论文信息 - FoldX 5.0: working with RNA, small molecules and a new graphical interface

FoldX 5.0: working with RNA, small molecules and a new graphical interface

Abstract Summary A new version of FoldX, whose main new features allows running classic FoldX commands on structures containing RNA molecules and includes a module that allows parametrization of ligands or small molecules (ParamX) that were not previously recognized in old versions, has been released. An extended FoldX graphical user interface has also being developed (available as a python plugin for the YASARA molecular viewer) allowing user-friendly parametrization of new custom user molecules encoded using JSON format. Availability and implementation http://foldxsuite.crg.eu/

[1] François Stricher,et al. The FoldX web server: an online force field , 2005, Nucleic Acids Res..

[2] François Stricher,et al. A graphical interface for the FoldX forcefield , 2011, Bioinform..

[3] M. Bulyk,et al. Using protein design algorithms to understand the molecular basis of disease caused by protein–DNA interactions: the Pax6 example , 2010, Nucleic acids research.

[4] Andreu Alibés,et al. DNA-binding specificity prediction with FoldX. , 2011, Methods in enzymology.

[5] Andreu Alibés,et al. Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases , 2008, Nature.

[6] L. Serrano,et al. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. , 2002, Journal of molecular biology.

[7] Philip R. Evans,et al. Crystal structure of the spliceosomal U2B″–U2A′ protein complex bound to a fragment of U2 small nuclear RNA , 1998, Nature.