Verify3D was used to validate and evaluate the model's quality (Luthy et al. 1997). Molecular docking was used to elucidate the possible differences in binding of OUC-Csngly with two types of ligands: COSs and cello-oligosaccharides.... Biochemical characterization and cleavage pattern analysis of a novel chitosanase with cellulase activity
What are the advantages of using 3D profiles for testing models?
Verify3D was used to validate and evaluate the model's quality (Luthy et al. 1997). Molecular docking was used to elucidate the possible differences in binding of OUC-Csngly with two types of ...
What are the applications of 3D protein profiles?
01/01/1997 · The use of 3D profiles to verify protein models, illustrated with the correct and misfolded structures of hemerythrin, 1° both having 113 residues. The model on the left is the X-ray-derived structure. 11 A 3D profile calculated from its coordinates matches the sequence of hemerythrin with a score S c°r = 38.
What are 3D-1D scores?
VERIFY3D: assessment of protein models with three-dimensional profiles Methods Enzymol. 1997;277:396-404. doi: 10.1016/s0076-6879(97)77022-8. Authors D Eisenberg 1 , R Lüthy, J U Bowie. Affiliation 1 Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles 90095, USA. PMID: 9379925 DOI: 10.1016/s0076-6879(97)77022-8 No …
How does verify 3D determine the compatibility of an atomic model?
The three-dimensional (3D) profile of a protein structure is a table computed from the atomic coordinates of the structure that can be used to score the compatibility of the 3D structure model with any amino acid sequence. Three-dimensional profiles computed from correct protein structures match their own sequences with high scores.
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
How do you read 3D results?
On verify3D, a score of more than 80% means that your model has good quality - however you must check with other evaluation tolls such as voromqa, Proq3 etc to make sure you have a high quality model.
What is Q mean score?
QMEAN, which stands for Qualitative Model Energy ANalysis, is a composite scoring function describing the major geometrical aspects of protein structures. Five different structural descriptors are used. The local geometry is analyzed by a new kind of torsion angle potential over three consecutive amino acids.
What is a good GMQE?
In general a higher QSQE is "better", while a value above 0.7 can be considered reliable to follow the predicted quaternary structure in the modelling process. This complements the GMQE score which estimates the accuracy of the tertiary structure of the resulting model.
What does GMQE mean?
GMQE (Global Model Quality Estimation) is is expressed as a number between 0 and 1, reflecting the expected accuracy of a model built with that alignment and template, normalized by the coverage of the target sequence. Higher numbers indicate higher reliability.
What is SWISS-MODEL used for?
SWISS-MODEL (http://swissmodel.expasy.org) is a server for automated comparative modeling of three-dimensional (3D) protein structures. It pioneered the field of automated modeling starting in 1993 and is the most widely-used free web-based automated modeling facility today.