NovaFold, DNASTAR’s 3D protein structure prediction program, can use a sequence file to predict ligand binding sites and protein function and to build 3-D protein structure models based on iterative assembly simulations. DNASTAR provides NovaFold as a local or cloud-based, separately licensed service within Protean 3D. The NovaFold client provides an easy to use interface for submitting structure prediction tasks to a high performance computing cluster on the Amazon EC2 web service.

For step-by-step instructions, see Run NovaFold through Protean 3D, Run Nova applications through the DNASTAR website, or Run Nova applications locally.

NovaFold uses the I-TASSER algorithm developed by Professor Yang Zhang of the Department of Computational Medicine and Bioinformatics at the University of Michigan. This algorithm utilizes a combination of "threading" and "ab initio folding" in predicting protein structure.

  • Threading attempts to match portions of the query sequence to template sequences. The template sequences, and their experimentally solved structures, are part of the RCSB Protein Data Bank (PDB).
  • Ab initio folding uses biophysical properties of the query sequence and simulations to determine the likely structure(s) of the protein.

Professor Zhang’s algorithms have won the Protein Structure Prediction Center’s five most recent Critical Assessment of Protein Structure Prediction (CASP) experiments. Each CASP experiment is a biennial, world-wide evaluation of structure prediction methods, with approximately 100 participating laboratories.

  • CASP9 Results - #1 Zhang-Server and QUARK (another Zhang service)

For references related to the I-TASSER algorithm, see Research References.

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