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Neural tube defects (NTDs) is a serious birth defect disease which can be effectively prevented through folic acid and vitamins supplement during perinatal stage.Here, we tried to establish a "prediction-validation" model for the mechanism research of such nutritional intervention (NI).The prediction part was carried out by inverse molecular docking to find the potential target proteins of the three nutrients (folic acid, vitamin B1 and vitamin B2) followed by pathway analysis, while the validation part was carried out by a metabonomics study.