PMID- 15700409
OWN - NLM
STAT- MEDLINE
DCOM- 20050315
LR  - 20061115
IS  - 1066-5277 (Print)
IS  - 1066-5277 (Linking)
VI  - 11
IP  - 5
DP  - 2004
TI  - Algorithm and data structures for efficient energy maintenance during Monte Carlo 
      simulation of proteins.
PG  - 902-32
AB  - Monte Carlo simulation (MCS) is a common methodology to compute pathways and 
      thermodynamic properties of proteins. A simulation run is a series of random 
      steps in conformation space, each perturbing some degrees of freedom of the 
      molecule. A step is accepted with a probability that depends on the change in 
      value of an energy function. Typical energy functions sum many terms. The most 
      costly ones to compute are contributed by atom pairs closer than some cutoff 
      distance. This paper introduces a new method that speeds up MCS by exploiting the 
      facts that proteins are long kinematic chains and that few degrees of freedom are 
      changed at each step. A novel data structure, called the ChainTree, captures both 
      the kinematics and the shape of a protein at successive levels of detail. It is 
      used to efficiently detect self-collision (steric clash between atoms) and/or 
      find all atom pairs contributing to the energy. It also makes it possible to 
      identify partial energy sums left unchanged by a perturbation, thus allowing the 
      energy value to be incrementally updated. Computational tests on four proteins of 
      sizes ranging from 68 to 755 amino acids show that MCS with the ChainTree method 
      is significantly faster (as much as 10 times faster for the largest protein) than 
      with the widely used grid method. They also indicate that speed-up increases with 
      larger proteins.
FAU - Lotan, Itay
AU  - Lotan I
AD  - Department of Computer Science, Stanford University, Stanford, CA 94305, USA.
FAU - Schwarzer, Fabian
AU  - Schwarzer F
FAU - Halperin, Dan
AU  - Halperin D
FAU - Latombe, Jean-Claude
AU  - Latombe JC
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PL  - United States
TA  - J Comput Biol
JT  - Journal of computational biology : a journal of computational molecular cell 
      biology
JID - 9433358
RN  - 0 (Proteins)
SB  - IM
MH  - Algorithms
MH  - *Computational Biology
MH  - Computer Simulation
MH  - Data Interpretation, Statistical
MH  - Kinetics
MH  - *Models, Molecular
MH  - *Monte Carlo Method
MH  - Proteins/*chemistry
EDAT- 2005/02/11 09:00
MHDA- 2005/03/16 09:00
CRDT- 2005/02/11 09:00
PHST- 2005/02/11 09:00 [pubmed]
PHST- 2005/03/16 09:00 [medline]
PHST- 2005/02/11 09:00 [entrez]
AID - 10.1089/cmb.2004.11.902 [doi]
PST - ppublish
SO  - J Comput Biol. 2004;11(5):902-32. doi: 10.1089/cmb.2004.11.902.