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CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.
Kozlikova B, Sebestova E, Sustr V, Brezovsky J, Strnad O, Daniel L, Bednar D, Pavelka A, Manak M, Bezdeka M, Benes P, Kotry M, Gora A, Damborsky J, Sochor J. Kozlikova B, et al. Among authors: pavelka a. Bioinformatics. 2014 Sep 15;30(18):2684-5. doi: 10.1093/bioinformatics/btu364. Epub 2014 May 29. Bioinformatics. 2014. PMID: 24876375
CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
Chovancova E, Pavelka A, Benes P, Strnad O, Brezovsky J, Kozlikova B, Gora A, Sustr V, Klvana M, Medek P, Biedermannova L, Sochor J, Damborsky J. Chovancova E, et al. Among authors: pavelka a. PLoS Comput Biol. 2012;8(10):e1002708. doi: 10.1371/journal.pcbi.1002708. Epub 2012 Oct 18. PLoS Comput Biol. 2012. PMID: 23093919 Free PMC article.
CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.
Jurcik A, Bednar D, Byska J, Marques SM, Furmanova K, Daniel L, Kokkonen P, Brezovsky J, Strnad O, Stourac J, Pavelka A, Manak M, Damborsky J, Kozlikova B. Jurcik A, et al. Among authors: pavelka a. Bioinformatics. 2018 Oct 15;34(20):3586-3588. doi: 10.1093/bioinformatics/bty386. Bioinformatics. 2018. PMID: 29741570 Free PMC article.
CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules.
Pavelka A, Sebestova E, Kozlikova B, Brezovsky J, Sochor J, Damborsky J. Pavelka A, et al. IEEE/ACM Trans Comput Biol Bioinform. 2016 May-Jun;13(3):505-17. doi: 10.1109/TCBB.2015.2459680. IEEE/ACM Trans Comput Biol Bioinform. 2016. PMID: 27295634
Haloalkane dehalogenases: biotechnological applications.
Koudelakova T, Bidmanova S, Dvorak P, Pavelka A, Chaloupkova R, Prokop Z, Damborsky J. Koudelakova T, et al. Among authors: pavelka a. Biotechnol J. 2013 Jan;8(1):32-45. doi: 10.1002/biot.201100486. Epub 2012 Sep 11. Biotechnol J. 2013. PMID: 22965918 Review.
17 results