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The EnCPdock server is built to perform the direct conjoint comparative analyses of complementarity and binding energetics in proteins. One of its prime components, the Complementarity Plot (CP) is an established validation tool () for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). Complementarities can be computed for docked/bound protein-protein complexes in a residue-wise manner as well as for the overall interfacial surfaces of the molecular partners. CP_dock is a version of CP that computes the overall shape and electrostatic complementarities (Sc, EC) at the protein-protein interface and plots them as an ordered pair {Sc, EC} in the two dimensional plot. CP_dock (standalone suite @GitHub) is built with knowledge-based probabilistic quality estimates of the bound (or, feasibility of the docked) PPI complex, indirectly rendering their affinity and stability. In EnCPdock, these complementarity-based and other judiciously chosen high-level structural descriptors are optimally combined to predict binding free energies (∆G_binding) using supervised learning. The server enables one to compute, correlate and analyze complementarity and other high-level structural descriptors along with the predicted energetics for protein-protein binding. It returns a prediction accuracy (in its predicted binding energetics) comparable to the state-of-the-art. In addition, EnCPdock also generates Mobile Molecular Graphics (JSMol) of the interfacial atomic contact networks (which, by definition would map to Bipartite Graphs). The inter-residue Contact Map is also made downloadbale for further analyses. The server also furnishes individual Feature Trends along with relative Probability estimates (Pr _fmax) of the obtained feature-scores. This functionality is built to determine and pin-point binding defects to the level of fine-grained structural descripotrs - a tool that would naturally aid in structural tinkering and intervention in context to the design of targeted protein-interfaces, peptide design, mutational and possibly other related studies.

If you find this server helpful, you might consider citing the following articles:

• EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations
  Biswas G., Mukherjee D., Dutta N., Ghosh P., Basu S*. J Mol Model (2023) 29:239
  doi: https://doi.org/10.1007/s00894-023-05626-0       (Main Reference)
• Combining Complementarity and Binding Energetics in the Assessment of Protein Interactions: EnCPdock—A Practical Manual
  Biswas G., Mukherjee D., Basu S.*. J Comp Biol, (2024)
  doi: http://dx.doi.org/10.1089/cmb.2024.0554
• Plausible blockers of Spike RBD in SARS-CoV2—molecular design and underlying interaction dynamics from high-level structural descriptors.
  Basu, S., Chakravarty, D., Bhattacharyya, D. et al. J Mol Model (2021) 27:191
  doi: 10.1007/s00894-021-04779-0
• CPdock: the complementarity plot for docking of proteins: implementing multi-dielectric continuum electrostatics.
  Basu S. J Mol Model. (2017) 24(1):8
  doi: 10.1007/s00894-017-3546-y.
• Applications of complementarity plot in error detection and structure validation of proteins.
  Basu S., Bhattacharyya D., Banerjee R. Indian J Biochem Biophys. (2014) 51(3):188-200
  PMID: 25204080
• Self-Complementarity within Proteins: Bridging the Gap between Binding and Folding.
  Basu S., Bhattacharyya D., Banerjee R. Biophys J (2012) 102:2605–2614
  doi: 10.1016/j.bpj.2012.04.029