MPTherm-pred is a webserver contains diferent topological specific models for predicting the membrane protein thermal stability upon missense mutations. This method is developed by a set of 929 membrane protein mutations in both membrane bound and aqueous (cytoplasmic/extra-cellular) regions, which are retrieved from MPTherm database. Each model was validated with different cross-validation procedures and tested against evolutionary independent protein mutations. The membrane models showed a pearson correlation of 0.73 with mean absolute error (MAE) of 2.75℃ between experimental and predicted ΔTm values for the test dataset. Similarly, the average correlation and MAE in aqueous regions were 0.75 and 3.5℃, respectively. This suite of predictive methods help in designing the new stable mutants for different applications and to elucidate the key factors influencing the membrane protein stability upon mutations.