ISLAND: In-Silico Prediction of Proteins Binding Affinity Using Sequence Descriptors
This work addresses the need for computational methods to replace expensive experimental binding affinity determination, focusing on sequence-based approaches that are more broadly applicable than structure-dependent methods.
The paper tackles the problem of predicting protein binding affinity using only sequence information, proposing ISLAND, a novel sequence-only predictor that achieves better accuracy than existing methods on both validation and independent test datasets.
Determination of binding affinity of proteins in the formation of protein complexes requires sophisticated, expensive and time-consuming experimentation which can be replaced with computational methods. Most computational prediction techniques require protein structures which limit their applicability to protein complexes with known structures. In this work, we explore sequence based protein binding affinity prediction using machine learning. Our paper highlights the fact that the generalization performance of even the state of the art sequence-only predictor of binding affinity is far from satisfactory and that the development of effective and practical methods in this domain is still an open problem. We also propose a novel sequence-only predictor of binding affinity called ISLAND which gives better accuracy than existing methods over the same validation set as well as on external independent test dataset. A cloud-based webserver implementation of ISLAND and its Python code are available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#island.