Towards the automatic crystal structure solution of nucleic acids: automated model building using the new CAB program

Abstract

CAB, a recently described automated model-building (AMB) program, has been modified to work effectively with nucleic acids. To this end, several new algorithms have been introduced and the libraries have been updated. To reduce the input average phase error, ligand heavy atoms are now located before starting the CAB interpretation of the electron-density maps. Furthermore, alternative approaches are used depending on whether the ligands belong to the target or to the model chain used in the molecular-replacement step. Robust criteria are then applied to decide whether the AMB model is acceptable or whether it must be modified to fit prior information on the target structure. In the latter case, the model chains are rearranged to fit prior information on the target chains. Here, the performance of the new AMB program CAB applied to various nucleic acid structures is discussed. Other well documented programs such as Nautilus, ARP/wARP and phenix.autobuild were also applied and the experimental results are described.

The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline

“…To address this, we decided to submit the phases and weights obtained by these programs to the same refinement and AMB procedure using SYNERGY and CAB, respectively. SYNERGY’s efficacy was demonstrated by Burla et al [ 39 ], while the ability of CAB was verified in a Paper III by Cascarano & Giacovazzo [ 56 ]. We implemented the three pipelines, REMO22 + SYNERGY + CAB, PHASER + SYNERGY + CAB and MOLREP +SYNERGY + CAB, into SIR22, a modified version of SIR2014 [ 62 ], for checking the automatic crystal structure solution via different MR techniques.…”

“…For the nucleic acid structures, we selected 56 structures deposited in the PDB database (solved using MR techniques), thereby having observed diffraction data, unit cell information, space group symmetry, published sequences, and MR models available. Among these, 46 were used by Cascarano & Giacovazzo [ 56 ] as test cases to assess the effectiveness of the CAB approach for nucleic acid structures. The first 31 structures are DNA (SET DNA), and the remaining 25 structures are RNA fragments (SET RNA).…”

“…Popular AMB programs include BUCCANEER [ 49 ] for proteins, NAUTILUS [ 50 ] for nucleic acids, ARP/wARP [ 51 ] for proteins and nucleic acids, and the PHENIX AUTOBUILD wizard [ 52 ] for proteins and nucleic acids. Recently, a new cyclic AMB procedure called CAB [ 53 ], which uses BUCCANEER for protein model building and NAUTILUS for nucleic acids building, has been developed and shown to be highly efficient in experimental applications (see Papers I–III [ 54 , 55 , 56 ]).…”

Extending Ab Initio Phasing up to 2.2 Å Resolution: New Superposition Techniques

“…The DSR step (see Section 5) was able to substantially reduce the average phase error of 10 over 12 test structures up to a level suitable for succeeding in the automatic model building process (1crm and 1z1y are excluded). The AMB procedure of our pipeline is CAB [24,25], an AMB approach which cyclically applies BUCCANEER [26] and NAUTILUS [27] algorithms, respectively. The high quality of CAB has been shown in a recent paper [28], but, unfortunately, it is a program specifically written for molecular replacement studies.…”

ModelCraft: an advanced automated model-building pipeline using Buccaneer

“…If the output model does not have sufficient sequence coverage then the pipeline is repeated with modified input phases. A newer CAB II pipeline has been released that builds nucleic acid structures using Nautilus (Cowtan, 2014) with an updated library of backbone conformations (Cascarano & Giacovazzo, 2021).…”