Version 0.2.25 - October 2018
CTraj is a simulation analysis framework for all-atom simulations of disordered proteins. It can support a variety of input types, and works with simulations generated via CAMPARI, GROMACS, NAMD, Amber, and various other simulation packages. CTraj provides a high-performance toolkit for the analysis of properties of relevance to intrinsically disordered proteins. It natively supports frame-weights for performing this analysis over weighted ensembles.
As of Oct 2018 CTraj development is being finalized, although it has been used for the analysis of a variety of different systems. We anticipate full over the next six months.
CTraj was developed by Alex Holehouse, with additional contributions from other members of the Pappu Lab. The automated generation of smFRET dyes was initially developed by Kiersten Ruff, while PRE profile generation was originally implemented by Nick Lyle.
Publications that use CTraj
Staller, M.V., Holehouse, A.S., Swain-Lenz, D., Das, R.K., Pappu, R.V., and Cohen, B.A. (2018). A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain. Cell Syst 6, 444–455.e6
Cohan, M.C., Posey, A.E., Grigsby, S.J., Mittal, A., Holehouse, A.S., Buske, P.J., Levin, P.A., and Pappu, R.V. (2018). Evolved sequence features within the intrinsically disordered tail influence FtsZ assembly and bacterial cell division.
Mittal, A., Holehouse, A.S., Cohan, M.C., and Pappu, R.V. (2018). Sequence-to-Conformation Relationships of Disordered Regions Tethered to Folded Domains of Proteins. J. Mol. Biol. 430, 2403–2421.
Mercadante, D., Wagner, J.A., Aramburu, I.V., Lemke, E.A., and Gräter, F. (2017). Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins. J. Chem. Theory Comput. 13, 3964–3974.
Wei, M.-T., Elbaum-Garfinkle, S., Holehouse, A.S., Chen, C.C.-H., Feric, M., Arnold, C.B., Priestley, R.D., Pappu, R.V., and Brangwynne, C.P. (2017). Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles. Nat. Chem. 9, 1118–1125.
Fuertes, G., Banterle, N., Ruff, K.M., Chowdhury, A., Mercadante, D., Koehler, C., Kachala, M., Estrada Girona, G., Milles, S., Mishra, A., et al. (2017). Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements. Proc. Natl. Acad. Sci. U. S. A. 114, E6342–E6351.