Verify3D is a web-based tool that evaluates the correctness of a protein structure model based on its 3D structural profile. It works by assigning structural classes to residues based on their location and environment, then comparing the results to profiles of good protein structures. The tool generates plots representing the average and raw scores for each residue, with higher average scores across residues indicating a more correct model structure. Verify3D is useful for protein structure prediction as it can verify models based on how well their 3D profiles match their amino acid sequences.

1. Verify 3D

2. Content
● Introduction
● Objectives
● Input & Output
● Methodology
● Results Analysis
● Conclusion

3. 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) and
comparing the results to good
structures.
Introduction

4. “VERIFY3D (Assessment of Protein Models
With Three-Dimensional Profiles) tool is
utilized to evaluate the correctness of a
protein model by its 3D profile.”

5. Objectives
Available on
Verify3D is a web
based tool that can
accessed through any
web browser.
Research
Outcome
The correctness of a
protein model can be
verified by its 3D
profile.
Analyzes
Verify3D is utilized
for protein model
evaluation by its 3D
Profile.

6. Input
The server requires
to upload the file
containing the
target protein
structure in PDB
format.
The server results in
plots depending
upon the chains
present in the
query protein.
Output
Input & Output

7. Plotting
Generates number
of plots depends
upon the number of
chains
Verify3D Test
Good predicted structure
of a protein must have
80% or more average
score.
Evaluation
Utilized for protein
model evaluation by its
3D Profile.
Plots
Greater the number of
chains present in the
protein model, greater
will be the number of
plots
Correctness
Correctness of a
protein model can be
verified by its 3D
profile
Methodology
3D Profiles
3D profile of a protein
structure can be used to
score the compatibility of
the 3D structure

8. This is how Verify3D evaluates the
protein models, generating plot
which represents averaged score
and raw score for each residue in
the predicted or experimentally
determined model.

9. Dots Interpretation
1st Green Raw Score (Score for each amino
acid residue)
2nd Blue Average Score (Score for overall
residues)
Results Analysis
Table represents the interpretation of plots:

10. Verify3D utilizes the three-
dimensional profiles
computed from correct
protein structures match
their own sequences with
high scores for protein
model evaluation.
Conclusion

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