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Biophys J, October 2001, p. 2422-2422, Vol. 81, No. 4
Merck Frosst Canada & Co.
Peter A. Kollman passed away on May 25, 2001, at the age of
56, shortly after being diagnosed with cancer. While his death leaves
an empty space in the computational chemistry community, it also gives
us the occasion to celebrate the now-completed opus of his life. From
the standpoint of the fashionable "scientific statistics," his
contribution was prodigious: over his 31-year career he was an author
on more than 400 journal articles (more than one per month, on
average), and more than 50 reviews and chapters, and he was the 11th
most-cited chemist between 1981 and 1997. Over most of this time he was
a Professor of Chemistry and Pharmaceutical Chemistry at the University
of California at San Francisco, starting in 1971 and becoming full
professor in 1980. Prior to this, he was a postdoctoral fellow with
David Buckingham (Cambridge), following his Ph.D. with Leland Allen
(Princeton). At UCSF, his early work using quantum chemistry to examine
hydrogen bonding slowly evolved toward molecular mechanics methods,
leading to the development in his laboratory of the AMBER suite of
programs in 1981 and an associated general force field in 1984. He
continued the development of the program, refusing to concede exclusive rights for its development commercially so he could ensure its availability to the academic community. He has since welcomed the
efforts of many collaborators, especially the major involvement of
David Case at Scripps, in developing the program. It is today one of
the most widely used academic packages for biomolecular simulation,
applied in over 1000 academic and industrial laboratories.
He maintained up to his death a strong effort in force field
development as a main focus of his research, refining his "simple but
general" two-body additive model, still widely used today, and then
pressing forward beyond the two-body approximation into polarizable
force fields. His sense of the importance of electrostatics led to his
championing the use of atomic charges fit from a
quantum-mechanically-derived electrostatic potential, and the
incorporation and use of Ewald sums, to capture critical long-range
effects. He had an uncanny ability to discern which experimental data
and which chemical interactions were the most important to account for;
this allowed his force fields to maintain surprising accuracy and
generality given the simplicity of his approach in both functional form
and parameterization. This, together with his insistence on generality of overall approach (e.g. for atomic charge fitting), enabled his group
to tackle with equal facility a wide spectrum of applied problems
involving proteins, nucleic acids, and small molecules. Another major
turning point in his research came with the incorporation of
free-energy calculations into AMBER in 1987. Recognizing the importance
to the biological community of calculating relative free energies of
binding, Peter's research group began a sustained effort in this area,
applying slow-growth perturbation and the more rigorous free-energy
perturbation methods, using windows or thermodynamic integration, to a
diverse variety of protein, nucleic acid, and small-molecule problems.
Recently, he had been extending approximate free-energy methods to
include enhanced sampling and continuum dielectric methods (the latter
again to improve the treatment of long-range electrostatics),
culminating in the MM-PBSA method.
While he will certainly be remembered for his excellent science
and breadth of knowledge, for those who knew him personally his legacy
will be as much associated with his strength of character and
joie de vivre. He fearlessly tackled a wide spectrum of
biological problems, many of them daunting in their complexity. Often
challenged on the validity of applying his then-current methodologies
to a particularly challenging problem, Peter was always very open with
a careful and knowledgeable assessment of the limitations of the
methods, but never failed in his optimism that these problems could
nevertheless be modeled in a meaningful way. He was widely acknowledged
by students, post-docs, and faculty alike as being universally
encouraging to those with whom he was in any kind of supervising or
mentoring capacity. Going over your project with him one-on-one, after
the fast-paced scientific discussion examining issues in the project
and making suggestions, he would inevitably conclude by reiterating the
progress made (no matter how small), and "cheer-lead" you on to
more. In group meetings, on occasions when a presentation by a post-doc
or student exposed to the group a potentially embarrassing shortcoming
in their approach, Peter would always give grace. His face would adopt
a studied, slightly puzzled expression and he would say something like,
"I don't quite understand why you did [description of
shortcoming]; why don't you take another look at [references] and
maybe talk to [group expert on issue] later"; then he would change
the topic. Experienced group members came to recognize this form;
everyone appreciated it (especially the person up front). With
successes, Peter was always generous in his recognition and praise of
those involved, both in public and in private. A gregarious man, his booming voice and ready laughter attracted a crowd at any kind of
professional or social meeting. His positive approach has had a lasting
impact on those who passed through his laboratory and serves for many
as a model of scientific interaction. Even as we miss him deeply, we
can rejoice at his rich life and count ourselves lucky to have had him
with us.
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FOOTNOTES |
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Former postdoctoral fellow with Peter Kollman at UCSF
Editorial note: At the time of his death, Peter Kollman was a member of the Biophysical Journal Editorial Board. With his passing the Journal has lost a counselor whose wisdom and energy will be sorely missed.
Biophys J, October 2001, p. 2422-2422, Vol. 81, No. 4
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