J. Appl. Cryst.の発刊に際して
10 Mar 1970-Vol. 12, Iss: 1, pp 1-1
About: The article was published on 1970-03-10 and is currently open access. It has received 8159 citations till now.
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TL;DR: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
Abstract: An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
81,116 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...These days such padding is less desirable and there are excellent programs such as enCIFer (Allen et al., 2004) for working with CIF files, so CIFTAB is now effectively redundant....
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TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
34,239 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...This dictionary contains among oth i ems descriptions of the solution components, the experime conditions, enumerated lists of the instruments used, as we information about structure refinement....
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TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.
28,425 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Multithreading is achieved using OpenMP along the lines suggested by Diederichs (2000), and the program is particularly suitable for multiple-core processors....
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TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.
27,505 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...…e-mail: emsley@ysbl.york.ac.uk # 2004 International Union of Crystallography Printed in Denmark ± all rights reserved CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and…...
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...The introduction of FRODO (Jones, 1978) and then O (Jones et al., 1991) to the ®eld of protein crystallography was in each case revolutionary, each in their time breaking new ground in demonstrating what was possible with the current hardware....
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TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
18,531 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...After ensuring that the diffraction data are sound and understood, the next critical necessity for solving a structure is the determination of phases using one of several strategies (Adams, Afonine et al., 2009)....
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...Tools such as efficient rigid-body refinement (multiplezones algorithm; Afonine et al., 2009), simulated-annealing refinement (Brünger et al., 1987) in Cartesian or torsion-angle space (Grosse-Kunstleve et al., 2009), automatic NCS detection and its use as restraints in refinement are important at…...
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References
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TL;DR: Characterization of 23 pentapeptide insertions in TEM-1beta-lactamase demonstrated the utility of the new insertion method, which relies on the random insertion of transposon Tn 4430 and subsequent in vitro deletion of the bulk of the transpos on the target gene.
Abstract: A new insertion method for probing protein functional organization was developed The method relies on the random insertion of transposon Tn 4430 and subsequent in vitro deletion of the bulk of the transposon after which a 15 bp insertion remains within the target gene This results in pentapeptide insertions randomly distributed in the target protein Characterization of 23 pentapeptide insertions in TEM-1beta-lactamase demonstrated the utility of the method The phenotypes associated with the mutated beta-lactamase proteins equated both with the sorts of local peptide structures in which the pentapeptide insertions occurred and their position in the three-dimensional structure of the enzyme
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TL;DR: Two webservers are presented for multiple alignment and recognition of binding patterns shared by a set of protein structures, which often involve energetically important hot-spot residues that are crucial for protein–protein associations.
Abstract: Analysis of protein–ligand complexes and recognition of spatially conserved physico-chemical properties is important for the prediction of binding and function Here, we present two webservers for multiple alignment and recognition of binding patterns shared by a set of protein structures The first webserver, MultiBind (http://bioinfo3dcstauacil/MultiBind), performs multiple alignment of protein binding sites It recognizes the common spatial chemical binding patterns even in the absence of similarity of the sequences or the folds of the compared proteins The input to the MultiBind server is a set of protein-binding sites defined by interactions with small molecules The output is a detailed list of the shared physico-chemical binding site properties The second webserver, MAPPIS (http://bioinfo3dcstauacil/MAPPIS), aims to analyze protein–protein interactions It performs multiple alignment of protein–protein interfaces (PPIs), which are regions of interaction between two protein molecules MAPPIS recognizes the spatially conserved physico-chemical interactions, which often involve energetically important hot-spot residues that are crucial for protein–protein associations The input to the MAPPIS server is a set of protein-protein complexes The output is a detailed list of the shared interaction properties of the interfaces
99 citations
TL;DR: In this article, single crystals of A$1-x}$K$_x$Fe$_2$As$2$ (A=Ba, Sr) with high quality have been grown successfully by FeAs self-flux method.
Abstract: Single crystals of A$_{1-x}$K$_x$Fe$_2$As$_2$ (A=Ba, Sr) with high quality have been grown successfully by FeAs self-flux method. The samples have sizes up to 4 mm with flat and shiny surfaces. The X-ray diffraction patterns suggest that they have high crystalline quality and c-axis orientation. The non-superconducting crystals show a spin-density-wave (SDW) instability at about 173 K and 135 K for Sr-based and Ba-based compound, respectively. After doping K as the hole dopant into the BaFe$_2$As$_2$ system, the SDW transition is smeared, and superconducting samples with the compound of Ba$_{1-x}$K$_x$Fe$_2$As$_2$ (0 $< x \leqslant$ 0.4) are obtained. The superconductors characterized by AC susceptibility and resistivity measurements exhibit very sharp superconducting transition at about 36 K, 32 K, 27 K and 23 K for x= 0.40,0.28,0.25 and 0.23, respectively.
99 citations
TL;DR: The unexpected double helical chirality of the metallo-prisms observed in the solid state persists in solution giving rise to two different stereodynamic processes as demonstrated by NMR enantiodifferentiation experiments.
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TL;DR: Shape analysis of LMM and HMM structures revealed how symmetric association of dimers could lead to minimal HMM variants, implying that the disruption of cellular HMM particles may require regulation of protein-RNA, as well as protein-protein interactions, which has implications for therapeutic development.
99 citations