What is MolProbity used for?

What is MolProbity used for?

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes.

What is MolProbity?

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.

How do you cite MolProbity?

Cite MolProbity: Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21.

What is the PDB code?

Every molecular model (atomic coordinate file) in the Protein Data Bank (PDB) has a unique accession or identification code. These codes are always 4 characters in length. Plans for an expanded identification code system that handle more entries have been announced.

What does Ramachandran plot tell you?

The Ramachandran plot is a plot of the torsional angles – phi (φ)and psi (ψ) – of the residues (amino acids) contained in a peptide. By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides.

Why we use Ramachandran plot?

What angle is phi?

Typical values are phi = -140 degrees and psi = 130 degrees. In contrast, alpha-helical residues have both phi and psi negative.

How do I find my PDB ID for protein?

To find it, simply enter the PDB code in the search slot found at the left of this (and every) page in Proteopedia. Proteopedia is updated once each week, shortly following the weekly new release cycle at the PDB.

What does Rcsb PDB stand for?

Research Collaboratory for Structural Bioinformatics
RCSB PDB (Research Collaboratory for Structural Bioinformatics PDB) operates the US data center for the global PDB archive, and makes PDB data available at no charge to all data consumers without limitations on usage (Policies).

What is the PSI angle?

A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the union of a line and two half-planes that have this line as a common edge.

What kind of web server is MolProbity for?

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes.

What do you need to know about MolProbity?

MolProbity is a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules and can calculate and display the H-bond and van der Waals contacts in the interfaces between components.

How does MolProbity improve the Protein Data Bank?

Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity’s unique all-atom clashscore.

Where can I find a mirror of MolProbity?

There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria.

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