Difference between revisions of "Part:BBa K3468088:Experience"
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===Applications of BBa_K3468088=== | ===Applications of BBa_K3468088=== | ||
| + | We builded a model of the mutant (A202C-E231c), using Pymol for visual inspection (geometric criteria, see Figure 4 and Table 1), and finally using FoldX for evaluation. During visual inspection in Pymol, we found that this disulfide bond is far from the catalytic triad, far from the inside of the protein, and met the disulfide bond geometry criteria. DDG is -2.454kcal/mol evaluated by FoldX. | ||
| + | Reference: | ||
| + | [1] Craig and Dombkowski: Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins. BMC Bioinformatics 2013 14:346. | ||
| + | [2] Hein J.Wijma, Robert J.Floor, Peter A.Jekel1,David Baker, Siewert J.Marrink and Dick B.Janssen. Computationally designed libraries for rapid enzyme stabilization. Protein Engineering, Design & Selection vol. 27 no. 2 pp. 49– 58, 2014. | ||
| + | [3] Vardhan S.Dani, C.Ramakrishnan and Raghavan Varadarajan. MODIP revisited: re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins. Protein Engineering vol.16 no.3 pp.187–193, 2003. | ||
===User Reviews=== | ===User Reviews=== | ||
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Applications of BBa_K3468088
We builded a model of the mutant (A202C-E231c), using Pymol for visual inspection (geometric criteria, see Figure 4 and Table 1), and finally using FoldX for evaluation. During visual inspection in Pymol, we found that this disulfide bond is far from the catalytic triad, far from the inside of the protein, and met the disulfide bond geometry criteria. DDG is -2.454kcal/mol evaluated by FoldX. Reference: [1] Craig and Dombkowski: Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins. BMC Bioinformatics 2013 14:346. [2] Hein J.Wijma, Robert J.Floor, Peter A.Jekel1,David Baker, Siewert J.Marrink and Dick B.Janssen. Computationally designed libraries for rapid enzyme stabilization. Protein Engineering, Design & Selection vol. 27 no. 2 pp. 49– 58, 2014. [3] Vardhan S.Dani, C.Ramakrishnan and Raghavan Varadarajan. MODIP revisited: re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins. Protein Engineering vol.16 no.3 pp.187–193, 2003.
User Reviews
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