TY - GEN
T1 - An evolutionary framework to sample near-native protein conformations
AU - Saleh, Sameh
AU - Olson, Brian
AU - Shehu, Amarda
PY - 2012
Y1 - 2012
N2 - Structural characterization of the protein native state is an important problem in computational biology. Thermodynamically, the native state is that of lowest free energy in the protein conformational space [1]. Predicting it ab initio from the amino-acid sequence can be posed as an optimization problem that has proven to be NP-hard [2]. Due to imperfect modeling of interatomic interactions, the native state often does not correspond to the global minimum. As a result, the goal in ab-initio protein structure prediction is to first arrive at a diverse ensemble of low-energy (decoy) conformations potentially relevant for the native state. Decoys are often computed using a coarse-grained energy function that expedites sampling of low-energy conformations. Select decoys are then refined with heavy-duty protocols using fine-grained energy functions to allow prediction of the native state.
AB - Structural characterization of the protein native state is an important problem in computational biology. Thermodynamically, the native state is that of lowest free energy in the protein conformational space [1]. Predicting it ab initio from the amino-acid sequence can be posed as an optimization problem that has proven to be NP-hard [2]. Due to imperfect modeling of interatomic interactions, the native state often does not correspond to the global minimum. As a result, the goal in ab-initio protein structure prediction is to first arrive at a diverse ensemble of low-energy (decoy) conformations potentially relevant for the native state. Decoys are often computed using a coarse-grained energy function that expedites sampling of low-energy conformations. Select decoys are then refined with heavy-duty protocols using fine-grained energy functions to allow prediction of the native state.
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U2 - 10.1109/BIBMW.2012.6470268
DO - 10.1109/BIBMW.2012.6470268
M3 - Conference contribution
AN - SCOPUS:84875602426
SN - 9781467327466
T3 - Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012
SP - 933
BT - Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012
T2 - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012
Y2 - 4 October 2012 through 7 October 2012
ER -