TY  - JOUR
AU  - Klenin, K.
AU  - Strodel, B.
AU  - Wales, D.J.
AU  - Wenzel, W.
TI  - Modelling Proteins: Conformational Sampling and Reconstruction of Folding Kinetics
JO  - Biochimica et biophysica acta / Proteins and proteomics
VL  - 1814
SN  - 1570-9639
CY  - Amsterdam [u.a.]
PB  - Elsevier
M1  - PreJuSER-16597
SP  - 977 - 1000
PY  - 2011
N1  - KK and WW acknowledge the support from the DFG Center for Functional Nanostructures (C5.1) and the Landesstiftung Baden-Wurttemberg (Biomaterials program and HPC program).
AB  - In the last decades biomolecular simulation has made tremendous inroads to help elucidate biomolecular processes in-silico. Despite enormous advances in molecular dynamics techniques and the available computational power, many problems involve long time scales and large-scale molecular rearrangements that are still difficult to sample adequately. In this review we therefore summarise recent efforts to fundamentally improve this situation by decoupling the sampling of the energy landscape from the description of the kinetics of the process. Recent years have seen the emergence of many advanced sampling techniques, which permit efficient characterisation of the relevant family of molecular conformations by dispensing with the details of the short-term kinetics of the process. Because these methods generate thermodynamic information at best, they must be complemented by techniques to reconstruct the kinetics of the process using the ensemble of relevant conformations. Here we review recent advances for both types of methods and discuss their perspectives to permit efficient and accurate modelling of large-scale conformational changes in biomolecules. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
KW  - Algorithms
KW  - Evolution, Molecular
KW  - Kinetics
KW  - Models, Molecular
KW  - Monte Carlo Method
KW  - Protein Conformation
KW  - Protein Folding
KW  - Proteins: chemistry
KW  - Proteins (NLM Chemicals)
KW  - J (WoSType)
LB  - PUB:(DE-HGF)16
C6  - pmid:20851219
UR  - <Go to ISI:>//WOS:000292350200007
DO  - DOI:10.1016/j.bbapap.2010.09.006
UR  - https://juser.fz-juelich.de/record/16597
ER  -