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## Reference
If you use the results of the CS23D2.0 server in a publication, please cite the following paper: ## Tables
et al. Structure
validation by Calpha geometry: phi,psi and Cbeta deviation.
2003 Feb 15;50(3):437-50. The fewer violations, the better the structure. Ideally there should
be no violations.trans# Omega violations - indicates the number of residues that have Omega angles that are not in the range 180.0 ± 12.5 degrees or 0.0 ± 15.0 degrees. Ideal Omega angles for peptide bonds are 180 degrees while Ideal Omega angles for cis peptide bonds are 0
degrees.J. Mol. BiolMean chemical shift correlation - indicates the Pearson correlation coefficient calculated between input chemical shifts and those calculated by SHIFTX for the structure generated by CS23D2.0. Values closer to 0.9 are optimal. Values less than 0.7 indicate possible problems with the structure. HCount (%) - indicates the percentage of residues in the protein that are involved in canonical hydrogen bonds. Good structures have higher percentages of "good" or canonical hydrogen bonds. Values approaching 80% are ideal. To ensure consistency, hydrogen atoms for all structures were replaced by those from Reduce v3.10 (Word, et al.(1999) "Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation" . Biopolymers285, 1733-1745).
Average H-bond energy - indicates the average H-bond energy calculated in kcal/mol (using the DSSP definitions of Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. .
1983 Dec;22(12):2577-637). Average H-bond energy indicates how close H-bonds are to ideal
geometry. The lower the average H-bond energy, the better the structure is.
## Figure 1. Dependence of backbone RMSD of CS23D2.0 models on template sequence identity for different methods of structure generationA scatter plot showing the performance of CS23D2.0´s three approaches to structure generation (subfragment assembly + homology modeling, chemical shift threading and ab initio structure generation) relative to the level of sequence identity of the matching templates or subfragments. Data from Tables 3-6 in the CS23D2.0 web documentation pages was used to assemble this graph.## Energy Function## SummaryCS23D2.0 uses an energy function consisting of several statistics-based pseudo-potentials:Chemical shift correlation scores for HA, HN, N, CA, CB, and CO chemical shifts.
Chemical shifts for the CS23D2.0 models are predicted using SHIFTX, and,
after subtraction of random coil shifts for CA and CB shifts, correlation
coeffecients are determined between these predicted chemical shifts and the experimental
chemical shifts submitted by the user. A threading potential. Bump score for backbone atoms plus C-Beta and C-Gamma atoms. Hydrogen bond count. Ramachandran score counting phi and psi torsion angle violations. Omega score counting omega angle violations. Chi score based on expected chi angles for different phi and psi combinations. Radius of gyration, giving a penalty if the calculated radius of gyration
deviates from the expected value by more than 10%. Hydrogen bond energy. Disulphide bond count. Secondary structure score, based on the similarity between the secondary structure
of the CS23D2.0 3-D model and the expected secondary structure. The expected secondary
structure is normally based on that predicted by a sequence homology match to the PPT-DB 2º Structure (Cytoplasmic)
database.
If, however, this predicted secondary structure is more than 50% different from the
secondary structure predicted from the chemical shifts by CSI,
the CSI-predicted secondary structure is used as the expected secondary structure. ## Score WeightingEach of the initial terms in the energy function are transformed through a series of steps: (1) They are multiplied so that they behave as energy-like terms, i.e. more negative scores indicate a better structure. (2) They are scaled so that they all have close to the same order of magnitude (about ± 1 to 100). (3) All scores except for the chemical shifts scores and the radius of gyration score are normalized by dividing by the number of residues in the peptide, and then multiplying by 100 to re-scale them. (4) All scores are multiplied by weights that were determined based on training of the energy function on CASP7 decoys and decoys generated by Rosetta.The initial score calculations, plus the results of steps (1) and (2) are: Chemical shift correlation values (0.0 to 1.0) is multiplied by -10.0. threading potential is multiplied by 0.2. bump score, for all pairs of atoms that are closer than the
allowed threshold distances, the magnitude of the difference between the observed distance
and the threshold, in Angstroms, is added to the score. Any distances closer than 70% of
the threshold receive an additional penalty of +10. The initial bump score is multiplied
by 0.5. hydrogen bond count (the number of hydrogen bonds) is multiplied by -1.1. Ramachandran score is calculated based on Ramachandran tables with four
angle classes: 3 (good), 2 (acceptable), 1 (minimal), 0 (disallowed). For each residue,
this class number r is used to generate a Rama score value of (3 - r)²,
and the sum of all these values over all residues is calculated. To the final score is then
added the fraction of residues that did not have an r value of 3. omega score, if an omega angle is not within ±12.5° of 180°
or within ±15° of 0°, then the magnitude of the difference between the
omega angle and these thresholds is added to the omega score. chi score is based on the fact that chi angles cluster into three main groups
for each residue. Each chi angle is assigned to the chi group to which it is closest, and
the probability of observing that chi group given the phi and psi angles of the residue is
subtracted from the chi score. radius of gyration score, if the calculated radius of gyration is not
within 10% of the expected radius of gyration, the magnitude of the difference between
the real and expected values is used as the intial radius of gyration score. The initial
score is multiplied by 2.5. hydrogen bond energy score, the sum of all the hydrogen bond energies is
calculated. The sum is divided by the number of residues and multiplied by 40.0. disulphide bond count is multiplied by -3.0. secondary structure score, the sum of all secondary structure mismatch
scores in the peptide is calculated: +4 for Beta-strand or helix matched with coil, and
+8 for Beta-strand residues matched with helix residues. The weightings for step (4) for the above scores, other than the chemical shift scores, were trained on decoys from CASP7 using linear regression-based fitting. The weights for the chemical shift scores were trained separately on Rosetta decoys of structures with known chemical shifts; both ab-initio Rosetta decoys and Rosetta decoys generated from relaxing the native structures. The relative weighting between the chemical shift scores and the other scores was then determined based on linear regression. The weights in step (4) are multiplied by the values in step (3) to obtain the final scores. The step (4) weights are:
† Adjusted manually to a low value because training set it to 0. ## CS23D2.0 Results AssessmentA CS23D2.0 results summary for a structure prediction includes the mean chemical shift correlation values before and after energy minimization. The reliability of the final structure is guaged by looking at the final mean chemical shift correlation:0.75 - 1.00 = High 0.65 - 0.75 = Good 0.55 - 0.65 = Moderate 0.00 - 0.55 = PoorA CS23D2.0 results summary also prints information on torsion angle violations. The expected number of torsion angles in the core, allowed, generous and disallowed regions is estimated based on the following percentages: #res in phi/psi core 90% #res in phi/psi allowed 7% #res in phi/psi generous 1% #res in phi/psi disallowed 0% #res in omega allowed 99% #res in omega disallowed 1%Note: The first and last residues are not use for phi/psi, and the last residue is not used for omega. ## Torsion Angle Mapping for ThriftyCS23D2.0 performs a homolog search based torsion similarity against a non-redundant database of all cytoplasmic proteins in the PDB. This search uses an updated version of Thrifty that assigns each residue a letter based on its torsion angle class. The torsion angle mappings for each of the 9 letters in this torsion angle alphabet are shown below. |
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