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NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB

J. F. Doreleijers, W. F. Vranken, C. Schulte, J. L. Markley, E. L. Ulrich, G. Vriend, G. W. Vuister
2011 Nucleic Acids Research  
We appreciated Akira Kinjo's advice for setting up a local slave of PDBj Mine. We are especially indebted to all the authors providing wwPDB with the fruits of their labor.  ...  We enjoyed the advice and constructive criticism from all CCPN developers in Cambridge and Tim te Beek, Karen Berntsen, Vincent Breukels, Maarten Hekkelman, Wilmar Teunissen and Wouter Touw in Nijmegen  ...  AVAILABILITY Reports Currently all wwPDB members (RCSB-PDB, PDBe, PDBj and BMRB) include links to the NRG-CING reports. These pointers drive the vast majority of traffic to the NRG-CING database.  ... 
doi:10.1093/nar/gkr1134 pmid:22139937 pmcid:PMC3245154 fatcat:4e3djnotandizjix7im24lesja

The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries

Jurgen F. Doreleijers, Wim F. Vranken, Christopher Schulte, Jundong Lin, Jonathan R. Wedell, Christopher J. Penkett, Geerten W. Vuister, Gert Vriend, John L. Markley, Eldon L. Ulrich
2009 Journal of Biomolecular NMR  
et al. in Proteins 59:662-672, 2005; Saccenti and Rosato in J Biomol NMR 40:251-261, 2008).  ...  Several pilot experiments have indicated that improvements in older NMR structures can be expected by applying modern software and new protocols (Nabuurs et al. in Proteins 55:483-186, 2004; Nederveen  ...  use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.  ... 
doi:10.1007/s10858-009-9378-z pmid:19809795 pmcid:PMC2777234 fatcat:gdnkbqlzivebvfy3s6kksbuvem

CING: an integrated residue-based structure validation program suite

Jurgen F. Doreleijers, Alan W. Sousa da Silva, Elmar Krieger, Sander B. Nabuurs, Christian A. E. M. Spronk, Tim J. Stevens, Wim F. Vranken, Gert Vriend, Geerten W. Vuister
2012 Journal of Biomolecular NMR  
We present a suite of programs, named CING for Common Interface for NMR Structure Generation that provides for a residue-based, integrated validation of the structural NMR ensemble in conjunction with  ...  the experimental restraints and other input data.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s)  ... 
doi:10.1007/s10858-012-9669-7 pmid:22986687 pmcid:PMC3483101 fatcat:qi4f6yatcvczbevdljn2kfntc4

Structural basis for proteintrans-splicing by a bacterial intein-like domain - protein ligation without nucleophilic side chains

A. Sesilja Aranko, Jesper S. Oeemig, Hideo Iwaï
2013 The FEBS Journal  
Database The resonance assignments and structure coordinates have been deposited in BMRB (18653) and RCSB (2LWY) Abbreviations Cth, Clostridium thermocellum; BIL, bacterial intein-like; GB1, the B1 domain  ...  We determined the first solution NMR structure of a BIL domain, CthBIL4, to guide engineering of split BIL domains for protein ligation.  ...  This project was supported by the Academy of Finland (137995), the Sigrid Juselius Foundation and Biocenter Finland (NMR and mass-spectrometry facilities at the Institute of Biotechnology).  ... 
doi:10.1111/febs.12307 pmid:23621571 fatcat:at4hx2dyafha5hnnjytkjyv35u