Because of the different structure and structural changes of proteins， the tradi-tional shape descriptor algorithm is not ideal for the retrieval of protein datasets.In order to improve the retrieval performance， a new protein shape descriptor and protein retrieval framework based on mixed spectrum features were proposed.The shaped escritor was made by combining Bag of Feature of Wave Kernel Signature and Heat Kernel Signature， namely WKS_HKS algorithm.The WKS_HKS algorithm and several existing shape descriptor al- gorithms were compared comprehensively on three different types of molecular datasets.Experimental results show that this algorithm is better than a single algorithm， and better than several comparative shape descriptor algorithms.