Biomolecular modeling: Goals, problems, perspectives.
Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling.
van Gunsteren
Wilfred F
WF
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland. wfvgn@igc.phys.chem.ethz.ch
Bakowies
Dirk
D
Baron
Riccardo
R
Chandrasekhar
Indira
I
Christen
Markus
M
Daura
Xavier
X
Gee
Peter
P
Geerke
Daan P
DP
Glättli
Alice
A
Hünenberger
Philippe H
PH
Kastenholz
Mika A
MA
Oostenbrink
Chris
C
Schenk
Merijn
M
Trzesniak
Daniel
D
van der Vegt
Nico F A
NF
Yu
Haibo B
HB
D003198:Computer Simulation; D008954:Models, Biological; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D011506:Proteins