Application of constrained real-space refinement of flexible molecular fragments to automatic model building of RNA structures

Pavelčík, F.

doi:10.1107/s0021889812007546

Cited by 5 publications

(3 citation statements)

References 38 publications

(40 reference statements)

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“…NAUTILUS [10] RCRANE [6] in COOT [54] NAFIT, NABUILD in LAFIRE [5] AMBER [55] ARP/wARP [9] ERRASER [56] FARFAR [57,58] PHENIX.AUTOB [3] ROSETTA [59] NUT/DHL/RSR [60,61] 3DNA [62] CAB…”

Section: Sub1mentioning

confidence: 99%

Cyclic Automated Model Building (CAB) Applied to Nucleic Acids

et al. 2020

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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.Crystals 2020, 10, 280 2 of 15 at all [8]. Rebuilding and refining current models is often a time-consuming manual practice, so AMB promise to save time.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. All such AMB procedures are based on an intensive use of prior crystallochemical knowledge. Indeed, nucleotides contain three rigid groups: the pentose sugar, the phosphate group and the base. Different programs use different tools for the AMB: some programs use the planarity of the base (e.g., in ARP/wARP), others exploit the sugar and the phosphate groups as the first tool for identifying the main chain (e.g., in NAUTILUS). All try to extend possible nucleotide chains and match the built chains to the nucleotide sequence. Models so found may be refined via REFMAC [11] or PHENIX. REFINE [12]; usually, calculations are iterated to obtain more complete models. It is typical that a good percentage of nucleotides are correctly built in the final model.Recently, the cyclic automated model building (CAB) package for protein-automated model building was described [13]. CAB uses BUCCANEER in a cyclic procedure aimed at increasing its rate of success and the quality of the provided molecular models. In other words, CAB wraps around BUCCANEER. This program is itself cyclic; a standard BUCCANEER run performs five cycles of model building and 10 cycles of model refinement via REFMAC. CAB is highly automated and not very time consuming because BUCCANEER is fast, efficient, simple to use, and rather insensitive to the resolution limit of the data. CAB was ...

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“…NAUTILUS [10] RCRANE [6] in COOT [54] NAFIT, NABUILD in LAFIRE [5] AMBER [55] ARP/wARP [9] ERRASER [56] FARFAR [57,58] PHENIX.AUTOB [3] ROSETTA [59] NUT/DHL/RSR [60,61] 3DNA [62] CAB…”

Section: Sub1mentioning

confidence: 99%

Cyclic Automated Model Building (CAB) Applied to Nucleic Acids

et al. 2020

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“…As crystals containing nucleic acids do not usually diffact to high resolution, several authors have made a great deal of effort to tackle the difficulties involved. Initial model-building programs such as phenix.autobuild (Terwilliger et al, 2008;Adams et al, 2010), ARP/wARP (Hattne & Lamzin, 2008), NUT/DHL/RSR (Pavelcik & Schneider, 2008;Pavelcik, 2012) and Nautilus (Cowtan, 2012) utilize features that can be observed in lower resolution electron-density maps. Semi-automated model building can be performed with RCrane (Keating & Pyle, 2012).…”

Section: Introductionmentioning

confidence: 99%

New model-fitting and model-completion programs for automated iterative nucleic acid refinement

Yamashita

Zhou

Tanaka

et al. 2013

Acta Crystallogr D Biol Cryst

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In the past decade many structures of nucleic acids have been determined, which have contributed to our understanding of their biological functions. However, crystals containing nucleic acids often diffract X-rays poorly. This makes electron-density interpretation difficult and requires a great deal of expertise in crystallography and knowledge of nucleic acid structure. Here, new programs called NAFIT and NABUILD for fitting and extending nucleic acid models are presented. These programs can be used as modules in the automated refinement system LAFIRE, as well as acting as independent programs. NAFIT performs sequential grouped fitting with empirical torsion-angle restraints and antibumping restraints including H atoms. NABUILD extends the model using a skeletonized map in a coarse-grained manner. It has been shown that NAFIT greatly improves electron-density fit and geometric quality and that iterative refinement with NABUILD significantly reduces the Rfree factor.

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“…In the past years, important advances have been made in the field of auto tracing of nucleic acids, with a wide number of available programs, e.g. NUT/DHL/RSR [1,2], arp/warp [3], NAFIT/NABUILD [4] nautilus [5], knuspr [6], RCrane [7]. The program knuspr [6] places phosphates and bases into electron density maps at a high degree of reliability even at moderate resolution ( 3 ∥ 4Å).…”

mentioning

confidence: 99%