Root-mean-square-deviation (RMSD) is an indicator in protein-structure-prediction-algorithms (PSPAs). Goal of PSP algorithms is to obtain 0 Å RMSD from native protein structures. Protein structure and RMSD prediction is very essential. In 2013, the estimated RMSD proteins based on nine features were obtained best results using D2N (Distance to the native). We presented in This paper proposed approach to reduce predicted RMSD Error Than the actual amount for RMSD and calculate mean absolute error (MAE), through feed forward neural network, adaptive neuro fuzzy method. ANFIS is achieved better and more accurate results.