Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NEF and NMR-STAR formats provide...
[NMR paper] Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank
Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank
Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NMR exchange (NEF) and NMR-STAR...
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[NMR paper] The accuracy of NMR protein structures in the Protein Data Bank
The accuracy of NMR protein structures in the Protein Data Bank
The program ANSURR measures the accuracy of NMR structures by comparing rigidity obtained from experimental backbone chemical shifts and from structures. We report on ANSURR analysis of 7,000 PDB NMR ensembles within the Protein Data Bank, which can be found at ansurr.com. The accuracy of NMR structures progressively improved up until 2005, but since then, it has plateaued. Most structures have accurate secondary structure, but are generally too floppy, particularly in loops. Thus, there is a...
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[NMR paper] PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.
PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.
PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.
J Biomol NMR. 2013 Jul 30;
Authors: Tejero R, Snyder D, Mao B, Aramini JM, Montelione GT
Abstract
The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use...
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07-31-2013 12:00 PM
PDBe Protein Data Bank in Europe
PDBe Protein Data Bank in Europe
PDBe, Protein Data Bank in Europe, is part of the EBI-EMBL, and serves as a European resource for PDB protein structure deposition annotation to the wwPDB. We provide powerful 3D structure search services and analysis tools for PDB data related to structures of proteins, nucleic acids, carbohydrates, small molecules, ligands, drugs and antibiotics.We integrate data from Interpro, Uniprot, GO, CATH, SCOP, Pfam, etc. through the SIFTS project to enrich the data held in the Protein Data Bank
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Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Proteins. 2011 Jan 6;
Authors: Bernard A, Vranken WF, Bardiaux B, Nilges M, Malliavin TE
The classical procedure for nuclear magnetic resonance structure calculation allocates empirical distance ranges and uses historical values for weighting factors. However, Bayesian analysis suggests that there are more optimal...
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03-03-2011 12:34 PM
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Open Biochem J. 2010;4:83-95
Authors: Sikic K, Tomic S, Carugo O
Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in...
Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank
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