PROTEINS"
   Dickerson and Geis,
   W.A. Benjamin, Inc., 1969

- "Protein Engineering"
   D.L. Oxender and C. F. Fox
   Alan R. Liss, Inc, 1987

- "Proteins, A theoretical perspective of dynamics, Structure, and
thermodynamics"
   Charles L. Brooks III, Martin Karplus,  B. Montgomery Pettitt, John Wiley,
1988.

- "Dynamics of proteins and nucleic acids" by J. Andrew McCammon
   and Stephen C. Harvey, Cambridge University Press, 1987.

- "Prediction of protein structure and the principles of protein conformation"
   G. D. Fasman Ed.
   Plenum Press, New York, 1989

- "Density Functional Methods in Chemistry"
   J. K. Labanowski, J. W. Andzelm,
   Springer-Verlag (New York : 1991)

- "Ab Initio Molecular Orbital Theory",
   W. J. Hehre, L. Radom, P. v. R. Schleyer, J. A. Pople,
   Wiley-Interscience Publication (New York : 1986)


I hope this helps.

Philippe Youkharibache.
youkha at.at biosym.com


PS:  I'll ge gone until July 1.  So if you send me mail I will not be able
to respond before then, and even then I'll probably have to trim out hundreds
of messages.  That's the price to pay with E-mail !


A few original e-mail messages follow:

*******************************************************
From Galen Gawboy (gawboy -8 at 8- sodium.mps.ohio-state.edu)

>  Philippe,
>
>        >Question for everyone?  Is there really a shortage of computational
>        >chemists/chemists in general?
>
>>And my answer is : there is an incredible shortage of computational
>>chemists in the chemical industry, all over the world.  In fact, it is
>>much worse in Europe and Japan. (So it is not only a green card issue)
>
>   As someone who is nearing completion of my PhD, and facing a grim
>job market for post docs I find this heartening. I for one have absolutely
>no idea what industry would look for in a computational chemist.
>
>   I looked in Chemical Engineering News recently and saw only 3 openings
>for computational chemists. I have also heard from a head hunter that
>personnell department types tend to throw out the theory resume's on the
>grounds that they don't see the need to hire someone with "esoteric" skills
>with the hope that that person would fit in to the "results oriented" R&D
>that their company does.
  
>So if there is huge shortage
>of computational chemists where are the openings? How do we sidestep
>the personnell "professionals"? What does industry look for?
>
>  Some practical advice of how to get past the resume' screeners and get word
>to people who value the skills of computational chemists would be a valued
>contribution to the list. For that matter identifying the types of companies
>that value computational chemists would be of much use. I tried to have
>an informal chat with a representative from a petroleum company to try to
>guage what type of general studies their company would be interested in
>to try to steer my research direction towards a more real world emphasis.
>It turned out that her husband was their group computational chemist. He
>has had no training in the field what so ever and seemed to winging it,( I
>kept this opinion to myself), surprisingly she was quite hostile towards me.
>
>  Perhaps it is hard for computational chemists to break into industry because
>attitudes like this permeate other companies. In other words they hire their
>computational chemists from the ranks of their bench chemists and expect them
>to pick some black box package and crunch out numbers. I have nothing against
>black box packages, but I suspect that they would get more bang for their buck
>if they went outside their company and hired somebody who knows how the black
>box works.
>
>Gee, this was longer than I thought it would be. Sorry.
>
>-galen
>
*******************************************************
From markb &$at$& orl.mmc.com
From: burke[ AT ]tbone.agouron.com (Ben Burke)
From: "Frederick F. Ignatz-Hoover"
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