findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM

Abstract

Although experimental protein-structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or appear as a contaminant. Regardless of the source of the problem, the unknown protein always requires characterization. Here, an automated pipeline is presented for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. The method's application to characterize the crystal structure of an unknown protein purified from a snake venom is presented. It is also shown that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures.

Keywords

• protein structures
• protein sequences
• simbad
• cryo-em
• bioinformatics
• structure determination
• findmysequence
• neural networks