ReferenceSRSD: a single residue substitution structural database drived from PDB (In preparation.)
Ask: How is the data collected?
Answer: All the protein X-ray structures were first obtained from PDB (Latest update: July 20th, 2014). Chains with missing backbone atoms were removed, and chains with the same sequences were merged to get a non-redundant single chain database. Next, those non-redundant single chains were aligned using a demestic developed software to identify the pairs of proteins with single residue substitution. To reduce the structural fluctuation by thermal oscillations or disorder, residue substitutions occur in terminal residues (< 10) were removed. The final nonredundant protein pairs were filtered with the criterion of resolution < 3.0 Å. Function annotation information is obtained by inspecting the articles of protein structures from the NCBI PubMed manually.
Ask: What is this database used for?
Answer: This database aims (i) to facilitate our analysis of protein structural & functional changes induced by single residue difference, (ii) to deeper understand protein folding mechanism and (iii) to infer possible rules for protein structure optimization and protein design.
Ask: What does Positions mean?
Answer: This value is obtained from the Residue sequence nunmber of PDB file which may be not the same as the number according to the amino acid sequences themselves. We hope the numbers are consistant with the numbering system of biochemical and biophysical communities.
Ask: What does Ramachandran Plots mean?
Answer: Ramachandran plots are wildly used to measure the variation of backbone conformations from the objective of finding stable ones. It illustrates the backbone dihedral angles (ψ and φ ) which are possible for an amino-acid residue in a protein. ψ and φ outside the colored regions are of very low possibilities in real proteins. One of our study (in preparing) shows that the changes of Ramachandran probabilities have significant correlation with backbone displacement upon residue substitutions. Please note the distance between '+' and 'x' versus the colored regions of their location.
Ask: What does SSEs mean?
Answer: SSEs indicates eight types of secondary structure accoding to DSSP, which are the 310 helix (G), α helix (H) and π helix (I), beta bridge (B), beta bulges (E), turns(T), regions of high curvature (S) and other loops (_). These eight types are usually grouped into three larger classes: helix (G, H and I), strand (E and B) and loop (all others).
Ask: What is the difference of Nonredundant and Redundant data sets?
Answer: Nonredundant data set eliminates protein pairs with the same sequences from Redundant data set.
Ask: Why cannot I view 3D structures?
Answer: You do not have Java applets enabled in your web browser, or your browser is blocking this applet. Check the warning message from your browser and/or enable Java applets in your web browser preferences, or install the Java Runtime Environment from www.java.com . If you using windows, please set the security level to be Medium (Please see more information at http://www.java.com/en/download/help/jcp_security.xml )
Ask: Why cannot I view Ramachandran Plots?
Answer: Ramachandran Plots are implemented using JSXGraph (http://jsxgraph.uni-bayreuth.de) technique. Some browsers (IE 7) may be incompatible with JSXGraph. We suggest users try Chrome or Firefox to view the plots.
Please send us an email (cy_scu [AT] yeah.net) if you have any more question in using SRSD.