The Job Name is used to identify the status in the queue and to display the results.
To use the evaluation server, input of the MODELLER license key is required. For further information, please consult http://salilab.org/modeller/registration.html.
An email will be sent to the input email address, once the calculations are finished.
Input model file in PDB format (see http://www.pdb.org)
Optional input alignment file in PIR format (see MODELLER manual).
Please note that the second field in line two of the structure entry should
contain a pdb code (without chain) of a template file currently available in
the PDB database.
The TSVMod score is significantly more reliable if:
The calculation of the GA341 score requires the target-template sequence identity. For model files produced by MODELLER, this information will be taken from the PDB header.
TSVMod predicts the RMSD and the Native Overlap (at 3.5 Å cutoff) of
a model with its native structure, using a support vector machine (SVM).
The predicted root-mean-squared deviation (RMSD) between the coordinates of the Cα atoms in the model and in the native structure.
Fraction of model Cα atoms that are predicted to be within 3.5 Å of their positions in the native structure.
The standard relax count is 1. If not enough similar structures are found in the training set, the default boundaries are relaxed incrementally.
Number of similar structures used to compute the results
Using probability theory, we derive an atomic distance- dependent statistical potential from a sample of native structures that does not depend on any adjustable parameters (Discrete Optimized Protein Energy, or DOPE). DOPE is based on an improved reference state that corresponds to noninteracting atoms in a homogeneous sphere with the radius dependent on a sample native structure; it thus accounts for the finite and spherical shape of the native structures. The evaluation server reports the normalized z-DOPE score.
DOPE energy profile, smoothed over a 15 residue window, normalized over the number of DOPE restraints acting on each residue.
Score for the reliability of a model, derived from statistical potentials (F. Melo, R. Sanchez, A. Sali, 2002). A model is predicted to be reliable when the model score is higher than a pre-specified cutoff (0.7). A reliable model has a probability of the correct fold that is larger than 95%. A fold is correct when at least 30% of its Cα atoms superpose within 3.5Å of their correct positions.
A surface statistical potential that contributes to GA341.
A pairwise statistical potential that contributes to GA341.
A combined statistical potential that contributes to GA341.
For more information, please consult the following publications: TSVMod: D. Eramian, N. Eswar, M.Y. Shen, A. Sali. How well can the accuracy of comparative protein structure models be predicted? Protein Sci 17, 1881-1893, 2008. DOPE: M.Y. Shen, A. Sali. Statistical potential for assessment and prediction of protein structures. Protein Sci 15, 2507-2524, 2006. GA341: F. Melo, R. Sanchez, A. Sali. Statistical potentials for fold assessment. Protein Sci 11, 430-448, 2002.