EnCPdock Help :
Protocol Reference (J Comp Biol, 2024)
File Name and File Format specifications:
An atomic coordinate file in Brookhaven formatInput file features :
Only the naturally occuring 20 amino acids and ions (listed below) will be considered for the calculation. Large prosthetic groups or co-factors (i.e., a non-protein chemical component with MW > 200 Da), e.g., proto-porphyrin rings, NADP, acetyl CoA, etc. or RNA/DNA chains will be ignored during calculation. We recommend users to provide/use protein-protein/peptide complexex with/without ions, listed below, for the optimum result. When pdb files contain multiple occupancies for atoms, the 'hieghest occupancy conformers' are selected (& first conformer for equal occupancies).
NA => Sodium MG => Magnesium AL => Aluminium K => Potassium CA => Calcium MN => Manganese FE => Iron CO => Cobalt NI => Nickel CU => Copper ZN => Zinc AG => Silver CD => Cadmium PT1 => Platinum AU => Gold HG => Mercury
The present version of the server is for binary complexes, we are in the process of implementing higher order assemblies.
Abbreviation:
| Files (extensions) | Abbreviations | Descriptions |
|---|---|---|
| *.ScEC | Sc | Shape complementarity |
| EC | Electrostatic complementarity | |
| *.asaAngsq | sum(∆ASA) | Net change in solvent Accessible Surface Area (upon complexation) |
| ASAcomplex | ASAreceptor + ASAligand | |
| nBSA | normalized Buried Surface Area | |
| nBSAp | normalized Buried Surface Area (polar) | |
| nBSAnp | normalized Buried Surface Area (non-polar) | |
| fracI | Fraction of atoms buried upon association | |
| *.Nintres | Nintres | number of Interfacial residues |
| *.netlen | Ld | Link density of the interfacial contact network |
| ACI | Average Contact Intensity of the interfacial contact network | |
| slopedd | Slope of degree-distribution profile of the interfacial contact network (plotted in a log-log scale) | |
| Yinterdd | Y-intercept of the same degree-distribution profile | |
| CCpdd (r) | Goodness of fit (linear) of the same degree-distribution profile | |
| Nrec | Number of residues pertaining to the receptor chain | |
| Nlig | Number of residues pertaining to the ligand chain | |
| Ntot | Total number of residues pertaining to the protein-protein complex | |
| logN | log10(Nrec+Nlig) | |
| logasp | log10(Nrec/Nlig) | |
| *.delGp | ∆Gper-res (kcal.mol-1) | per residue free energy of interaction (binding) |
| *.delGp | ∆Gtot (kcal.mol-1) | Total free energy of interaction (binding) |
| *.Pr_fmax | Features | Input feature vectors (Structural Descriptors) |
| *.Pr_fmax | Scores | Scores for each feature obtained by the input PPI complex |
| *.Pr_fmax | Prfmax | Relative Probabilities of each feature-score with respect to the event of the highest observed frequency for that feature |
Start Page:
EnCPDock is capable of analyzing complementarities for docked/bound protein-protein complexes either directly from PDB or uploaded files in *.pdb format 
. Once pdbid is selected the file upload option will be disabled automatically and vice versa. To re-enable the options click on "Reset Values" button. After selecting a pdbid or selecting a local pdb formated file click the "Submit" button. Theare is an optional box provided for the user to add their email id. If provided, the user will be notified by email once the job has completed. The email would also contain the link for accessing the result. The result is available for next 24hrs.
| Enter PDB ID: Or, Upload an atomic coordinate file in brookhaven format | |
| Email (optional) | |
Chains (Protein/peptide) and Integral Metal Ion(s) Selection Page:
After submission the server takes user to a chain selection page. Left section of the page provides the deader information of the file. In case user provides only the coordinate information this section remains empty. The top right section of the page shows pictorial depction of the whole complex. The detail of the chains and metals are provided below the picture of the whole complex. User must select only two chains and/or metals from the whole complex for further analysis.
Once the "Proceed" button is pressed after optimal selection, job is submitted. User can see the job id and the selected chains for analysis. The page refreshes automatically every 10 sec. User can wait on this page for the analysis to be done or can provide the email id in the start page to be notified about job completion.
Results Page:
The Results are displayed in a tabular page with four distinct tabs (windows) built with distinct and definite purposes.
Tab-1: Scores and Plots
The first of these four tabs, Scores and Plots is the main Result-window which outputs the feature scores for all features (high-level Structural Descriptors) used as Input feature vectors in training EnCPdock along with the predicted binding energetics (ΔG) values (Total as well as per-residue contributions) on the left half of the window. The right half locates the ordered-pair {Sc, EC} point pertaining to the complex in the two-dimensional Complementarity Plot (CPdock) with demonstrated applications in docking scoring and protein/peptide design.
Tab-2: Molecular Graphics (3D)
The second tab, Molecular Graphics (3D), provides a structural window (JSmol) for a dynamic Molecular Visualization of the input PPI complex along with the interfacial atomic contacts (serving as Links in the Contact Network) displayed as thick Red lines (JSmol object: struts). The structure can be easily rotated and oriented for optimum visualization as per requirement. Users can export specific orientations of the complex as high resolution still images by right clicking on the window and then following the options: File > Export > Export PNG image.
Tab-3: Contact Map
The third tab portrays the Contact Map of the interface in an Edge List format along with link weightages for each link/edge. One can download the map as a formatted textfile by clicking "Download Contact Map" at the right-top of the window. Adjacency matrices can then be easily derived from the contact map for subsequent Network analyses. We have also provided a download button on the top right tab bar (
) for downloading the entire OUTPUT folder (zipped) for local analyses/visualization.
Tab-4: Feature Trends
The fourth tab portrays Feature Trends for each feature (high-level Structural Descriptors) used as Input feature vectors in training EnCPdock in the background of their corresponding Native kernel density distributions. It further computes the relative probabilities of each feature-score with respect to the event of the highest observed frequency for that feature (Prfmax) and locates them in the corresponding plots as red dots (points of intersection between the curves/profiles and vertical dashed lines). These relative probability estimates reflect whether an input PPI complex is regular or terminal with respect to the obtained feature-scores for each feature. This functionality is built with the aim to aid structural tinkering and intervention as might be relevant to targeted design of protein-interfaces, mutational studies and peptide design.
