actually ,I am working on enzyme design by computational methods ,and i want improve enzyme activity and stability ,so can i used some other tools ??
thanks !!
Hi Shahid,
enzyme engineering is an established field with a plethora of available tools. However, it's easy to feel lost as descriptions and user interfaces of most of them are frequently rather unclear and chaotic. Maybe it's worth to try read a few review articles which could provide you basic navigation and understanding of essential principles, such as those ones:
http://www.sciencedirect.com/science/article/pii/S1367593117300248
http://www.sciencedirect.com/science/article/pii/S1367593113002354
Above mentioned tool, HotSpot Wizard (http://loschmidt.chemi.muni.cz/hotspotwizard), which I co-developed with my colleagues in my former lab, is certainly a good starting point. We spent substantial time trying to make it user-friendly. The tool provides good results for a broad variety of enzyme structures.
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw416
If the improvement of protein stability is your prime interest, I recommend you FireProt (http://loschmidt.chemi.muni.cz/fireprot). It integrates FoldX and Rosetta protocols together with smart filtering function to propose multi-point mutation with possible synergistic effect.
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004556
Finally, if you want to work directly with Rosetta, this set of molecular benchmarks could help you find the most useful setting:
https://guybrush.ucsf.edu/benchmarks
Since you aim at increasing stability and want to use rosetta, I would use the Point-mutant-scan application (pmut) to look for the positions which are most likely to have a positive effect (https://www.rosettacommons.org/docs/latest/application_documentation/design/pmut-scan-parallel)
Hi Shahid,
enzyme engineering is an established field with a plethora of available tools. However, it's easy to feel lost as descriptions and user interfaces of most of them are frequently rather unclear and chaotic. Maybe it's worth to try read a few review articles which could provide you basic navigation and understanding of essential principles, such as those ones:
http://www.sciencedirect.com/science/article/pii/S1367593117300248
http://www.sciencedirect.com/science/article/pii/S1367593113002354
Above mentioned tool, HotSpot Wizard (http://loschmidt.chemi.muni.cz/hotspotwizard), which I co-developed with my colleagues in my former lab, is certainly a good starting point. We spent substantial time trying to make it user-friendly. The tool provides good results for a broad variety of enzyme structures.
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw416
If the improvement of protein stability is your prime interest, I recommend you FireProt (http://loschmidt.chemi.muni.cz/fireprot). It integrates FoldX and Rosetta protocols together with smart filtering function to propose multi-point mutation with possible synergistic effect.
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004556
Finally, if you want to work directly with Rosetta, this set of molecular benchmarks could help you find the most useful setting:
https://guybrush.ucsf.edu/benchmarks
thanks a lot for your answers. special thanks to @ Jaroslav Bendl sir!!!
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