Audrey Lee et al 2005 Phys. Biol. 2 S108 doi:10.1088/1478-3975/2/4/S05
A methodology for efficiently sampling the conformation space of molecular structures
Audrey Lee1, Ileana Streinu2 and Oliver Brock1
Show affiliationsMotivated by recently developed computational techniques for studying protein flexibility, and their potential applications in docking, we propose an efficient method for sampling the conformational space of complex molecular structures. We focus on the loop closure problem, identified in the work of Thorpe and Lei (2004 Phil. Mag. 84 1323–31) as a primary bottleneck in the fast simulation of molecular motions. By modeling a molecular structure as a branching robot, we use an intuitive method in which the robot holds onto itself for maintaining loop constraints. New conformations are generated by applying random external forces, while internal, attractive forces pull the loops closed. Our implementation, tested on several model molecules with low number of degrees of freedom but many interconnected loops, gives promising results that show an almost four times speed-up on the benchmark cube-molecule of Thorpe and Lei.
- PACS
-
87.15.H- Dynamics of biomolecules
36.20.Ey Conformation (statistics and dynamics)
87.15.A- Theory, modeling, and computer simulation
- Subjects
- Dates
-
Issue 4 (December 2005)
Received 1 June 2005, accepted for publication 29 July 2005
Published 9 November 2005
-
-
A methodology for efficiently sampling the conformation space of molecular structures
Audrey Lee et al 2005 Phys. Biol. 2 S108
-
Dynamical mean field theory of the repulsive BCS+U model
Kwon Park 2009 New J. Phys. 11 073027
-
Lax pairs for ultra-discrete Painlevé cellular automata
N Joshi et al 2004 J. Phys. A: Math. Gen. 37 L559
-
Connection matrices for ultradiscrete linear problems
Chris Ormerod 2007 J. Phys. A: Math. Theor. 40 12799
-
On the Contribution of Large-Scale Structure to Strong Gravitational Lensing
C. Faure et al. 2009 ApJ 695 1233
-
Creating pure nanostructures from electron-beam-induced deposition using purification techniques: a technology perspective
A Botman et al 2009 Nanotechnology 20 372001
-
The Present-Day Star Formation Rate of the Milky Way Determined from Spitzer-Detected Young Stellar Objects
Thomas P. Robitaille and Barbara A. Whitney 2010 ApJ 710 L11
-
Risks of the oil transition
A E Farrell and A R Brandt 2006 Environ. Res. Lett. 1 014004
-
Moving black holes via singularity excision
Deirdre Shoemaker et al 2003 Class. Quantum Grav. 20 3729
-
Universal scalings of universal scaling exponents
Rafael de la Llave et al 2007 J. Phys. A: Math. Theor. 40 F427
Users also read
What's this?Related review articles
What's this?- Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems—an analytical theory
- Molecular energy transducers of the living cell. Proton ATP synthase: a rotating molecular motor
- Generalized-ensemble molecular dynamics and Monte Carlo algorithms beyond the limit of the multicanonical algorithm