PROTDES: CHARMM toolbox for computational protein design

Springer Science and Business Media LLC - Tập 2 - Trang 105-113 - 2009
María Suárez1,2, Pablo Tortosa1, Alfonso Jaramillo1,2
1Biochemistry Laboratory, CNRS—UMR 7654, Ecole Polytechnique, Palaiseau, France
2SYNTH-BIO group Epigenomics Project, Evry Cedex, France

Tóm tắt

We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html .

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