Server For Computing/Predicting DEPTH, Ligand Binding Sites, pKa, Disulfide engineering

  1. 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>
  2. 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
  3. Residue depth: a novel parameter for the analysis of protein structure and stability. Suvobrata Chakravarty and Raghavan Varadarajan(1999). Structure 7,723-732.
  4. Patel, S.; Indu, S.; Ramakrishnan, C.; Varadarajan, R. Protein disulfide analysis and design. In Biomolecular Forms and Functions; World Scientific/Indian Inst of Science: Bangalore, India, 2013; pp. 296–311.
  5. Indu S, Kumar ST, Thakurela S, Gupta M, Bhaskara RM, Ramakrishnan C, Varadarajan R. Disulfide conformation and design at helix N-termini. Proteins. 2010 Apr;78(5):1228-42. doi: 10.1002/prot.22641. PMID: 19938155; PMCID: PMC7167797.
  6. Das M, Kobayashi M, Yamada Y, Sreeramulu S, Ramakrishnan C, Wakatsuki S, Kato R, Varadarajan R. Design of disulfide-linked thioredoxin dimers and multimers through analysis of crystal contacts. J Mol Biol. 2007 Oct 5;372(5):1278-92. doi: 10.1016/j.jmb.2007.07.033. Epub 2007 Aug 2. PMID: 17727880.
  7. Dani VS, Ramakrishnan C, Varadarajan R. MODIP revisited: re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins. Protein Eng. 2003 Mar;16(3):187-93. doi: 10.1093/proeng/gzg024. PMID: 12702798.
  8. Sowdhamini R, Srinivasan N, Shoichet B, Santi DV, Ramakrishnan C, Balaram P. Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis. Protein Eng. 1989 Nov;3(2):95-103. doi: 10.1093/protein/3.2.95. PMID: 2594728.

For NGL plugin:
  1. 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
  2. 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
  3. H Nguyen, DA Case and AS Rose. (2017). NGLview - Interactive molecular graphics for Jupyter notebooks. Bioinformatics, btx789. doi:10.1093/bioinformatics/btx789
  4. 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