Fold Assessment Software
General Description
This web site contains a
fold assessment software that relies on the GA341 multivariate scoring
function. A benchmark of the performance of this scoring function in fold
assessment has been recently described (Melo and Sali, 2007).
The general working pipeline
of this scoring function is shown in Figure 1. The GA341 scoring function depends on
three independent variables: 1) The compactness of the model, 2) a combined
statistical potential z-score of the model, and 3) the percentage sequence
identity of the target-template alignment that was used to build the model.
Figure 1:
Fold assessment scheme.
The GA341 score depends on
three variables: the percentage sequence identity is calculated from the
alignment that was used to build the model, while the compactness (Methods) and
the combined statistical potential z-score (Melo et al. 2002) are calculated from the 3D
model itself. Next, the length of the model and the GA341 score are plugged into a
naive Bayesian classifier to obtain the conditional probability that the model
is correct, pC(GA341, length).
Typically, pC of at least 0.7
predicts that the model is correct; otherwise it is classified as incorrect.
The software is distributed
as a bunch of executable programs for LINUX OS. The programs can be easily
integrated with a simple script. The software is distributed with no warranties
and it is responsibility of the user how the software is used and how the
results are interpreted.
Raw data
|
File
name |
Type |
File
format |
General
description |
|
Programs |
Binary files |
This archive contains all the executable programs for LINUX OS and the
required data libraries. |
|
|
Help file |
Plain text |
README file that explains how to run each program and what each program does. |
References
|
Melo, F. and Sali, A. (2007) |
|
Melo, F., Sánchez, R., and
Sali, A. (2002) |
|
Sali,
A., Fiser, A., Sanchez, R., Marti-Renom, M.A., Jerkovic, B., Badretdinov, A.,
Melo, F., Overington, J., and Feyfant, E. (2001). MODELLER, A Protein Structure Modeling Program,
Release 6v0. |