The MolProbity server, developed by the Richardson group [1,2], is a site for the evaluation of single X-ray structures and NMR structure ensembles. The server performs a number of validations including all-residue Ramachandran analysis, rotamer analysis, and all-atom clash analysis.
Full Answer
What is MolProbity used for?
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.
What does MolProbity score mean?
"[The MolProbity score] is a log-weighted combination of the clashscore, percentage Ramachandran not favored and percentage bad side-chain rotamers, giving one number that reflects the crystallographic resolution at which those values would be expected.
How do you reference MolProbity?
Cite MolProbity: Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21. Davis et al.
What are favored rotamers?
In the new system developed here, a score of <0.3% qualifies as a rotamer outlier – its score is worse than 99.7% of the good data. Scores ≥ 0.3% and < 2.0% are considered allowed while those ≥ 2.0% are considered favored, as is traditional for Ramachandran criteria [18, 28].
What does a Ramachandran plot show?
The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. In theory, the allowed regions of the Ramachandran plot show which values of the Phi/Psi angles are possible for an amino acid, X, in a ala-X-ala tripeptide (Ramachandran et al., 1963).
How do you cite Pdbsum?
PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank....PDBsum.ContentAuthorsRoman Laskowski & al. (1997)Primary citationPMID 9433130AccessWebsitewww.ebi.ac.uk/pdbsum/8 more rows
What is verify3d?
Determines the compatibility of an atomic model (3D) with its own amino acid sequence (1D) by assigning a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures.
What is CaBLAM outlier?
As a general rule, CaBLAM outliers usually indicate a problem with the orientations for one or more peptide planes. Look for a way to reorient the peptide either to remove clashes or establish hydrogen bonds.
What is a Rotamer?
rotamer (plural rotamers) (chemistry) any of a set of conformers that arise from restricted rotation around a single bond.
What is a Rotamer protein?
In proteins, the sidechain of an amino acid can take different positions. These positions are called rotamers. Foldit puzzles may also contain non-protein molecules called ligands. In some cases, small molecule ligands may have multiple rotamers as well.
What is a Ramachandran outlier?
Ramachandran outliers are those amino acids with non-favorable dihedral angles, and the Ramachandran plot is a powerful tool for making those evident. Most of the time, Ramachandran outliers are a consequence of mistakes during the data processing.
Uploading a PDB
PDB files are quickly uploaded, and in the case of NMR ensembles, divided into individual PDB files. One next analyzes all-atom contacts and geometry (Figure 1). There is also an “add hydrogens” tool for X-ray structures, which is useful for comparison of NMR/X-ray structure pairs.
Structure Analysis in KiNG
Structures can be analyzed using the interactive 3D software package KiNG (Figure 2). The kinemage files feature various structure validation metrics mapped onto the structures (s), including close contacts (pink dots), Ramachandran outliers (green lines) and bad rotamers (yellow side chains).
Ramachandran Analysis
The MolProbity output also includes a complete Ramachandran analysis of all residues in all models, which can be downloaded as a pdf file. Here is an example Ramachandran output file: 2KIF-rama.pdf.
What is molprobity web service?
MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculates global and local validation for all-atom contacts (steric clashes, H-bonds & vdW), covalent geometry, and conformation (Ramachandran & rotamers for protein, ribose puckers & suite conformers for RNA). Results are displayed online as 3D graphics and sortable charts.
Why are pro and gly important?
Pro, and Gly (important because Gly φ,ψ angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of α-helix, which rates as favorable in energy yet rarely occurs.
Authors
MolProbity is a web application that integrates validation programs from the Richardson lab at Duke University.
Purpose
MolProbity provides the user with an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. It combines all atom contact analysis with updated versions of more traditional tools for validating geometry and dihedral-angle combinations.
Usage
The integrated MolProbity web application is at http://molprobity.biochem.duke.edu/ . The user is guided through a work-flow that typically consists of:
Literature
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids I. W. Davis, A. Leaver-Fay, V. B. Chen, J. N. Block, G. J. Kapral, X. Wang, L. W. Murray, W. B. Arendall, III, J. Snoeyink, J. S. Richardson, and D. C. Richardson. Nucl. Acids Res. 35: W375-W383 (2007)
How to access MolProbity?
MolProbity is typically accessed by pointing a web browser to http://kinemage.biochem.duke.edu (where related software and documentation are available) and then clicking the MolProbity logo. The current interface has a main page that evolves during the session as the user makes choices.
What is molprobity used for?
MolProbity also uses carefully filtered, high-accuracy Ramachandran and rotamer distributions to check mainchain and sidechains for conformational outliers. Finally, it reports on some novel geometric indicators of misfitting, such as the Cβ deviation ( 18) and the base-phosphate perpendicular distance.
What is moleprobity analysis?
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.
What is molprobity workflow?
MolProbity is a flexible tool and can be used for many different purposes, but typical use follows one of two patterns, depending on whether the user is a ‘producer’ of structures or a ‘consumer’ of someone else's structures.
How long has MolProbity been around?
The MolProbity server has been operating continuously for more than 5 years now, with hundreds of different users per month and thousands of sessions. Thousands of different scientists have accessed it since its inception, and more structure files have been run through MolProbity than the number of files deposited in the PDB. About 80% of MolProbity sessions use uploaded files, and 20% fetch database files.
What is sugar pucker in RNA?
RNA sugar pucker (C3′ endo or C2′ endo) is strongly correlated to the perpendicular distance between the following (3′) phosphate and either the plane of the base or the C1′–N1/9 glycosidic bond vector . Incorrectly chosen sugar puckers also often result in out-of-range values for the epsilon dihedral. This is important information, because a sugar pucker is very difficult to determine directly from the electron density at resolutions typical for large RNAs. MolProbity checks epsilon angles and checks the modeled sugar pucker against the base-phosphate distance; it flags outliers as potentially having the wrong pucker.
Is MolProbity a job submission form?
However, MolProbity is not a mere job-submission form; it is a complex web application that offers multiple modes of use, integrates many different kinds of information and suggests courses of action based on that information. MolProbity uses a variety of physics- and knowledge-based algorithms to analyze a structure.