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.Dec 21, 2009
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.
What is a good Clashscore?
Summary statistics. Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms. * 100th percentile is the best among structures of comparable resolution; 0th percentile is the worst.
What are poor Rotamers?
Rotamers: Refers to the geometry of the amino acid side chains. The number indicates the number of amino acids in the poor or favored category and the percentage of amino acids that fall into those categories. If there is a high percentage of poor rotamers (>1.5%), this can be concerning.Aug 31, 2020
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 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).
What are steric clashes?
Steric clash is one of the artifacts prevalent in low-resolution structures and homology models. Steric clashes arise due to the unnatural overlap of any two nonbonding atoms in a protein structure.
What is VERIFY3D?
The program VERIFY3D provides this link by reducing a 3D structure to 1D string of environmental classes. Therefore the method can be used to evaluate any protein model or to measure the compatibility of any protein structure with its amino-acid sequence.
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.
What is Cablam outlier?
Residues that fall outside these contours are considered outliers and are reported in validation feedback. cablam_validate also compares local CA geometry measures which are robust at low resolution against contours of expected secondary structure behavior.
How is Ramachandran plot generated?
The plot was developed in 1963 by G. N. Ramachandran, et. al. by plotting the φ values on the x-axis and the ψ values on the y-axis, as for the image at left.
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)
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.
What is molprobity software?
MolProbity is a research, software, and service project that deals with large volumes of complex data. The service component performs comprehensive validation on individual macromolecular structures, where it pays special attention to the local anomalies which are usually errors but sometimes valid and biologically important. After producing effective, user-friendly software that creates user demand, the over-riding requirement for service is near-24/7 uptime of the website. That both requires long-term management and equipment upgrades to maintain capacity, run speed, and security, and also requires constant short-term attention: automatic monitoring where feasible, attention to user alerts, and frequent checks of the server state for possible hardware failures, persistent attack trials, or hung jobs. Our team, especially the system manager, almost always notice and fix problems within a few hours, nearly all of which is set up so it can be done remotely.
What is molprobity analysis?
MolProbity performs covalent bond geometry analysis for both mainchain and sidechain atoms in protein and nucleic acids, now using the Phenix geometry libraries. Bond lengths or angles more than 4σ from the expected value are considered outliers, and are flagged in both chart and graphical forms. Another validation unique to MolProbity is the Cβ deviation, 11 a combination of covalent angles and chirality around the Cα that flags geometry problems there much more effectively than simply analyzing individual variables. Large Cβ deviations usually mean that either the sidechain or the backbone has been misfit at that residue.
What is moleprobity?
MolProbity is a widely used system of model validation for protein and nucleic acid structures, accessed at http://molprobity.biochem.duke.edu. It builds upon the work of earlier systems such as ProCheck, 1 WhatIf, 2 and Oops, 3 which introduced the use of validation by Ramachandran-plot and sidechain rotamer criteria. It complements systems for validating data 4, 5 and model-to-data match such as Rfree 6 or real-space residual. 7 MolProbity has some features specifically tailored for X-ray crystallography, and is also suitable, and used, for cryoEM, neutron, NMR, and computational models. MolProbity's unique feature of all-atom contact analysis (including hydrogens) was described in 1999, 8, 9 followed by its complementary rotamer, Ramachandran, and Cβ deviation criteria, 10, 11 and the initial MolProbity web service. 12 Validation of RNA backbone, interfaces, and NMR ensembles, a large speedup for Reduce, and an entirely new web interface were described in 2007. 13 Implementation of many MolProbity validations inside the Phenix crystallography package, an emphasis on helping users correct specific types of outliers, and the resulting improvements in clashscore and Asn/Gln/His flips were reported in 2010. 14
Why is macromolecular structure validation important?
More recently, its importance is recognized as a way for end-users of those structures to evaluate reliability both overall and in local detail, and especially for structural biologists to improve the accuracy of their models throughout the process of structure solution. MolProbity continues to enhance its capability at performing all those functions. That enhancement process requires ongoing infrastructure improvement and also the development of new or extended validation criteria that can be optimally helpful for molecular systems at lower resolutions and for the characteristics of new structural biology techniques. New criteria typically come from solidly researched empirical or theoretical recognition of further regularities and relationships in macromolecular structure, and then formulating them in ways that can reliably improve the practice and the results of structural biology. We do such research ourselves, and also seek to apply it from the results of others.