NESG

    		 For academic use only. For commercial use, please contact Nooriel Banayan (neb2154@columbia.edu), John F. Hunt (jfh21@columbia.edu), or Columbia Science and Technology Ventures (techventures@columbia.edu)
    Crystal Packing Analysis and Epitope Engineering Server

    Crystal Packing Analysis & Epitope Engineering Server

    Retreive by PDB id:
    Or submit a .pdb file:

    Packing Similarity Analysis

    Upload one or two PDB files and view the packing similarities between the chains/interfaces in the crystal or between the two crystals.
    PDB file
    Second PDB file (optional)

    Epitope Lookup

    Enter an epitope sequence and structure (from dimer up to hexamer), like KVDK EEEE or ExxxR HxxxH, and see PDB crystal packing interfaces where it is present. Secondary structure codes: C=loop, E=sheet, H=helix.
    Sequence
    Structure

    Epitope Engineering

    Upload a fasta file with the sequence of a protein and couple dozen of its homologues, and a PROF secondary structure prediction file, and receive crystallization engineering mutagenesis suggestions (example result).
    .faa file (target protein first)
    Perform automated search of the NR database
    .prof file [get here (select text format) or here (select "native Prof")]
     

    Guidelines of Sequence File Submission

    For fasta sequence file submitted for Epitope Engineering, please follow the guidelines below:
    1. Each block of letters representing a protein sequence must be preceeded by a single comment line containing the gene name
    2. A comment line is a line beginning with a ">" character
    3. The gene name is the sequence of characters after the ">" character and up to the first space or end-of-line
    4. Gene name cannot be longer than 30 characters
    5. Multiple genes/sequences with the same name are not allowed
    6. The first gene/sequence is the target for engineering