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|a (DE-627)NLM149101023
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|a (NLM)15224387
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|a DE-627
|b ger
|c DE-627
|e rakwb
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|a eng
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|a Xiang, Yun
|e verfasserin
|4 aut
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|a Fully quantum mechanical energy optimization for protein-ligand structure
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|c 2004
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|a Text
|b txt
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|a ohne Hilfsmittel zu benutzen
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|a Band
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|a Date Completed 29.04.2005
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|a Date Revised 24.11.2016
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|a published: Print
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|a Citation Status MEDLINE
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|a Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1431-1437, 2004
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|a We present a quantum mechanical approach to study protein-ligand binding structure with application to a Adipocyte lipid-binding protein complexed with Propanoic Acid. The present approach employs a recently develop molecular fractionation with a conjugate caps (MFCC) method to compute protein-ligand interaction energy and performs energy optimization using the quasi-Newton method. The MFCC method enables us to compute fully quantum mechanical ab initio protein-ligand interaction energy and its gradients that are used in energy minimization. This quantum optimization approach is applied to study the Adipocyte lipid-binding protein complexed with Propanoic Acid system, a complex system consisting of a 2057-atom protein and a 10-atom ligand. The MFCC calculation is carried out at the Hartree-Fock level with a 3-21G basis set. The quantum optimized structure of this complex is in good agreement with the experimental crystal structure. The quantum energy calculation is implemented in a parallel program that dramatically speeds up the MFCC calculation for the protein-ligand system. Similarly good agreement between MFCC optimized structure and the experimental structure is also obtained for the streptavidin-biotin complex. Due to heavy computational cost, the quantum energy minimization is carried out in a six-dimensional space that corresponds to the rigid-body protein-ligand interaction
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|a Journal Article
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|a Carrier Proteins
|2 NLM
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|a Fatty Acid-Binding Proteins
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|a Ligands
|2 NLM
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|a Propionates
|2 NLM
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|a Proteins
|2 NLM
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|a propionic acid
|2 NLM
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|a JHU490RVYR
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|a Zhang, Da W
|e verfasserin
|4 aut
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|a Zhang, John Z H
|e verfasserin
|4 aut
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 25(2004), 12 vom: 05. Sept., Seite 1431-7
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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|g volume:25
|g year:2004
|g number:12
|g day:05
|g month:09
|g pages:1431-7
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