Combining Complementarity and Binding Energetics in the Assessment of Protein Interactions: EnCPdock-A Practical
Gargi Biswas1, Debasish Mukherjee2, Sankar Basu3
1Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
Abstract:
The combined effect of shape and electrostatic complementarities (Sc, EC) at the interface of the interacting protein partners (PPI) serves as the physical basis for such associations and is a strong determinant of their binding energetics. EnCPdock (https://www.scinetmol.in/EnCPdock/) presents a comprehensive web platform for the direct conjoint comparative analyses of complementarity and binding energetics in PPIs. It elegantly interlinks the dual nature of local (Sc) and nonlocal complementarity (EC) in PPIs using the complementarity plot. It further derives an AI-based ΔGbinding with a prediction accuracy comparable to the state of the art. This book chapter presents a practical manual to conceptualize and implement EnCPdock with its various features and functionalities, collectively having the potential to serve as a valuable protein engineering tool in the design of novel protein interfaces.
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