Methods and Datasets

  1. A fragement based method for modeling of protein segments into cry-EM density maps. Ismer, J. et al. BMC Bioinformatics (2017) 18(1):475
  2. The RCSB Protein Data Bank: new resources for research and education. Rose, P.W. et al. Nucleic Acids Res. (2013) 41, D475—82
  3. SL2. an interactive webtool for modeling of missing segments in proteins. Ismer, J. et al. Nucleic Acids Res. (2016) 44, W390—W394
  4. NGL Viewer: a web application for molecular visualization. Rose, A.S. and Hildebrand, P.W. Nucleic Acids Res. (2015) 43, W576—W579
  5. TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates. Tusnády, G.E. et al. Bioinformatics (2005) 21, 1276—7
  6. SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins. Hildebrand, P.W. et al. Nucleic Acids Res. (2009) 37, W571—4.
  7. Loops In Proteins (LIP)--a comprehensive loop database for homology modelling. Michalsky, E. et al. Protein Eng. (2003) 16, 979—85.
  8. ModLoop: automated modeling of loops in protein structures. Fiser, A. and Sali, A. Bioinformatics (2003) 19, 2500—2501
  9. Loopholes and missing links in protein modeling. Rossi, K.A. et al. Protein Sci. (2007) 16, 1999—2012
  10. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. Frank,J. et al. J. Struct. Biol. (1996) 116, 190—9
  11. Further reading

  12. FREAD revisited: Accurate loop structure prediction using a database search algorithm. Choi, Y. and Deane, C.M. Proteins (2010) 78, 1431—40
  13. Fragment-based modeling of membrane protein loops: successes, failures, and prospects for the future. Kelm, S. et al. Proteins (2014) 82, 175—86