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72. Kadam RU, Juraszek J, Brandenburg B et al (2017) Potent peptidic fusion inhibitors of
influenza virus. Science 358(80):496–502. https://doi.org/10.1126/science.aan051
73. Chang YS, Graves B, Guerlavais V et al (2013) Stapled a-helical peptide drug development:
a potent dual inhibitor of MDM2 and MDMX for p53-dependent cancer therapy. Proc Natl
Acad Sci 110:E3445–E3454. https://doi.org/10.1073/pnas.1303002110
74. Shadfan M, Lopez-Pajares V, Yuan Z-M (2012) MDM2 and MDMX: alone and together in
regulation of p53. Transl Cancer Res 1:88–89. https://doi.org/10.3978/j.issn.2218-676x.
2012.04.02
75. Tiwari G, Verma CS (2017) Toward understanding the molecular recognition of albumin by
p53-activating stapled peptide ATSP-7041. J Phys Chem B 121:657–670. https://doi.org/10.
1021/acs.jpcb.6b09900
76. Schindler CEM, De Vries SJ, Zacharias M (2015) Fully blind peptide-protein docking with
pepATTRACT. Structure 23:1507–1515. https://doi.org/10.1016/j.str.2015.05.021
77. Leder L, Berger C, Bomhauser S et al (1995) Spectroscopic, calorimetric, and kinetic
demonstration of conformational adaptation in peptide-antibody recognition. Biochemistry
34:16509–16518. https://doi.org/10.1021/bi00050a035
78. Ferrari AM, Wei BQ, Costantino L, Shoichet BK (2004) Soft docking and multiple receptor
conformations in virtual screening. J Med Chem 47:5076–5084. https://doi.org/10.1021/
jm049756p
79. Totrov M, Ferna J, Abagyan R (2002) Soft protein–protein docking in internal coordinates.
Protein Sci 11:280–291. https://doi.org/10.1110/ps.19202.ical
80. Li CH, Ma XH, Chen WZ, Wang CX (2003) A soft docking algorithm for predicting the
structure of antibody-antigen complexes. Proteins Struct Funct Genet 52:47–50. https://doi.
org/10.1002/prot.10382
81. Alonso H, Bliznyuk AA, Gready JE (2006) Combining docking and molecular dynamic
simulations in drug design. Med Res Rev 26:531–568. https://doi.org/10.1002/med.20067
82. Leach AR (1994) Ligand docking to proteins with discrete side-chain flexibility. J Mol Biol
235:345–356. https://doi.org/10.1016/s0022-2836(05)80038-5
83. Schnecke V, Kuhn LA (2000) Virtual screening with solvation and ligand-induced
complementarity. Perspect Drug Discov Des 20:171–190. https://doi.org/10.1023/a:
1008737207775
84. Källblad P, Dean PM (2003) Efficient conformational sampling of local side-chain
flexibility. J Mol Biol 326:1651–1665. https://doi.org/10.1016/s0022-2836(03)00083-4
85. Frimurer TM, Peters GH, Iversen LF et al (2003) Ligand-induced conformational changes:
Improved predictions of ligand binding conformations and affinities. Biophys J 84:2273–
2281. https://doi.org/10.1016/s0006-3495(03)75033-4
86. Gaudreault F, Chartier M, Najmanovich R (2012) Side-chain rotamer changes upon ligand
binding: common, crucial, correlate with entropy and rearrange hydrogen bonding.
Bioinformatics 28:423–430. https://doi.org/10.1093/bioinformatics/bts395
87. Apostolakis J, Plückthun A, Caflisch A (1998) Docking small ligands in flexible binding
sites. J Comput Chem 19:21–37. https://doi.org/10.1002/(sici)1096-987x(19980115)19:1%
3c21::aid-jcc2%3e3.0.co;2-0
88. Davis IW, Baker D (2009) RosettaLigand docking with full ligand and receptor flexibility.
J Mol Biol 385:381–392. https://doi.org/10.1016/j.jmb.2008.11.010
89. Meiler J, Baker D (2006) ROSETTALIGAND: protein-small molecule docking with full
side-chain flexibility. Proteins Struct Funct Bioinform 65:538–548. https://doi.org/10.1002/
prot.21086
90. Perryman AL, Lin JH, McCammon JA (2006) Optimization and computational evaluation of
a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1
protease: an application of the relaxed complex method of structure-based drug design.
Chem Biol Drug Des 67:336–345. https://doi.org/10.1111/j.1747-0285.2006.00382.x
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
165
models. J Chem Theory Comput 6:2547–2557
72. Kadam RU, Juraszek J, Brandenburg B et al (2017) Potent peptidic fusion inhibitors of
influenza virus. Science 358(80):496–502. https://doi.org/10.1126/science.aan051
73. Chang YS, Graves B, Guerlavais V et al (2013) Stapled a-helical peptide drug development:
a potent dual inhibitor of MDM2 and MDMX for p53-dependent cancer therapy. Proc Natl
Acad Sci 110:E3445–E3454. https://doi.org/10.1073/pnas.1303002110
74. Shadfan M, Lopez-Pajares V, Yuan Z-M (2012) MDM2 and MDMX: alone and together in
regulation of p53. Transl Cancer Res 1:88–89. https://doi.org/10.3978/j.issn.2218-676x.
2012.04.02
75. Tiwari G, Verma CS (2017) Toward understanding the molecular recognition of albumin by
p53-activating stapled peptide ATSP-7041. J Phys Chem B 121:657–670. https://doi.org/10.
1021/acs.jpcb.6b09900
76. Schindler CEM, De Vries SJ, Zacharias M (2015) Fully blind peptide-protein docking with
pepATTRACT. Structure 23:1507–1515. https://doi.org/10.1016/j.str.2015.05.021
77. Leder L, Berger C, Bomhauser S et al (1995) Spectroscopic, calorimetric, and kinetic
demonstration of conformational adaptation in peptide-antibody recognition. Biochemistry
34:16509–16518. https://doi.org/10.1021/bi00050a035
78. Ferrari AM, Wei BQ, Costantino L, Shoichet BK (2004) Soft docking and multiple receptor
conformations in virtual screening. J Med Chem 47:5076–5084. https://doi.org/10.1021/
jm049756p
79. Totrov M, Ferna J, Abagyan R (2002) Soft protein–protein docking in internal coordinates.
Protein Sci 11:280–291. https://doi.org/10.1110/ps.19202.ical
80. Li CH, Ma XH, Chen WZ, Wang CX (2003) A soft docking algorithm for predicting the
structure of antibody-antigen complexes. Proteins Struct Funct Genet 52:47–50. https://doi.
org/10.1002/prot.10382
81. Alonso H, Bliznyuk AA, Gready JE (2006) Combining docking and molecular dynamic
simulations in drug design. Med Res Rev 26:531–568. https://doi.org/10.1002/med.20067
82. Leach AR (1994) Ligand docking to proteins with discrete side-chain flexibility. J Mol Biol
235:345–356. https://doi.org/10.1016/s0022-2836(05)80038-5
83. Schnecke V, Kuhn LA (2000) Virtual screening with solvation and ligand-induced
complementarity. Perspect Drug Discov Des 20:171–190. https://doi.org/10.1023/a:
1008737207775
84. Källblad P, Dean PM (2003) Efficient conformational sampling of local side-chain
flexibility. J Mol Biol 326:1651–1665. https://doi.org/10.1016/s0022-2836(03)00083-4
85. Frimurer TM, Peters GH, Iversen LF et al (2003) Ligand-induced conformational changes:
Improved predictions of ligand binding conformations and affinities. Biophys J 84:2273–
2281. https://doi.org/10.1016/s0006-3495(03)75033-4
86. Gaudreault F, Chartier M, Najmanovich R (2012) Side-chain rotamer changes upon ligand
binding: common, crucial, correlate with entropy and rearrange hydrogen bonding.
Bioinformatics 28:423–430. https://doi.org/10.1093/bioinformatics/bts395
87. Apostolakis J, Plückthun A, Caflisch A (1998) Docking small ligands in flexible binding
sites. J Comput Chem 19:21–37. https://doi.org/10.1002/(sici)1096-987x(19980115)19:1%
3c21::aid-jcc2%3e3.0.co;2-0
88. Davis IW, Baker D (2009) RosettaLigand docking with full ligand and receptor flexibility.
J Mol Biol 385:381–392. https://doi.org/10.1016/j.jmb.2008.11.010
89. Meiler J, Baker D (2006) ROSETTALIGAND: protein-small molecule docking with full
side-chain flexibility. Proteins Struct Funct Bioinform 65:538–548. https://doi.org/10.1002/
prot.21086
90. Perryman AL, Lin JH, McCammon JA (2006) Optimization and computational evaluation of
a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1
protease: an application of the relaxed complex method of structure-based drug design.
Chem Biol Drug Des 67:336–345. https://doi.org/10.1111/j.1747-0285.2006.00382.x
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
165