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115. Jorgensen WL, Chandrasekhar J, Madura JD
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(2010) Implementation of the CHARMM
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stability effects from correction Maps, virtual
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LINCS: a linear constraint solver for molecular
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J
Comput
Chem
12:1463–1472
118. Essmann U, Perera L, Berkowitz ML et al
(1995) A smooth particle mesh Ewald
method. J Chem Phys 103:8577
119. Bussi G, Donadio D, Parrinello M (2007)
Canonical sampling through velocity rescaling. J Chem Phys 126:014101
120. Amadei A, Linssen AB, Berendsen HJ (1993)
Essential dynamics of proteins. Proteins
17:412–425
121. Papaleo E, Pasi M, Tiberti M et al (2011)
Molecular dynamics of mesophilic-like
mutants of a cold-adapted enzyme: insights
into distal effects induced by the mutations.
PLoS One 6:e24214
122. Atilgan AR, Akan P, Baysal C (2004) Smallworld communication of residues and significance for protein dynamics. Biophys J
86:85–91
123. Bussi G, Gervasio FL, Laio A et al (2006)
Free-energy landscape for beta hairpin folding
from combined parallel tempering and metadynamics.
J
Am
Chem
Soc
128:13435–13441
124. Bonomi M, Barducci A, Parrinello M (2009)
Reconstructing the equilibrium Boltzmann
distribution from well-tempered metadynamics. J Comput Chem 30:1615–1621
125. Mellacheruvu D, Wright Z, Couzens AL et al
(2013) The CRAPome: a contaminant repository for affinity purification – mass spectrometry data. Nat Methods 10:730–736
126. Kuzu G, Gursoy A, Nussinov R et al (2014)
Exploiting conformational ensembles in
modeling protein-protein interactions on the
proteome
scale.
J
Proteome
Res
12:2641–2653
127. Gao M, Skolnick J (2011) New benchmark
metrics for protein-protein docking methods.
Proteins 79:1623–1634
244
Elena Papaleo
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures
for molecular simulations. Nucleic Acids Res
35:522–525
111. Mackerell AD, Feig M, Brooks CL (2004)
Extending the treatment of backbone energetics in protein force fields: limitations of
gas-phase quantum mechanics in reproducing
protein conformational distributions in
molecular dynamics simulations. J Comput
Chem 25:1400–1415
112. Piana S, Lindorff-Larsen K, Shaw DE (2011)
How robust are protein folding simulations
with respect to force field parameterization?
Biophys J 100:L47–L49
113. Mackerell AD, Banavali NK (2000) All atom
empirical force field for nucleic acids:
II. Application to molecular dynamics simulations of DNA and RNA in solution. J Comput
Chem 21:105–120
114. Parsons DW, Li M, Zhang X et al (2011) The
genetic landscape of the childhood cancer
medulloblastoma. Science 331:435–439
115. Jorgensen WL, Chandrasekhar J, Madura JD
et al (1983) Comparison of simple potential
functions for simulating liquid water. J Chem
Phys 79:926
116. Bjelkmar P, Larsson P, Cuendet MA et al
(2010) Implementation of the CHARMM
force field in GROMACS: analysis of protein
stability effects from correction Maps, virtual
interaction sites, and water models. J Chem
Theory Comput 6:459–466
117. Hess B, Bekker H, Berendsen H et al (1993)
LINCS: a linear constraint solver for molecular
simulations.
J
Comput
Chem
12:1463–1472
118. Essmann U, Perera L, Berkowitz ML et al
(1995) A smooth particle mesh Ewald
method. J Chem Phys 103:8577
119. Bussi G, Donadio D, Parrinello M (2007)
Canonical sampling through velocity rescaling. J Chem Phys 126:014101
120. Amadei A, Linssen AB, Berendsen HJ (1993)
Essential dynamics of proteins. Proteins
17:412–425
121. Papaleo E, Pasi M, Tiberti M et al (2011)
Molecular dynamics of mesophilic-like
mutants of a cold-adapted enzyme: insights
into distal effects induced by the mutations.
PLoS One 6:e24214
122. Atilgan AR, Akan P, Baysal C (2004) Smallworld communication of residues and significance for protein dynamics. Biophys J
86:85–91
123. Bussi G, Gervasio FL, Laio A et al (2006)
Free-energy landscape for beta hairpin folding
from combined parallel tempering and metadynamics.
J
Am
Chem
Soc
128:13435–13441
124. Bonomi M, Barducci A, Parrinello M (2009)
Reconstructing the equilibrium Boltzmann
distribution from well-tempered metadynamics. J Comput Chem 30:1615–1621
125. Mellacheruvu D, Wright Z, Couzens AL et al
(2013) The CRAPome: a contaminant repository for affinity purification – mass spectrometry data. Nat Methods 10:730–736
126. Kuzu G, Gursoy A, Nussinov R et al (2014)
Exploiting conformational ensembles in
modeling protein-protein interactions on the
proteome
scale.
J
Proteome
Res
12:2641–2653
127. Gao M, Skolnick J (2011) New benchmark
metrics for protein-protein docking methods.
Proteins 79:1623–1634
244
Elena Papaleo