From Protein Structure to Function with Bioinformatics.pdf

184 N.J. Burgoyne and R.M. Jacksonchemical character propensities, residue neighbour propensity, residue conservation,secondary structure, residue sequence separation, the length of loops and the locationof crystallographic water to similar effect. Several other related approaches arealso listed in Table 7.1. A comparison of the performance of these methods hasbeen made (Zhou and Qin 2007).7.6 SummaryThis chapter has detailed the current approaches which use surface properties in anumber of important applications including: protein function prediction; predictingbinding site location and druggability; annotation of ligand binding sites for structure-baseddrug design; and protein interface prediction. The various online toolsand methods have been introduced and the interested reader is referred to the publishedarticles for further details. We have attempted to give a broad overview of themethods and their practical applications; however, this is not a comprehensivereview of all methods in this important and emerging area.ReferencesAntosiewicz J, McCammon JA, Gilson MK (1994) Prediction of pH-dependent properties ofproteins. J Mol Biol 238:415–436.Beadle BM, Shoichet BK (2002) Structural bases of stability-function tradeoffs in enzymes. J MolBiol 321:285–296.Berchanski A, Shapira B, Eisenstein M (2004) Hydrophobic complementarity in protein-proteindocking. Proteins 56:130–142.Binkowski TA, Naghibzadeh S, Liang J (2003) CASTp: computed atlas of surface topography ofproteins. Nucleic Acids Res 31:3352–3355.Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces. J Mol Biol280:1–9.Bordner AJ, Abagyan R (2005) Statistical analysis and prediction of protein-protein interfaces.Proteins 60:353–366.Bradford JR, Westhead DR (2005) Improved prediction of protein-protein binding sites using asupport vector machines approach. Bioinformatics 21:1487–1494.Brady GP Jr, Stouten PF (2000) Fast prediction and visualization of protein binding pockets withPASS. J Comput Aided Mol Des 14:383–401.Brown D, Superti-Furga G (2003) Rediscovering the sweet spot in drug discovery. Drug DiscovToday 8:1067–1077.Burgoyne NJ, Jackson RM (2006) Predicting protein interaction sites: binding hot-spots in protein-proteinand protein-ligand interfaces. Bioinformatics 22:1335–1342.Cheng AC, Coleman RG, Smyth KT, et al. (2007) Structure-based maximal affinity model predictssmall-molecule druggability. Nat Biotechnol 25:71–75.Chothia C., Janin J (1975) Principles of protein-protein recognition. Nature 256: 705–708.Clackson T, Wells JA (1995) A hot spot of binding energy in a hormone-receptor interface.Science 267:383–386.Connolly ML (1984) Analytical molecular surface calculation. J Appl Cryst 16:548–558.