MSU ProFlex (formerly called FIRST) is a patented computational tool for identifying rigid and flexible regions in protein structures and protein-ligand complexes. Analysis of a single, static three-dimensional protein structure can capture the essential conformational flexibility of the protein. Hydrogen bonds, salt bridges and hydrophobic contacts are identified by geometric and energetic criteria once polar hydrogens have been placed using an external program (such as What If). Using a constraint counting algorithm, all-atom calculations on proteins of over 1000 residues can be completed within seconds. This software is available as source code and has been applied to many proteins and their complexes (see publications below).
Selected publications related to ProFlex:
- M. I. Zavodszky, M. Lei, A. R. Day, M. F. Thorpe, and L. A. Kuhn (2004)
Modeling Correlated Main-chain Motions in Proteins for Flexible Molecular Recognition (pdf) Proteins: Struct. Funct. Bioinf., 57(2), 243-261.
- H. Gohlke, L. A. Kuhn, and D. A. Case (2004)
Change in Protein Flexibility Upon Complex Formation: Analysis of Ras-Raf Using Molecular Dynamics and a Molecular Framework Approach (pdf) Proteins: Struct. Funct. Bioinf., 56, 322-337.
- Brandon M. Hespenheide, A.J. Rader, M.F. Thorpe, and Leslie A. Kuhn (2002)
Identifying protein folding cores from the evolution of flexible regions during unfolding (pdf) J. Molec. Graphics and Modelling, 21, 195-207.
- A. J. Rader, B. M. Hespenheide, L. A. Kuhn, and M. F. Thorpe (2002)
Protein Unfolding: Rigidity Lost (pdf) Proceedings of the National Academy of Sciences USA 99, 3540-3545.
- D. J. Jacobs, A. J. Rader, L. A. Kuhn, and M. F. Thorpe (2001)
Protein Flexibility Predictions Using Graph Theory (pdf) Proteins: Structure, Function, and Genetics 44, 150-165.
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