Compares the protein structure from multiple viewpoints. 3D Protein Retrieval is based on LightField descriptors to match 3D protein structures in visual-based similarity. The concept of the visual-based matching method is based on human perception, therefore, the result of retrieval can be used and manipulated more intuitively and quickly. It can also provide some clues for protein classification. The retrieval process is divided into off-line feature extraction and on-line protein retrieval. It takes less than three seconds for each query with 90% accuracy on an average.