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2015 ; 62
(4
): 481-95
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NMRFAM-SDF: a protein structure determination framework
#MMPMID25900069
Dashti H
; Lee W
; Tonelli M
; Cornilescu CC
; Cornilescu G
; Assadi-Porter FM
; Westler WM
; Eghbalnia HR
; Markley JL
J Biomol NMR
2015[Aug]; 62
(4
): 481-95
PMID25900069
show ga
The computationally demanding nature of automated NMR structure determination
necessitates a delicate balancing of factors that include the time complexity of
data collection, the computational complexity of chemical shift assignments, and
selection of proper optimization steps. During the past two decades the
computational and algorithmic aspects of several discrete steps of the process
have been addressed. Although no single comprehensive solution has emerged, the
incorporation of a validation protocol has gained recognition as a necessary step
for a robust automated approach. The need for validation becomes even more
pronounced in cases of proteins with higher structural complexity, where
potentially larger errors generated at each step can propagate and accumulate in
the process of structure calculation, thereby significantly degrading the
efficacy of any software framework. This paper introduces a complete framework
for protein structure determination with NMR--from data acquisition to the
structure determination. The aim is twofold: to simplify the structure
determination process for non-NMR experts whenever feasible, while maintaining
flexibility by providing a set of modules that validate each step, and to enable
the assessment of error propagations. This framework, called NMRFAM-SDF
(NMRFAM-Structure Determination Framework), and its various components are
available for download from the NMRFAM website
(http://nmrfam.wisc.edu/software.htm).
|*Nuclear Magnetic Resonance, Biomolecular/methods
[MESH]
free
free
free
