PeptiDesCalculator: Software for computation of peptide descriptors. Definition, implementation and case studies for 9 bioactivity endpoints

Abstract

We present a novel Java‐based program denominated PeptiDesCalculator for computing peptide descriptors. These descriptors include: redefinitions of known protein parameters to suite the peptide domain, generalization schemes for the global descriptions of peptide characteristics, as well as empirical descriptors based on experimental evidence on peptide stability and interaction propensity. The PeptiDesCalculator software provides a user‐friendly Graphical User Interface (GUI) and is parallelized to maximize the use of computational resources available in current work stations. The PeptiDesCalculator indices are employed in modeling 8 peptide bioactivity endpoints demonstrating satisfactory behavior. Moreover, we compare the performance of a support vector machine (SVM) classifier built using 15 PeptiDesCalculator indices with that of a recently reported deep neural network (DNN) antimicrobial activity classifier, demonstrating comparable test set performance notwithstanding the remarkably lower degree of freedom for the former. This software will facilitate the development of in silico models for the prediction of peptide properties.

Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery

“…With an increase in the dimensionality of the descriptor class, information content about the descriptors is also expanding. Several software resources like Open Babel [ 40 ], PaDEL [ 41 ], Dragon [ 42 ], MOE [ 43 ], PeptiDesCalculator [ 44 ], AlvaDes [ 45 ], QuBiLS-MAS [ 46 ] are currently available which can calculate a wide set of different descriptors (OD/1D/2D/3D) from the SMILES format or 2D structure of the chemical compounds.…”