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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.
Useful links
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 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 Legobody and megabody, but suffer from inherent flexibility, resulting in poorly resolved targets. NovoAb's proprietary AbEM3D cryo-EM service platform employs novel Rigidbody (rigid antibody formats) technology to overcome these limitations, making cryo-EM a more accessible and affordable methodology to the structural biology community.
Our Rigidbody based AbEM3D cryo-EM mapping technology enables high-resolution 3D epitope mapping and paratope mapping for antibody-antigen complexes and binding site mapping for proteins and ligands, at single amino acid and atomic resolution. AbEM3D integrates modern biochemistry, automation, the most advanced hardware and software, and AI-powered image processing into a solution which can facilitate high-resolution structural characterization for even the most challenging targets, from very small proteins to large and complex protein assemblies. Samples are optimized, flash frozen in a wide range of naturally occurring conditions, and then used to collect hundreds of thousands of cryo-EM images and build precise empirical 3D structural models.
Key features:
- Minimal sample consumption (often <100 ug)
- Single amino acid to atomic resolution
- No crystals needed
- Linear and conformational epitope mapping
- Whole antibody, Fab, nanobody, scFv etc.
- Simutaneous epitope and paratope mapping
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Simultaneous mapping of binding sites on all protein partners
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Structure validation for AI-designed antibodies, nanobodies and proteins
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Structure validation for alphafold-predicted proteins
