XPLOR

The full potenhal of RDCs, however, can be seen by the incorporation of RDC data in structure calculations. Several programs hke XPLOR-NIH, DISCOVER or GROM ACS allow the incorporation of RDCs as angular or combined angular and distance dependent restraints. Several studies on sugars have been reported (see, e.g. Ref [43] and references therein) and Fig. 9.8 shows the comparison of three structural models for the backbone of the cyclic undecapeptide cyclosporin A, derived from X-ray crystahography, ROE data in CDCI3 as the solvent, and RDCs and ROEs obtained in a PDMS/CDCfi stretched gel [22]. Due to the sensitivity to... 

Brunger, A. T. (1992). XPLOR Version 3.1. Yale University Press, New Haven and London. 

Molecular Replacement. The tertiary structure of crystalline ALBP was solved by using the molecular replacement method incorporated into the XPLOR computer program (Brunger et al., 1987). The refined crystal structure of myelin P2 protein without solvent and fatty acid was used as the probe structure throughout the molecular replacement studies. We are indebted to Dr. A. Jones and his colleagues for permission to use their refined P2 coordinates before publication. 

XPLOR produces a sorted list of the correlation results simplifying final interpretation (Branger 1990). 

XPLOR is a modern package of refinement programs that includes powerful procedures for energy refinement by simulated annealing, in addition to more traditional tools like least-squares methods and molecular-replacement searches. The package is available for use on many different computer systems. Simulated annealing for large molecules usually requires supercomputers. 

Patterson Correlation Refinement. To select which of the orientations determined from the rotation search is the correct solution a Patterson correlation refinement of the peak list of the rotation function was performed. This was carried out by minimization against a target function defined by Brunger (1990) and as implemented in XPLOR. The search model, P2, was optimized for each of the selected peaks of the rotation function. 

Structure Refinement. The refinement of the structure was based on an energy function approach (Brunger etal., 1987) arbitrary combinations of empirical and effective energy terms describing crystallographic data as implemented in XPLOR. Molecular model building was done on an IRIS Workstation (Silicon Graphics) with the software TOM, a version of FRODO (Jones, 1978). 

A translation search as implemented in XPLOR was used to find the molecular position of the now oriented P2 probe in the ALBP unit cell. Only a single position... 

Figure 16 Yearly number of publications in the CJACS file mentioning the Cambridge Structural Database or the Protein Data Bank. The search queries for each curve were (1) protein w)data(w)bank, (2) xplor or x(w)plor, and (3) cam-bridge(w)structural(w)database. To minimize extraneous hits and to ensure have comparable curves, alternate names of the databases, such as CSD, Brookhaven, or PDB, were not used.

Schwieters CD, et al. The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 2003 160 65-73. Brunger AT, et al. Crystallography NMR system A new software suite for macromolecular structure determination. Acta Crystallogr. D. Biol. Crystallogr. 1998 54 905-921. 

Finally, NMR-derived distance information as well as information about dihedral angles (obtained from chemical shifts) is incorporated into structure calculations performed using molecular dynamics and simulated annealing programs such as CNS (48) and XPLOR-NIH (49) to calculate the protein stmcture. 

A. Briinger, in XPLOR 3.1 A System for X-ray Crystallography and NMR, Yale University Press, New Haven, 1992. 

A. T. Brunger, XPLOR Manual, Ver. 3.1 Yale University Press New Haven, 1993. 

The molecular dynamics for NMR structure determination and the torsion angle dynamics were extensively reviewed by Giintert.35 The method was also reviewed by Clore and Schwieters.20 The molecular dynamics programs, e.g., CHARMM,42 AMBER,43 and GROMACS44 can be used for the structure determination. XPLOR,38 its successor CNS,45 and XPLOR-NIH12... 

The procedure also used random array initial structures for molecular dynamics algorithm using XPLOR-NIH.12 Sixteen thousand initial structures were subjected to an initial simulated annealing (5,000 K, 80 ps). This means that the initial structures did not cover the entire conformational space, but were randomly distributed all over the space. The conformational... 

Rao, Teeter [148] Can be implemented in XPLOR Part of MD simulation AMBER — 4r counterions present... 

---