Kmalo is a free web tool for predicting lysine malonylation sites. As a newly discovered lysine post-translational modification (PTM), malonylation plays an essential part in many biological functions, such as cellular regulation and disease processes. For better understanding the mechanisms of malonylation, identifying malonylation sites with an efficient methodology has become an essential issue. In this study, Kmalo, a deep learning-based framework was proposed for the prediction of malonylation sites. Physicochemical properties, evolutionary information and sequenced-based features were used to encode the peptides as the inputs of convolutional neural network.