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Zhu, Hongbo, and M. Teresa Pisabarro. “MSPocket: an Orientation-Independent Algorithm for the Detection of Ligand Binding Pockets.” Bioinformatics, vol. 27, no. 3, June 2010, pp. 351–358., doi:10.1093/bioinformatics/btq672.
Connolly, M. “Solvent-Accessible Surfaces of Proteins and Nucleic Acids.” Science, vol. 221, no. 4612, 1983, pp. 709–713., doi:10.1126/science.6879170.
Ezzat, Ali, and Chee Keong Kwoh. “Comparison of Structure-Based Tools for the Prediction of Ligand Binding Site Residues in Apo-Structures.” Procedia Computer Science, vol. 11, 2012, pp. 115–126., doi:10.1016/j.procs.2012.09.013.
Fathi, Seyed Saberi, and Jack A Tuszynski. “A Simple Method for Finding a Protein’s Ligand-Binding Pockets.” BMC Structural Biology, vol. 14, no. 1, 2014, p. 18., doi:10.1186/1472-6807-14-18.
Guilloux, Vincent Le, et al. “Fpocket: An Open Source Platform for Ligand Pocket Detection.” BMC Bioinformatics, vol. 10, no. 1, 2009, p. 168., doi:10.1186/1471-2105-10-168.
Hendlich, Manfred, et al. “LIGSITE: Automatic and Efficient Detection of Potential Small Molecule-Binding Sites in Proteins.” Journal of Molecular Graphics and Modelling, vol. 15, no. 6, 1997, pp. 359–363., doi:10.1016/s1093-3263(98)00002-3.
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne. (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.
Huang, Bingding, and Michael Schroeder. “LIGSITEcsc: Predicting Ligand Binding Sites Using the Connolly Surface and Degree of Conservation.” BMC Structural Biology, vol. 6, no. 1, 2006, p. 19., doi:10.1186/1472-6807-6-19.
Jr., G. Patrick Brady, and Pieter F.w. Stouten. “Fast Prediction and Visualization of Protein Binding Pockets with PASS.” Journal of Computer-Aided Molecular Design, vol. 14, no. 4, May 2000, pp. 383–401., doi:10.1023/a:1008124202956.
Kalidas, Yeturu, and Nagasuma Chandra. “PocketDepth: A New Depth Based Algorithm for Identification of Ligand Binding Sites in Proteins.” Journal of Structural Biology, vol. 161, no. 1, 2008, pp. 31–42., doi:10.1016/j.jsb.2007.09.005.
Krivák, Radoslav, and David Hoksza. “P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features.” Algorithms for Computational Biology Lecture Notes in Computer Science, 2015, pp. 41–52., doi:10.1007/978-3-319-21233-3_4.
Krivák, Radoslav, and David Hoksza. “Improving Protein-Ligand Binding Site Prediction Accuracy by Classification of Inner Pocket Points Using Local Features.” Journal of Cheminformatics, vol. 7, no. 1, Jan. 2015, doi:10.1186/s13321-015-0059-5.
Laskowski, Roman A. “SURFNET: A Program for Visualizing Molecular Surfaces, Cavities, and Intermolecular Interactions.” Journal of Molecular Graphics, vol. 13, no. 5, 1995, pp. 323–330., doi:10.1016/0263-7855(95)00073-9.
Levitt, David G., and Leonard J. Banaszak. “POCKET: A Computer Graphies Method for Identifying and Displaying Protein Cavities and Their Surrounding Amino Acids.” Journal of Molecular Graphics, vol. 10, no. 4, 1992, pp. 229–234., doi:10.1016/0263-7855(92)80074-n.
Pan, Xiaoyong, and Hong-Bin Shen. “RNA-Protein Binding Motifs Mining with a New Hybrid Deep Learning Based Cross-Domain Knowledge Integration Approach.” BMC Bioinformatics, vol. 18, no. 1, 2017, doi:10.1186/s12859-017-1561-8.
Sarafianos, Stefan G., et al. “Structure and Function of HIV-1 Reverse Transcriptase: Molecular Mechanisms of Polymerization and Inhibition.” Journal of Molecular Biology, vol. 385, no. 3, 2009, pp. 693–713., doi:10.1016/j.jmb.2008.10.071.
Tubbs, Julie L., et al. “Flipping of Alkylated DNA Damage Bridges Base and Nucleotide Excision Repair.” Nature, vol. 459, no. 7248, 2009, pp. 808–813., doi:10.1038/nature08076.
Weisel, Martin, et al. “PocketPicker: Analysis of Ligand Binding-Sites with Shape Descriptors.” Chemistry Central Journal, vol. 1, no. 1, 2007, p. 7., doi:10.1186/1752-153x-1-7.
Yu, Jian, et al. “Roll: a New Algorithm for the Detection of Protein Pockets and Cavities with a Rolling Probe Sphere.” Bioinformatics, vol. 26, no. 1, 2009, pp. 46–52., doi:10.1093/bioinformatics/btp599.
Zhu, Hongbo, and M. Teresa Pisabarro. “MSPocket: an Orientation-Independent Algorithm for the Detection of Ligand Binding Pockets.” Bioinformatics, vol. 27, no. 3, June 2010, pp. 351–358., doi:10.1093/bioinformatics/btq672.