MD-trajectory processing librabry for FRET experiments using LabelLib and MDTraj
AvTraj is tool to calculate FRET observables from MD-trajectories. Read, write and analyze accessible volumes (AVs) using MD trajectories as an input with only a few lines of Python code. By the use of LabelLib AvTraj provides programmatic access to latest developments in implicit dye models for FRET experiments. AvTraj is a python library that allows users to perform simulations of accessible volumes for molecular dynamics (MD) trajectories. AvTraj serves as a high-level interface for the development of new methodologies for structure-based fluorescence spectroscopy. Details are provided in the publications 1. Kalinin, S., T. Peulen, S. Sindbert, P. J. Rothwell, S. Berger, T. Restle, R. S. Goody, H. Gohlke and C. A. M. Seidel (2012). A toolkit and benchmark study for FRET-restrained high-precision structural modeling. Nature Methods 9(12) 1218-U1129.
Dimura, M., T. O. Peulen, C. A. Hanke, A. Prakash, H. Gohlke and C. A. M. Seidel (2016). Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems." Current Opinion in Structural Biology 40 163-185.
Sindbert, S., S. Kalinin, N. Hien, A. Kienzler, L. Clima, W. Bannwarth, B. Appel, S. Muller and C. A. M. Seidel (2011). Accurate Distance Determination of Nucleic Acids via Forster Resonance Energy Transfer - Implications of Dye Linker Length and Rigidity. Journal of the American Chemical Society 133(8) 2463-2480.
