1. A computer-implemented system for predicting binding information relating to a binding of a protein and a ligand, comprising the following computer components stored in one or more memory storage devices and executable by one or more processors: a trained binding model comprising a hidden variable representing an unknown alignment of the ligand with the protein at a binding site of the protein, the trained binding model further comprising one or more parameters selected from a group Major Histocompatibility Complex (MHC)-specific weights, learnable contact potentials, and a learnable soft-step function; the one or more parameters of the trained binding model being estimated based at least in part on machine learning algorithms to minimize an error between the predicted binding information and a true binding information; a prediction component configured to predict the binding information by employing information about a protein's sequence, a ligand's sequence, and the trained binding model; and the trained binding model using a shift variable to influence predicting the binding information by altering a predicted amino acid composition.