Discrimination and Prediction of Protein-Protein Binding Affinity Using Deep Learning Approach

  • Rahul Nikam
  • K. Yugandhar
  • M. Michael GromihaEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10955)


Protein-protein interactions (PPIs) mediate myriad biological functions. Estimating the binding affinity for PPIs help us to understand the underlying molecular recognition mechanism. In this work, we utilized deep learning approach to discriminate protein-protein complexes based on their binding affinity. We setup a database of 464 protein-protein complexes along with their experimental binding affinities and developed a deep learning based binary classification model, which showed an accuracy of 81.75% using 5-fold cross-validation. Furthermore, we refined the method for predicting the binding affinity of protein-protein complexes using a large set of complexes (PPA-Pred2). It could predict the binding affinity of the training set and blind test set with a mean absolute error of 1.24 kcal/mol and 1.31 kcal/mol, respectively. We suggest that our methods could serve as efficient tools to study PPIs and provide crucial insights about the underlying mechanism for the molecular recognition process.


Protein-protein interaction Binding affinity Deep learning Machine learning 



We thank Indian Institute of Technology Madras and the High-Performance Computing Environment (HPCE) for computational facilities. The work was partially supported by the Department of Science and Technology, Government of India (DST/INT/SWD/P-05/2016) and of the Swedish Research Council.


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© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biotechnology, Bhupat and Jyoti Metha School of BiosciencesIndian Institute of Technology MadrasChennaiIndia

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