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with PASS. J Comput Aided Mol Des 14:383–401
130. Czirják G (2015) PrinCCes: continuity-based geometric decomposition and systematic
visualization of the void repertoire of proteins. J Mol Graph Model 62:118–127
131. Yu J, Zhou Y, Tanaka I, Yao M (2009) Roll: a new algorithm for the detection of protein
pockets and cavities with a rolling probe sphere. Bioinformatics 26:46–52
132. Sheffler W, Baker D (2009) RosettaHoles: rapid assessment of protein core packing for
structure prediction, refinement, design, and validation. Protein Sci 18:229–239
133. Laskowski RA (1995) SURFNET: a program for visualizing molecular surfaces, cavities,
and intermolecular interactions. J Mol Graph 13:323–330
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
167
the titratable residues on the inhibitor affinity to BACE-1. Biochemistry 49:7255–7263.
https://doi.org/10.1021/bi100637n
112. Perryman AL, Lin J (2004) HIV-1 protease molecular dynamics of a wild-type and of the
V82F / I84V mutant: possible contributions to drug resistance and a potential new target site
for drugs. Protein Sci 13:1108–1123. https://doi.org/10.1110/ps.03468904.importance
113. Trylska J, Tozzini V, Chang CEA, McCammon JA (2007) HIV-1 protease substrate binding
and product release pathways explored with coarse-grained molecular dynamics. Biophys J
92:4179–4187. https://doi.org/10.1529/biophysj.106.100560
114. Liu Z-P, Wu L-Y, Wang Y et al (2008) Bridging protein local structures and protein
functions. Amino Acids 35:627–650
115. Ratnaparkhi GS, Varadarajan R (2000) Thermodynamic and structural studies of cavity
formation in proteins suggest that loss of packing interactions rather than the hydrophobic
effect dominates the observed energetics. Biochemistry 39:12365–12374
116. DesJarlais RL, Sheridan RP, Seibel GL et al (1988) Using shape complementarity as an
initial screen in designing ligands for a receptor binding site of known three-dimensional
structure. J Med Chem 31:722–729
117. Anderson AC (2003) The process of structure-based drug design. Chem Biol 10:787–797.
https://doi.org/10.1016/j.chembiol.2003.09.002
118. Lee B, Richards FM (1971) The interpretation of protein structures: estimation of static
accessibility. J Mol Biol 55:379–400
119. Connolly ML (1983) Analytical molecular surface calculation. J Appl Crystallogr 16:548–
558
120. Connolly ML (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science
221:709–713
121. Liang J, Woodward C, Edelsbrunner H (1998) Anatomy of protein pockets and cavities:
measurement of binding site geometry and implications for ligand design. Protein Sci
7:1884–1897
122. Edelsbrunner H (1995) Smooth surfaces for multi-scale shape representation. In:
International conference on foundations of software technology and theoretical computer
science, pp 391–412
123. Mücke EP (1998) A robust implementation for three-dimensional Delaunay triangulations.
Int J Comput Geom Appl 8:255–276
124. Bryant R, Edelsbrunner H, Koehl P, Levitt M (2004) The area derivative of a space-filling
diagram. Discrete Comput Geom 32:293–308
125. Dundas J, Ouyang Z, Tseng J et al (2006) CASTp: computed atlas of surface topography of
proteins with structural and topographical mapping of functionally annotated residues.
Nucleic Acids Res 34:W116–W118
126. Benkaidali L, André F, Maouche B et al (2013) Computing cavities, channels, pores and
pockets in proteins from non-spherical ligands models. Bioinformatics 30:792–800
127. Huang B, Schroeder M (2006) LIGSITE csc: predicting ligand binding sites using the
Connolly surface and degree of conservation. BMC Struct Biol 6:19
128. Oliveira SHP, Ferraz FAN, Honorato RV et al (2014) KVFinder: steered identification of
protein cavities as a PyMOL plugin. BMC Bioinform 15:197
129. Brady GP, Stouten PFW (2000) Fast prediction and visualization of protein binding pockets
with PASS. J Comput Aided Mol Des 14:383–401
130. Czirják G (2015) PrinCCes: continuity-based geometric decomposition and systematic
visualization of the void repertoire of proteins. J Mol Graph Model 62:118–127
131. Yu J, Zhou Y, Tanaka I, Yao M (2009) Roll: a new algorithm for the detection of protein
pockets and cavities with a rolling probe sphere. Bioinformatics 26:46–52
132. Sheffler W, Baker D (2009) RosettaHoles: rapid assessment of protein core packing for
structure prediction, refinement, design, and validation. Protein Sci 18:229–239
133. Laskowski RA (1995) SURFNET: a program for visualizing molecular surfaces, cavities,
and intermolecular interactions. J Mol Graph 13:323–330
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
167