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General
Reference List 
- M.P. Allen and D.J.
Tildesley. Computer Simulation of Liquids. Oxford
University Press, New York, 1987. [Good advanced
reference book for molecular simulations]
- A.D. Bates and A.
Maxwell. DNA Topology. In Focus series,
Oxford University Press, New York, 1993. [Beautiful
paperback on the higher organizational forms of DNA]
- C. Branden and J. Tooze.
Introduction to Protein Structure. second
edition, Garland Publishing Inc., New York, 1999. [An
up-to-date and nicely illustrated protein structure
textbook dealing with basic structural principles as
well as the relationship among structure, function, and
engineering. The latter part includes chapters on
transcription regulation, signal transduction, immune
regulation, membrane and fibrous proteins, and virus
structures.]
- P. Bratley, B. L. Fox,
and L. E. Schrage. A Guide to Simulation.
Springer-Verlag, New York, 1987. [Good introduction
to Monte Carlo simulations]
- C. L. Brooks, III, M.
Karplus, and B.M. Pettitt. A Theoretical
Perspective of Dynamics, Structure, and Thermodynamics.
Wiley Interscience, New York, 1988. [Nice collection
on protein simulations]
- U. Burkert and N.L.
Allinger. Molecular Mechanics. American
Chemical Society, Washington D.C., 1980. [Basic
introductory monograph on molecular mechanics]
- C.R. Cantor and P.R.
Schimmel. Biophysical Chemistry.
Vol.1,2,3. W.H. Freeman and Company, San Fransisco,
1980. [Basic introductory monograph on molecular
mechanics]
- N. R. Cohen, Editor. Guidebook
on Molecular Modeling in Drug Design. Academic
Press, San Diego, 1996. [Modern reference for
molecular modeling as applied to drug design problems,
containing contributed chapters by industrial and
academic scientists, on problem formulation (database
analysis, docking), modeling tools, and medicinal
chemistry applications]
- Computational
Molecular Dynamics: Challenges, Methods, Ideas --
Proceedings of the 2nd International Symposium on
Algorithms for Macromolecular Modeling, Berlin, May
21-24, 1997, P. Deuflhard, J. Hermans, B. Leimkuhler, A.
E. Mark, S. Reich,. R. D. Skeel, Eds., Lecture Notes in
Computational Science and Engineering, Vol. 4 (Series
Editors M. Griebel, D. E. Keyes, R. M. Nieminen, D.
Roose, and T. Schlick), Springer-Verlag, Berlin and New
York, 1999. [Collection of articles from the
presentations invited to the May 1997 Berlin conference
on macromolecular-simulation algorithms. The books
contains sections on the following topics:
conformational dynamics, thermodynamic modeling,
enhanced time-stepping algorithms, quantum-classical
simulations, and parallel force field evaluation]
- T.E. Creighton, Editor. Protein
Folding. W.H. Freeman & Company, New York,
1992. [Nice collection with general topics regarding
proteins covered]
- D. Eisenberg and D.
Crothers. Physcial Chemistry with Applications to
the Life Science. Benjamin Cummings, Menlo Park,
California, 1979. [Wonderful physical chemistry
textbook, with useful biomolecular information]
- A. Fersht. Structure
and Mechanism in Protein Science: A Guide to Enzyme
Catalysis and Protein Folding. W. H. Freeman and
Company, New York, 1999. [A comprehensive perspective
of both enzyme catalysis and protein folding by a
pioneer researcher, an updated version of the author's
1995 text on Enzyme Structure and Mechanism; the text
reviews protein structure, emphasizing general
principles, as well as reviewing recent advances and
insights from theoretical approaches]
- D. Frenkel and B. Smit. Understanding
Molecular Simulations. From Algorithms to Applications.
Academic Press, San Diego, California, 1996. [Excellent
introduction to computer simulation of molecular
systems, containing a nice mix of mathematical details
and more informal, descriptive text. The focus is on
Monte Carlo and molecular dynamics methodologies,
through comparison and contrast analysis, including
simple algorithms and numerical illustrations. Some
important recent methodological advances are also
included]
- L.M. Gierasch and J.
King, Editors. Protein Folding, Deciphering the
Second Half of the Genetic Code. AAAS,
Washington D.C., 1990. [Interesting and beautifully
illustrated collection of articles; best bet: Jane
Richardson's origami analogues of protein folding
motifs!]
- H. Gould and J.
Tobochnik. An Introduction to Computer Simulation
Methods: Applications to Physical Systems. Part 1 and 2 Addison-Wesley,
Reading, MA, 1988. [A good introduction to computer
simulations, with a focus on classical mechanics in Part
1 and statistical physics in Part 2. The material is
made highly accessible to undergraduates by the
inclusion of many simple numerical examples, useful
illustrations, and programming segments.]
- A.Y. Grosberg and A.R.
Khokhlov. Giant Molecules. Here, There, and
Everywhere... Academic Press, San Diego,
California, 1997. [A lively introduction to polymer
physics, with nice illustrations and enticing color
plates, aptly fitting a beautiful subject. In the format
of a coffee-table book, the authors cover important
subjects like the wide range of polymeric subjects,
ideal chain models and their properties, Brownian
motion, biological polymers, and polymer dynamics. An
accompanying CD-ROM animates polymer motion, including
reputation and coil collapse.]
- J.M. Haile. Molecular
Dynamics Simulations: Elementary Methods. Wiley,
New York, 1992. [Elementary text on molecular
dynamics]
- M. Kalos and P. A.
Whitlock. Monte Carlo Methods. John Wiley
& Sons, New York, 1986. [Good introduction to
Monte Carlo techniques ]
- A. R. Leach. Molecular
Modeling. Principles and Applications. Addison
Wesley Longman, Essex, England, 1996. [Broad
introduction to many aspects of molecular modeling and
computational chemistry techniques, covering basic
concepts, quantum and molecular mechanics models,
techniques for energy minimization, molecular dynamics,
Monte Carlo sampling, free energy simulations, and drug
design applications]
- K.B. Lipkowitz and D.B.
Boyd, Editors. Reviews in Computational Chemistry.
VCH Publishers, New York, 1990 -- [Nice
series of book, with volumes appearing annually with
comprehensive reviews and tutorials on many aspects of
computational chemistry]
- J.A. McCammon and S.C.
Harvey. Dynamics of Proteins and Nucleic Acids. Cambridge
University Press, Cambridge, 1987. [First book on
bimolecular dynamics simulations]
- D.A. McQuarrie. Statistical
Mechanics. Harper Collins Publishers, New York,
1976. [Good reference text]
- National Research
Council report. Mathematical Challenges from Theoretical
/ Computational Chemistry, National Academy Press,
Washington D.C., 1995. [Panel report on the
opportunities for collaboration, past achievements, and
future possibilities between mathematical and chemical
scientists]
- D.C. Rapaport. The
Art of Molecular Dynamics Simulation. Cambridge
University Press, Cambridge, England., 1995. [Elementary
ext on molecular dynamics focusing on software details]
- W. Saenger. Principles
of Nucleic Acid Structure. Springer Advanced
Texts in Chemistry, Springer-Verlag, New York, 1984. [Wonderful
guide to the richness of DNA structure, with an amazing
breadth of topics]
- R.R. Sinden. DNA
Structure and Function. Academic Press, San
Diego, California, 1994. [Nice up-to-date textbook on
DNA structure]
- G.E. Schulz and R.H.
Schirmer. Principles of Protein Structure. Springer
Advanced Texts in Chemistry, Springer-Verlag, New York,
1990. [Nice advanced text on the rapidly-changing
field of protein folding]
- L. Stryer. Biochemistry.
W.H. Freeman, New York, latest edition (fourth
in 1995). [Wonderful biochemistry textbook, up to
date]
- W. Van Gunsteren and P.
Weiner, Editors (1989) and W. Van Gunsteren, P. Weiner,
and A.T. Wilkinson, Editors (1993, 1996): Computer
Simulation of Bimolecular Systems: Theoretical and
Experimentation Applications. Vol. 1,2,3. ESCOM,
Leiden, The Netherlands, 1989, 1993, 1996. [Good
series on biomolecular simulations, covering both
algorithms and applications]
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