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A free online tool for protein cleavage sites prediction with a chosen enzyme.
Calculate monoisotopic and average mass of a custom peptide or peptides predicted from a protein.
The cleavage specificities of selected enzymes.
A comprehensive and freely accessible resource of protein sequence and functional information.
Mass spectrum simulation tool for peptide/protein sequences. The number of charge can be custom defined.
An online tool predicts m/z values for SMS ions generated from selected fragmentation methods such as CID, ECD, or ETD. The ion type and maximum number of charge can be pre-defined.
PDB provides the most complete collection of information about the 3D structures of proteins, protein complexes and other biomolecules.
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Cryo-EM Service
High-resolution structures of proteins are crucial to understanding the molecular mechanism of biological processes and in the discovery of therapeutic agents. Single-particle analysis based cryo-electron microscopy (cryo-EM) has become an important structural biology technique for 3D characterization of bio-macromolecules and protein complexes at near atomic resolution. On the other hand, smaller proteins (< 50 kDa), many of which underlie human diseases, have been challenging for cryo-EM due to low signal-to-noise images and difficulties in particle alignment. Current strategies to overcome this problem are focused on increasing the overall size of small protein targets using scaffold proteins such as Levibody and Legebody, but suffer from inherent flexibility, resulting in poorly resolved targets compared to scaffolds. Our proprietary AbEM3D cryo-EM technology platform employs novel rigid antibody formats to overcome these limitations, making cryo-EM a more accessible, reliable, and affordable methodology to the structural biology community.
The AbEM3D cryo-EM platform enables high-resolution 3D epitope mapping and paratope mapping for antibodies (including whole antibody, Fab, nanobody, scFv etc.) and binding site mapping for proteins and ligands, at single amino acid and atomic resolution. AbEM3D brings together modern biochemistry, automation, the most advanced hardware and software, and artificial intelligence (AI) powered image processing into a solution which can facilitate high-resolution structural characterization for even the most challenging targets, including large, complex, and fragile protein assemblies. Samples are optimized, flash frozen in a broad range of naturally occurring conditions, and then used to build accurate empirical 3D structural models.
The AbEM3D cryo-EM platform is also an excellent option for interrogating the immune responses against biologics such as antibodies and vaccines. Our EMpEM (Epitope Mapping of pAb by Electron Microscopy) workflow allows you to study the polyclonal antibody responses against an immunogen/vaccine candidate. Antigen bound to these antibodies can directly be isolated from the serum and subjected to high-resolution cryo-EM analysis. Detailed structural information allows the mapping of different epitopes on the vaccine/biotherapeutics. These epitopes can then be engineered to enhance the immunogenicity for vaccine design and reduce the immunogenicity for protein/antibody therapeutics and gene therapy viral vectors. EMpEM is also a powerful tool for mapping antibody responses to each epitope in the serum, providing immediate feedback for mechanistic evaluation of epitope-targeting in vaccines. The abundance of pAbs to each epitope can also be calculated to show immune transitions over time.
