Abstract
Obtaining high-quality models for nucleic acid structures by automated model building programs (AMB) is still a challenge. The main reasons are the rather low resolution of the diffraction data and the large number of rotatable bonds in the main chains. The application of the most popular and documented AMB programs (e.g., PHENIX.AUTOBUILD, NAUTILUS and ARP/wARP) may provide a good assessment of the state of the art. Quite recently, a cyclic automated model building (CAB) package was described; it is a new AMB approach that makes the use of BUCCANEER for protein model building cyclic without modifying its basic algorithms. The applications showed that CAB improves the efficiency of BUCCANEER. The success suggested an extension of CAB to nucleic acids—in particular, to check if cyclically including NAUTILUS in CAB may improve its effectiveness. To accomplish this task, CAB algorithms designed for protein model building were modified to adapt them to the nucleic acid crystallochemistry. CAB was tested using 29 nucleic acids (DNA and RNA fragments). The phase estimates obtained via molecular replacement (MR) techniques were automatically submitted to phase refinement and then used as input for CAB. The experimental results from CAB were compared with those obtained by NAUTILUS, ARP/wARP and PHENIX.AUTOBUILD.
Highlights
Automated model building (AMB) programs try to replace the visual interpretation of the three-dimensional electron density map, which is usually time consuming and subjective, with automatic procedures to speed up the structure determination process and to minimize the modelling errors
The results showed that cyclic automated model building (CAB) gave more complete and accurate structures compared to the conventional use of BUCCANEER
In a previous paper [26], we selected from the Protein Data Bank (PDB) 38 nucleic acid structures for which phase solution attempts were made via molecular replacement (MR) techniques: we downloaded the observed diffraction data, unit cell dimensions, the space group symmetry, nucleotide sequence, and the structural models
Summary
Automated model building (AMB) programs try to replace the visual interpretation of the three-dimensional electron density map, which is usually time consuming and subjective, with automatic procedures to speed up the structure determination process and to minimize the modelling errors. Equivalent tools for nucleic acids exist, but most of them are still in progress Quite often, such AMB programs aid in detecting errors in crystallographic models [4], or extend and rebuild existing nucleotides chains [5] or perform semi-automatic building [6]. In spite of the above limitations, complete or almost complete AMB packages for nucleic acids exist: PHENIX.AUTOBUILD [3], ARP/wARP [9] and NAUTILUS [10]. These programs build nucleotide chains in a rather automatic manner.
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