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Thomas R. Schneider

Bio: Thomas R. Schneider is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Protein structure & Triclinic crystal system. The author has an hindex of 34, co-authored 102 publications receiving 9028 citations. Previous affiliations of Thomas R. Schneider include European Institute of Oncology & Max Planck Society.


Papers
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Book ChapterDOI
TL;DR: The program is designed to be easy to use and general for all space groups and uses a conventional structure-factor calculation rather than a fast Fourier transform (FFT) summation, which is much slower than programs written specifically for macromolecules.
Abstract: Publisher Summary SHELXL-93 was originally written as a replacement for the refinement part of the small-molecule program SHELX-76. The program is designed to be easy to use and general for all space groups and uses a conventional structure-factor calculation rather than a fast Fourier transform (FFT) summation. The latter would be faster but in practice involves some small approximations and is not suitable for the treatment of anomalous dispersion or anisotropic thermal motion. The price to pay for the extra precision and generality is that SHELXL is much slower than programs written specifically for macromolecules. This is compensated for, to some extent, by the better convergence properties, reducing the amount of manual intervention required. A new version, SHELXL-97, was released in May 1997; this is the version described in the chapter. The changes are primarily designed to make the program easier to use for macromolecules. Advances in cryogenic techniques, area detectors, and the use of synchrotron radiation enable macromolecular data to be collected to higher resolution than was previously possible. In practice, this tends to complicate the refinement because it is possible to resolve finer details of the structure. It is often necessary to model alternative conformations, and in a few cases, even anisotropic refinement is justified.

2,203 citations

Journal ArticleDOI
TL;DR: Iterative dual-space direct methods based on phase refinement in reciprocal space and peak picking in real space are able to locate relatively large numbers of anomalous scatterers efficiently from MAD or SAD data.
Abstract: Iterative dual-space direct methods based on phase refinement in reciprocal space and peak picking in real space are able to locate relatively large numbers of anomalous scatterers efficiently from MAD or SAD data. Truncation of the data at a particular resolution, typically in the range 3.0–3.5 A, can be critical to success. The efficiency can be improved by roughly an order of magnitude by Patterson-based seeding instead of starting from random phases or sites; Patterson superposition methods also provide useful validation. The program SHELXD implementing this approach is available as part of the SHELX package.

1,620 citations

Journal ArticleDOI
TL;DR: In this article, the SHELX suite of crystallographic programs are divided into three steps: (i) extraction of structure factors representing the substructure of heavy atoms and/or anomalous scatterers only (SHELXC; Sheldrick, 2004), (ii) determination of the sub-structures, and (iii) calculation of initial phases based on the knowledge of the substructures and improvement of these phases by density modi®cation.
Abstract: One approach to phasing of macromolecular crystal structure is to exploit the small changes in diffracted intensities induced by the inclusion of heavy atoms, to alter the wavelength in the presence of anomalous scatterers, or to use a combination thereof. In the SHELX suite of crystallographic programs, the computations involved in the respective phasing procedures are divided into three steps: (i) extraction of structure factors representing the substructure of heavy atoms and/or anomalous scatterers only (SHELXC; Sheldrick, 2004), (ii) determination of the substructure (SHELXD; Schneider & Sheldrick, 2002), (iii) calculation of initial phases based on the knowledge of the substructure and improvement of these phases by density modi®cation (SHELXE; Sheldrick, 2002). A number of crystal structures have been solved using the combination of the programs mentioned above. However, in particular for the inexperienced user, the creation of correct input ®les and the interpretation of the intermediate results can be a major obstacle.

754 citations

Journal ArticleDOI
TL;DR: The 1.9-Å resolution crystal structure of native c-Kit kinase in an autoinhibited conformation is reported and will facilitate the structure-guided design of specific inhibitors that target the activated andAutoinhibited conformations of c- Kit kinase.

603 citations

Journal ArticleDOI
TL;DR: The structure represents an intermediate state of activation of Aurora B in which the Aurora B C-terminal segment stabilizes an open conformation of the catalytic cleft, and a critical ion pair in the kinase active site is impaired.

400 citations


Cited by
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Journal ArticleDOI
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

Journal ArticleDOI
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

28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
10 Mar 1970

8,159 citations

Journal ArticleDOI
13 Oct 2000-Cell
TL;DR: Understanding of the complex signaling networks downstream from RTKs and how alterations in these networks are translated into cellular responses provides an important context for therapeutically countering the effects of pathogenic RTK mutations in cancer and other diseases.

7,056 citations