Computational Aspects of High‐Throughput Crystallographic Macromolecular Structure Determination

Adams, Paul D.; Brünger, A.T.

doi:10.1002/0471721204.ch4

Cited by 3 publications

(3 citation statements)

References 78 publications

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“…Except for the exceptionally rare case of well-ordered crystals from rigid molecules, disorder (which is commonly modeled as part of the refinement process) is a common phenomenon that occurs when some of the atoms in the structure adopt different orientations within different unit cells in the crystal (Ooi, 2010). Disorder may take on the form of discrete conformational sub-states for side chains or surface loops, or even small changes in the orientation of entire molecules throughout the crystal (Adams et al, 2003;Wilson & Brunger, 2000). In addition, crystal structures of multi-component systems and membrane proteins are still limited and refractory for structure determination (Liu & Hsu, 2005).…”

Section: Traditional Experimental Approaches To Structure Determinatimentioning

confidence: 99%

“…In addition, crystal structures of multi-component systems and membrane proteins are still limited and refractory for structure determination (Liu & Hsu, 2005). Despite these limitations, X-ray crystallography represents a mature approach (Adams et al, 2003) and continues to be regarded as the 'gold standard' for structure determination (Sali et al, 2003).…”

Section: Traditional Experimental Approaches To Structure Determinatimentioning

confidence: 99%

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Structure and Dynamics of Proteins from Nuclear Magnetic Resonance Spectroscopy

Valafar¹,

Irausquin²

2012

Protein Structure

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Section: Traditional Experimental Approaches To Structure Determinatimentioning

confidence: 99%

Section: Traditional Experimental Approaches To Structure Determinatimentioning

confidence: 99%

Structure and Dynamics of Proteins from Nuclear Magnetic Resonance Spectroscopy

Valafar¹,

Irausquin²

2012

Protein Structure

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“…Presently, X-ray crystallography is considered the more mature approach 1 and continues to be the most applied technique 2 . NMR, on the other hand, is still a relatively young approach 3 that allows for solution-state study of the structure of interest and typically focuses on collecting Nuclear Overhauser Effect (NOE) 4 data as structural restraints.…”

Section: Introductionmentioning

confidence: 99%

Dynafold: A Dynamic Programming Approach to Protein Backbone Structure Determination From Minimal Sets of Residual Dipolar Couplings

Mukhopadhyay

Irausquin

Schmidt

et al. 2014

J. Bioinform. Comput. Biol.

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Residual Dipolar Couplings (RDCs) are a source of NMR data that can provide a powerful set of constraints on the orientation of inter-nuclear vectors, and are quickly becoming a larger part of the experimental toolset for molecular biologists. However, few reliable protocols exist for the determination of protein backbone structures from small sets of RDCs. DynaFold is a new dynamic programming algorithm designed specifically for this task, using minimal sets of RDCs collected in multiple alignment media. DynaFold was first tested utilizing synthetic data generated for the N-H, Cα-Hα, and C-N vectors of 1BRF, 1F53, 110M and 3LAY proteins, with up to ±1 Hz error in 3 alignment media, and was able to produce structures with less than 1.9Å of the original structures. DynaFold was then tested using experimental data, obtained from the Biological Magnetic Resonance Bank, for proteins PDBID:1P7E and PDBID:1D3Z using RDC data from two alignment media. This exercise yielded structures within 1.0Å of their respective published structures in segments with high data density, and less than 1.9Å over the entire protein. The same sets of RDC data were also used in comparisons with traditional methods for analysis of RDCs, which failed to match the accuracy of DynaFold's approach to structure determination.

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Automated Structure Solution with the PHENIX Suite

Zwart

Afonine

Grosse‐Kunstleve

et al. 2008

Methods in Molecular Biology

515

513

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Running title: Automated structure solution with PHENIX Abstract Significant time and effort are often required to solve and complete a macromolecular crystal structure.The development of automated computational methods for the analysis, solution and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly 2 automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

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Computational Aspects of High‐Throughput Crystallographic Macromolecular Structure Determination

Cited by 3 publications

References 78 publications

Structure and Dynamics of Proteins from Nuclear Magnetic Resonance Spectroscopy

Structure and Dynamics of Proteins from Nuclear Magnetic Resonance Spectroscopy

Dynafold: A Dynamic Programming Approach to Protein Backbone Structure Determination From Minimal Sets of Residual Dipolar Couplings

Automated Structure Solution with the PHENIX Suite

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