Homology modeling and fold recognition programs
Use the programs in resources to model the PH domain in your assigned sequence. Document each result with the following:
1. Name of Program used
2. Name and PDB ID of the template used
3. Alignment on the model is based
4. Evaluation plots
5. Discussion - is the model good or bad in entirety or do specific regions look like they could be refined; is the template adequate; is the alignment accurate, etc
Note: Restrict the report to the best 5 models
Write a formal methods section for your assignment.
This material may consist of step-by-step explanations on how to solve a problem or examples of proper writing, including the use of citations, references, bibliographies, and formatting. This material is made available for the sole purpose of studying and learning - misuse is strictly forbidden.Part A
The structure of PH domain of Gab3 protein (Q8www8 sequence) was analyzed using 5 different programs [1-5]. All the programs are based on sequence homology with sequences of known PDB structures (PDB templates). The sequence (obtained by use of CDD program for prediction of protein domains) of PH domain of human Gab3 protein is:
The results obtained with different programs are presented in this report.
1. Swissmodel 
PDB template: Pleckstrin (Solution structure of the C-terminal PH domain of human pleckstrin) obtained by solution NMR
PDB ID: 1x05.1
The model is based on 28.04% of sequence similarity between target and template sequence. The alignment between the sequences is presented in Figure 1. It covers target sequence from 4 to 120 amino acid residue (coverage 0.86).
Structure showed was evaluated by QMEAN -4.05 and GMQE 0.57 values given by the program. QMEAN - Qualitative Model Energy ANalysis, is a composite scoring function describing the major geometrical aspects of protein structure . GMQE score estimates the accuracy of the tertiary structure of the resulting model, reflecting the expected accuracy of a model built with that alignment and template and the coverage of the target . Higher numbers indicate higher reliability. In this case, values suggest that results are satisfactory, but to test the reliability, evaluation programs have to be used. In this case, two evaluation programs – Verify 3D and ProSA [8, 9] were used
Verify3D analysis shows that 86.32% of the residues had a score greater than 0.2. This value is a threshold suggesting that residues are highly likely to give the same contribution to 3D structure in both, template and target sequences. 80% of ≥ 0.2 score residues is commonly taken as a value that confirms the reliability of a model. In this case, residues in range between 39 and 50, as well as residues 64 and 70 do not fit; as the score is lower than 0.2 (the lowest is about 0.01). The values in mentioned
range dip to the lowest value of 0.01. The major sequence that differs in both, target and template sequence are: