Technical Note
Version 1
Preserved in Portico This version is not peer-reviewed
Combining Complementarity and Binding Energetics in Protein Interactions: EnCPdock—A Practical Manual
Version 1
: Received: 17 October 2023 / Approved: 17 October 2023 / Online: 18 October 2023 (08:26:54 CEST)
A peer-reviewed article of this Preprint also exists.
Biswas, G., Mukherjee, D., & Basu, S. (2023). Combining Complementarity and Binding Energetics in Protein Interactions: EnCPdock—A Practical Manual. Biswas, G., Mukherjee, D., & Basu, S. (2023). Combining Complementarity and Binding Energetics in Protein Interactions: EnCPdock—A Practical Manual.
Abstract
The combined efect 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 detterminant 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 non-local complementarity (EC) in PPIs using the Complementarity Plot. It further derives an AI-based ∆Gbinding 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.
Keywords
EnCPdock; Complementarity Plot; Artificial Intelligence; Structure based Thermodynamics; web-server
Subject
Biology and Life Sciences, Biophysics
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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