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MolProbity: all-atom structure validation for macromolecular crystallography.

Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC - Acta Crystallogr. D Biol. Crystallogr. (2009)

Bottom Line: However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers.It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures.MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, Duke University, Durham, NC 27710, USA.

ABSTRACT
MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

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MolProbity-relevant quality criteria as a function of time for all structures in the PDB at a middle range of resolution, separately fitted before and after introduction of the web site. (a) All-atom clashscore (see §2.2); (b) percentage of Asn/Gln/His flips (see §2.1).
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fig8: MolProbity-relevant quality criteria as a function of time for all structures in the PDB at a middle range of resolution, separately fitted before and after introduction of the web site. (a) All-atom clashscore (see §2.2); (b) percentage of Asn/Gln/His flips (see §2.1).

Mentions: To evaluate the contribution MolProbity has made to crystallographic model quality in general, we have therefore plotted clashscore and Asn/Gln/His flips as a function of time in Fig. 8 ▶, with separate linear fits before and after the end of 2002. Gratifyingly, in both cases there is a clear trend of improvement since 2003. Median values also improve very steadily over that period. Anecdotal evidence indicates that this trend is mainly a consequence of thorough adoption of MolProbity-based methods by a small but growing fraction of crystallographers and there is therefore still much scope for further improvement in the future.


MolProbity: all-atom structure validation for macromolecular crystallography.

Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC - Acta Crystallogr. D Biol. Crystallogr. (2009)

MolProbity-relevant quality criteria as a function of time for all structures in the PDB at a middle range of resolution, separately fitted before and after introduction of the web site. (a) All-atom clashscore (see §2.2); (b) percentage of Asn/Gln/His flips (see §2.1).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2803126&req=5

fig8: MolProbity-relevant quality criteria as a function of time for all structures in the PDB at a middle range of resolution, separately fitted before and after introduction of the web site. (a) All-atom clashscore (see §2.2); (b) percentage of Asn/Gln/His flips (see §2.1).
Mentions: To evaluate the contribution MolProbity has made to crystallographic model quality in general, we have therefore plotted clashscore and Asn/Gln/His flips as a function of time in Fig. 8 ▶, with separate linear fits before and after the end of 2002. Gratifyingly, in both cases there is a clear trend of improvement since 2003. Median values also improve very steadily over that period. Anecdotal evidence indicates that this trend is mainly a consequence of thorough adoption of MolProbity-based methods by a small but growing fraction of crystallographers and there is therefore still much scope for further improvement in the future.

Bottom Line: However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers.It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures.MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, Duke University, Durham, NC 27710, USA.

ABSTRACT
MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

Show MeSH