Server For Computing/Predicting DEPTH, Cavity Sizes, Ligand Binding Sites and pKa

  • Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins Kuan Pern Tan, Thanh Binh Nguyen, Siddharth Patel, Raghavan Varadarajan and M. S. Madhusudhan Nucl. Acids Res. (1 July 2013) 41 (W1): W314-W321. doi: 10.1093/nar/gkt503>
  • DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins> Kuan Pern Tan; Raghavan Varadarajan; M. S. Madhusudhan Nucleic Acids Research 2011; doi: 10.1093/nar/gkr356
  • Residue depth: a novel parameter for the analysis of protein structure and stability. Suvobrata Chakravarty and Raghavan Varadarajan(1999). Structure 7,723-732.

  • For NGL plugin:
  • AS Rose, AR Bradley, Y Valasatava, JM Duarte, A Prlić and PW Rose. NGL viewer: web-based molecular graphics for large complexes. Bioinformatics: bty419, 2018. doi:10.1093/bioinformatics/bty419
  • AS Rose and PW Hildebrand. NGL Viewer: a web application for molecular visualization. Nucl Acids Res (1 July 2015) 43 (W1): W576-W579 first published online April 29, 2015. doi:10.1093/nar/gkv402
  • H Nguyen, DA Case and AS Rose. (2017). NGLview - Interactive molecular graphics for Jupyter notebooks. Bioinformatics, btx789. doi:10.1093/bioinformatics/btx789
  • JKS Tiemann, R Guixà-González, PW Hildebrand and AS Rose. (2017) .Viewing and sharing molecular dynamics simulations on the web. Nature Methods 14, 1123–1124 (2017). doi:10.1038/nmeth.4497