A new Robetta server is available for structure prediction.

Fragment Libraries    Alanine Scanning    DNA Interface Scan
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Welcome to the DNA Interface Scan Server

Dna Interface Scan Queue

Given the structure of a protein-DNA complex, this server estimates the changes to DNA binding affinity and specificity that result from exhaustive point mutations at individual amino acid positions in the interface. This protocol was inspired by an interest in estimating the extent to which each individual native amino acid is optimal for affinity and specificity. The underlying protocol reconfigures and minimizes amino acid sidechain orientations for enumerative single amino acid and basepair substitutions.

Submit a job to the DNA Interface Scan Server

NOTE: this server recently recovered from a disk failure. If you experience errors, please contact ashwortj [.ignore.this.bot.stopper.] uw.edu

Registered Username:
    or     Registered Email Address:
Job Name:
Upload PDB Complex:
DNA basepair definition(s): e.g. C.3,C.4

This modeling protocol was originally developed to assess the interfaces of native a representative set of high-resolution structures of protein-DNA complexes:

  • Ashworth J and Baker D (2009). Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Nucleic Acids Research 37(10):e73. PMC2691843
  • If this webserver is uncooperative please e-mail ashwortj [.ignore.this.bot.stopper.] uw.edu

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