- Ortiz-Sanchez JM, Nichols SE, Sayyah J,
Brown JH, McCammon JA, Grant BJ (2012)
Identification of potential small molecule bind-
ing pockets on rho family GTPases. PLoS One
7(7):e40809
- Sugita Y, Okamoto Y (2000) Replica-exchange
multicanonical algorithm and multicanonical
replica-exchange method for simulating sys-
tems with rough energy landscape. Chem
Phys Lett 329(3–4):261–270
- Voter AF (1997) Hyperdynamics: accelerated
molecular dynamics of infrequent events. Phys
Rev Lett 78(20):3908–3911
- Kerrigan JE (2013) Molecular dynamics simu-
lations in drug design. Methods Mol Biol
993:95–113
- Mortier J, Rakers C, Bermudez M, Murgueitio
MS, Riniker S, Wolber G (2015) The impact of
molecular dynamics on drug design: applica-
tions for the characterization of ligand-
macromolecule complexes. Drug Discov
Today 20(6):686–702
- Zhao H, Caflisch A (2015) Molecular dynam-
ics in drug design. Eur J Med Chem 91:4–14
- Li H, Kasam V, Tautermann CS, Seeliger D,
Vaidehi N (2014) Computational method to
identify druggable binding sites that target
protein-protein interactions. J Chem Inf
Model 54(5):1391–1400
- Alvarez-Garcia D, Barril X (2014) Molecular
simulations with solvent competition quantify
water displaceability and provide accurate inter-
action maps of protein binding sites. J Med
Chem 57(20):8530–8539
- Guvench O, MacKerell AD Jr (2009) Compu-
tational fragment-based binding site identifica-
tion by ligand competitive saturation. PLoS
Comput Biol 5(7):e1000435
- Lexa KW, Carlson HA (2011) Full protein
flexibility is essential for proper hot-spot
mapping. J Am Chem Soc 133(2):200–202
- Raman EP, Yu W, Lakkaraju SK, MacKerell AD
Jr (2013) Inclusion of multiple fragment types
in the site identification by ligand competitive
saturation (SILCS) approach. J Chem Inf
Model 53(12):3384–3398
- Beuming T, Che Y, Abel R, Kim B,
Shanmugasundaram V, Sherman W (2012)
Thermodynamic analysis of water molecules at
the surface of proteins and applications to
binding site prediction and characterization.
Proteins 80(3):871–883
- Masukawa KM, Kollman PA, Kuntz ID (2003)
Investigation of neuraminidase-substrate rec-
ognition using molecular dynamics and free
energy calculations. J Med Chem 46
(26):5628–5637
- Landon MR, Amaro RE, Baron R et al (2008)
Novel druggable hot spots in avian influenza
neuraminidase H5N1 revealed by computa-
tional solvent mapping of a reduced and repre-
sentative receptor ensemble. Chem Biol Drug
Des 71(2):106–116
- Shu M, Lin Z, Zhang Y, Wu Y, Mei H, Jiang Y
(2011) Molecular dynamics simulation of osel-
tamivir resistance in neuraminidase of avian
influenza H5N1 virus. J Mol Model 17
(3):587–592
- Dror RO, Pan AC, Arlow DH et al (2011)
Pathway and mechanism of drug binding to
G-protein-coupled receptors. Proc Natl Acad
Sci U S A 108(32):13118–13123
- Overington JP, Al-Lazikani B, Hopkins AL
(2006) Opinion - how many drug targets are
there? Nat Rev Drug Discov 5(12):993–996
- Kappel K, Miao Y, McCammon JA (2015)
Accelerated molecular dynamics simulations
of ligand binding to a muscarinic G-protein-
coupled receptor. Q Rev Biophys 48
(4):479–487
- Cimermancic P, Weinkam P, Rettenmaier TJ
(2016) CryptoSite: expanding the druggable
proteome by characterization and prediction
of cryptic binding sites. J Mol Biol 428
(4):709–719
- Petros AM, Olejniczak ET, Fesik SW (2004)
Structural biology of the Bcl-2 family of pro-
teins. Biochim Biophys Acta 1644(2–3):83–94
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