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PDBsum entry 1bny
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RNA binding protein
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PDB id
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1bny
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References listed in PDB file
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Key reference
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Title
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Homology modeling of an rnp domain from a human RNA-Binding protein: homology-Constrained energy optimization provides a criterion for distinguishing potential sequence alignments.
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Authors
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P.V.Sahasrabudhe,
R.Tejero,
S.Kitao,
Y.Furuichi,
G.T.Montelione.
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Ref.
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Proteins, 1998,
33,
558-566.
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PubMed id
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Abstract
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We have recently described an automated approach for homology modeling using
restrained molecular dynamics and simulated annealing procedures (Li et al,
Protein Sci., 6:956-970,1997). We have employed this approach for constructing a
homology model of the putative RNA-binding domain of the human RNA-binding
protein with multiple splice sites (RBP-MS). The regions of RBP-MS which are
homologous to the template protein snRNP U1A were constrained by "homology
distance constraints," while the conformation of the non-homologous regions were
defined only by a potential energy function. A full energy function without
explicit solvent was employed to ensure that the calculated structures have good
conformational energies and are physically reasonable. The effects of
mis-alignment of the unknown and the template sequences were also explored in
order to determine the feasibility of this homology modeling method for
distinguishing possible sequence alignments based on considerations of the
resulting conformational energies of modeled structures. Differences in the
alignments of the unknown and the template sequences result in significant
differences in the conformational energies of the calculated homology models.
These results suggest that conformational energies and residual constraint
violations in these homology-constrained simulated annealing calculations can be
used as criteria to distinguish between correct and incorrect sequence
alignments and chain folds.
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Secondary reference #1
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Title
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A unique human gene that spans over 230 kb in the human chromosome 8p11-12 and codes multiple family proteins sharing RNA-Binding motifs.
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Authors
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A.Shimamoto,
S.Kitao,
K.Ichikawa,
N.Suzuki,
Y.Yamabe,
O.Imamura,
Y.Tokutake,
M.Satoh,
T.Matsumoto,
J.Kuromitsu,
H.Kataoka,
K.Sugawara,
M.Sugawara,
M.Sugimoto,
M.Goto,
Y.Furuichi.
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Ref.
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Proc Natl Acad Sci U S A, 1996,
93,
10913-10917.
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PubMed id
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