BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank

  title={BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank},
  author={Jurgen F. Doreleijers and Steve Mading and Dimitri Maziuk and Kassandra Sojourner and Lei Yin and Jun Zhu and John L. Markley and Eldon L. Ulrich},
  journal={Journal of Biomolecular NMR},
Experimental constraints associated with NMR structures are available from the Protein Data Bank (PDB) in the form of `Magnetic Resonance' (MR) files. These files contain multiple types of data concatenated without boundary markers and are difficult to use for further research. Reported here are the results of a project initiated to annotate, archive, and disseminate these data to the research community from a searchable resource in a uniform format. The MR files from a set of 1410 NMR… 

BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures

We present two new databases of NMR-derived distance and dihedral angle restraints: the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED). These databases currently

A global analysis of NMR distance constraints from the PDB

  • W. Vranken
  • Computer Science
    Journal of biomolecular NMR
  • 2007
The analysis described here illustrates the importance of depositing constraints (and all other possible NMR derived information) along with the structure coordinates, as this type of information can greatly assist the NMR community.

RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank

The set of recalculated coordinates constitutes a unified database of protein structures in which potential user‐ and software‐dependent biases have been kept as small as possible and can be used by the structural biology community for further development of calculation protocols, validation tools, structure‐based statistical approaches and modeling.

Protein Data Bank: the single global archive for 3D macromolecular structure data

  • Stephen K Helen M Charmi Chunxiao Li Luigi Di Cole Jose M Burley Berman Bhikadiya Bi Chen Costanzo Christie S. Burley Y. Ioannidis
  • Chemistry
    Nucleic acids research
  • 2019
Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific ww PDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the

Refinement of Nmr-determined Protein Structures with Database Derived Distance Constraints

It is shown that with the increasing numbers of high quality protein structures being determined, a computational approach to enhancing the accuracy of the NMR-determined structures becomes possible by deriving additional distance constraints from the distributions of the distances in databases of known protein structures.


The BioMagResBank (BMRB: is a repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies of biological molecules. BMRB is a

PDBStat: a universal restraint converter and restraint analysis software package for protein NMR

The use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations is demonstrated, and the resulting protein NMR structure models are compared with those generated from the same NMR restraint data using more traditional structure determination methods.

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

A large-scale international collaborative effort to make all deposited experimental NMR data semantically and syntactically homogeneous, and thus useful for further research is described.

The accuracy of NMR protein structures in the Protein Data Bank

The use of ANSURR is reported to be used to analyse NMR ensembles within the Protein Data Bank (PDB), where most structures have accurate secondary structure, but are too floppy, particularly in loops.



The Protein Data Bank

The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.

Completeness of NOEs in protein structures: A statistical analysis of NMR data

The completeness of experimentally observed NOE restraints of a set of 97 NMR protein structures deposited in the PDB has been assessed. Completeness is defined as the ratio of the number of

STAR/mmCIF: An ontology for macromolecular structure

While the description of macromolecular structure and the x-ray crystallographic experiment used to derive it represent explicit data, the ontology is extensible and applicable to other less well-characterized data domains.

Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.

X-PLOR Version 3.1: A System for X-ray Crystallography and NMR

This manual to X-PLOR Version 3.1 presents the theoretical background, syntax and function of the programme and also provides a comprehensive list of references and sample input files with comments.


We present the development of a force field for simulation of nucleic acids and proteins. Our approach began by obtaining equilibrium bond lengths and angles from microwave, neutron diffraction, and

Solution structure of human GAIP (Galpha interacting protein): a regulator of G protein signaling.

It is suggested that other structural differences between the two proteins may be related to the process of binding as well as to a distinct efficiency in their respective GTPase activating function.