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ModRefiner is an algorithm for atomic-level, high-resolution protein structure refinement, which can start from either C-alpha trace, main-chain model or full-atomic model. Both side-chain and backbone atoms are completely flexible during structure refinement simulations, where conformational search is guided by a composite of physics- and knowledge-based force field. ModRefiner has an option to allow for the assignment of a second structure which will be used as a reference to which the refinement simulations are driven. One aim of ModRefiner is to draw the initial starting models closer to their native state, in terms of hydrogen bonds, backbone topology and side-chain positioning. It also generates significant improvement in physical quality of local structures. The standalone program also supports ab initio full-atomic relaxation, where the refined model is not restrainted by the initial model or the reference model.

Go to Job M11 to view an example of ModRefiner output. While the current webserver only supports single-chain model, the latest 64-bit Linux version also supports dimer refinement.

Cut and paste the structure you want to refine (C-alpha trace, main-chain model or full-atomic model) in PDB format here: Or upload the target structure file from your local computer: Upload a reference structure (only C-alpha trace required) to which the refined model will be driven (Optional): Email (Mandatory, where results will be sent to):

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Download the ModRefiner standalone program:

• WindowsXP version
• Linux 64-bit version Linux 32-bit version
• Mac version

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Update history (please always download the newest version):

• 2018/03/22: The 64-bit Linux version now does not depend on GSL shared library.
• 2017/08/21: The 64-bit Linux version now supports refinement of dimer models. The old 64-bit Linux version is still available.
• 2011/10/24: The residue number doesn't need to start from 1. The program terminates after a fixed number of cycles rather than running time.
• 2011/05/05: The first version is released.

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Reference:
Dong Xu and Yang Zhang. Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-step Atomic-level Energy Minimization. Biophysical Journal, vol 101, 2525-2534 (2011). (download the PDF file).