PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.
What is ProCheck software?
PROCHECK: validation of protein‐structure coordinates @article{Laskowski2012PROCHECKVO, title={PROCHECK: validation of protein‐structure coordinates}, author={Roman A. Laskowski and Malcolm W Macarthur and Janet M. Thornton}, journal={International Tables for Crystallography}, year={2012}, pages={684-687} } R. Laskowski, M. W. Macarthur, J. Thornton; Published 14 April …
What is Procheck-NMR?
14/04/2012 · Abstract The structure-validation program PROCHECK is described. Skip to Article Content; Skip to Article Information; Search within ... Search term. Advanced Search Citation Search. Search term. Advanced Search Citation Search. Login / Register. Chapter 21.4 PROCHECK: validation of protein-structure coordinates. Volume F. Crystallography of …
What is the best software for protein model validation?
14/04/2012 · PROCHECK: validation of protein-structure coordinates. Volume F. Crystallography of biological macromolecules. Second Online Edition (2012) Part 21. Structure validation. R. A. Laskowski, Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England. Search for more papers by this author. M. W. MacArthur, …
What programs are used to check the quality of protein structures?
PROCHECK: validation of protein structure coordinates, in International Tables of Crystallography, Volume F. Crystallography of Biological Macromolecules, eds. Rossmann M G & Arnold E, Dordrecht, Kluwer Academic Publishers, The Netherlands, pp. 722-725. Morris A L, MacArthur M W, Hutchinson E G & Thornton J M (1992). Stereochemical quality of protein structure …
How do you run Procheck?
To run PROCHECK:Enter the 4-letter PDB code of the protein of interest, its chain ID (if required) and its resolution.Click on RUN to run the program.Click on Reset to enter new code.
How do I validate a Ramachandran plot?
Ramachandran validation of protein structures is commonly performed using developments, such as MolProbity. We suggest tailoring such analyses by position-wise, geometry-specific steric-maps, which show (φ,ψ) regions with steric-clash at every residue position.
Which software is used for protein structure analysis?
Homology modelingNameMethodLinkESyPred3DTemplate detection, alignment, 3D modelingserverFoldXEnergy calculations and protein designdownloadPhyre and Phyre2Remote template detection, alignment, 3D modeling, multi-templates, ab initioserverHHpredTemplate detection, alignment, 3D modelingserver download article11 more rows
How do you test protein structure?
Specific Structure ChecksStereochemical Validation. All chiral centers of proteins and nucleic acids are checked for correct stereochemistry. ... Atom Nomenclature. ... Close Contacts. ... Ligand and Atom Nomenclature. ... Sequence Comparison. ... Distant Waters. ... Checks against Experimental Data. ... Validation Server.
What is Ramachandran plot used for?
The Ramachandran plot provides a way to view the distribution of torsion angles in a protein structure and shows that the torsion angles corresponding to the two major secondary structure elements (α-helices and β-sheets) are clearly clustered within separate regions.
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.
Which tool is used to find structural similarities in proteins?
MinRMS: A Tool for Determining Protein Similarity. MinRMS is a program for finding minimal root-mean-squared-distance (RMSD) alignments between two proteins as a function of the number of matching residue pairs within a heuristically limited search space.
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
Which one of the following tools can be used for both modeling the protein and structure visualization?
MODBASE stores comparative models for all protein sequences detectably related to a known protein structure and additionally links each model to a number of external databases. MODVIEW can be used to visualize the models and alignments stored in the databases.
What is validation of a structure?
Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids. ... Essential to their biological functions are the detailed 3D structures of the molecules and the changes in those structures.
How do you validate the 3D structure of a protein?
You may validate it through SAVES server. There are 4-5 servers in it like Errat, Verify3D, Ramachandran plot etc. You may run all of those to validate the structure. Also in addition, you may validate it through ProSA web server which analyze the protein structure and matches with X-Ray and NMR calculated structures.24-Dec-2014
What is a good Errat score?
ERRAT is a so-called “overall quality factor” for non-bonded atomic interactions, with higher scores indicating higher quality. The generally accepted range is >50 for a high quality model.02-Apr-2013
Key references
Laskowski R A, MacArthur M W, Moss D S, Thornton J M (1993). PROCHECK - a program to check the stereochemical quality of protein structures. J. App. Cryst., 26, 283-291.
Related references
Laskowski R A, MacArthur M W, Thornton J M (2001). PROCHECK: validation of protein structure coordinates, in International Tables of Crystallography, Volume F. Crystallography of Biological Macromolecules , eds. Rossmann M G & Arnold E, Dordrecht, Kluwer Academic Publishers, The Netherlands, pp. 722-725.