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104 citations found for Adams, P.D.

There are 120 articles by Adams, P. click here to see these.

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Acta Cryst. (2017). A73, a391
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X-ray and neutron crystallographic data have been combined in a joint structure-refinement procedure that has been developed using recent advances in modern computational methodologies, including cross-validated maximum-likelihood target functions with gradient-based optimization and simulated annealing.


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Homologous models of penicillopepsin were used to generate initial phases for the native crystal structure of the aspartic proteinase penicillopepsin by molecular replacement. It is shown that the combination of cross-validation, torsion-angle dynamics simulated annealing and maximum-likelihood target functions allow refinement to proceed efficiently, even when the initial molecular-replacement-phased electron-density maps do not allow manual rebuilding.


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Acta Cryst. (2006). A62, s85
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The non-iterative feature-enhancing approach improves crystallographic maps' interpretability by reducing model bias and noise and strengthening the existing signal.

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Modelling deformation electron density using interatomic scatters is simpler than multipolar methods, produces comparable results at subatomic resolution and can easily be applied to macromolecules.

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Application of phenix.model_vs_data to the contents of the Protein Data Bank shows that the vast majority of deposited structures can be automatically analyzed to reproduce the reported quality statistics. However, the small fraction of structures that elude automated re-analysis highlight areas where new software developments can help retain valuable information for future analysis.

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Acta Cryst. (2005). A61, c160
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A robust method for determining bulk-solvent and anisotropic scaling parameters for macromolecular refinement is described. A maximum-likelihood target function for determination of flat bulk-solvent model parameters and overall anisotropic scale factor is also proposed.

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A fast analytical method for calculating mask-based bulk-solvent scale factors and overall anisotropic correction factors is introduced.

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phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

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A description is provided of the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite and its application to the re-refinement of cryo-EM-derived models.

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New methods and PHENIX tools for quality assessment of cryo-EM maps, atomic models and model-to-map fitting are presented. Results of systematic application of these tools to high-resolution cryo-EM maps and corresponding atomic models are analyzed and discussed.

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The values of anisotropic atomic displacement parameters (ADPs) that correspond to concerted motions can be obtained from refined TLS matrices analytically or numerically. The difference between the ADPs obtained using these two methods can be used to assess the results of TLS refinement.

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Acta Cryst A. (2016). A72, s22
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