Methods, Datasets and Visualization

  1. The RCSB Protein Data Bank: new resources for research and education. Rose, P.W. et al. Nucleic Acids Res. (2013) 41, D475—82
  2. NGL Viewer: a web application for molecular visualization. Rose, A.S. and Hildebrand, P.W. Nucleic Acids Res. (2015) 43, W576—W579
  3. TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates. Tusnády, G.E. et al. Bioinformatics (2005) 21, 1276—7
  4. 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.
  5. Loopholes and missing links in protein modeling. Rossi, K.A. et al. Protein Sci. (2007) 16, 1999—2012
  6. ModLoop: automated modeling of loops in protein structures. Fiser, A. and Sali, A. Bioinformatics (2003) 19, 2500—2501
  7. Loops In Proteins (LIP)--a comprehensive loop database for homology modelling. Michalsky, E. et al. Protein Eng. (2003) 16, 979—85.
  8. Further reading

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