57. Rognan D, Lauemøller SL, Holm A, Buus S, Tschinke V (1999) Predicting binding affinities
of protein ligands from three-dimensional models: application to peptide binding to class I
major histocompatibility proteins. J Med Chem 42(22):4650–4658
58. Wang R, Lai L, Wang S (2002) Further development and validation of empirical scoring
functions for structure-based binding affinity prediction. J Comput Aided Mol Des 16(1):
11–26
59. Muegge I (2000) A knowledge-based scoring function for protein-ligand interactions:
probing the reference state. Perspect Drug Discov Des 20(1):99–114
60. Muegge I (2001) Effect of ligand volume correction on PMF scoring. J Comput Chem 22(4):
418–425
61. Muegge I, Martin YC (1999) A general and fast scoring function for protein-ligand
interactions: a simplified potential approach. J Med Chem 42(5):791–804
62. Gohlke H, Hendlich M, Klebe G (2000) Knowledge-based scoring function to predict
protein-ligand interactions. J Mol Biol 295(2):337–356
63. DeWitte RS, Shakhnovich EI (1996) SMoG: de novo design method based on simple, fast,
and accurate free energy estimates. 1. Methodology and supporting evidence. J Am Chem
Soc 118(47):11733–11744
64. Momany FA, McGuire RF, Burgess AW, Scheraga HA (1975) Energy parameters in
polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions,
hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring
amino acids. The J Phys Chem 79(22):2361–2381
65. Nemethy G, Pottle MS, Scheraga HA (1983) Energy parameters in polypeptides. 9.
Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. The J Phys Chem 87(11):1883–1887
66. Lifson S, Warshel A (1968) Consistent force field for calculations of conformations,
vibrational spectra, and enthalpies of cycloalkane and n-alkane molecules. J Chem Phys 49
(11):5116–5129
67. Hagler AT, Huler E, Lifson S (1974) Energy functions for peptides and proteins.
I. Derivation of a consistent force field including the hydrogen bond from amide crystals.
J Am Chem Soc 96(17):5319–5327
68. Hagler AT, Lifson S (1974) Energy functions for peptides and proteins. II. Amide hydrogen
bond and calculation of amide crystal properties. J Am Chem Soc 96(17):5327–5335
69. Jorgensen WL (1981) Quantum and statistical mechanical studies of liquids. 10.
Transferable intermolecular potential functions for water, alcohols, and ethers. Application
to liquid water. J Am Chem Soc 103(2):335–340
70. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S, Weiner P
(1984) A new force field for molecular mechanical simulation of nucleic acids and proteins.
J Am Chem Soc 106(3):765–784
71. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC,
Fox T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation
of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117(19):5179–5197
72. Damm W, van Gunsteren WF (2000) Reversible peptide folding: dependence on molecular
force field used. J Comput Chem 21(9):774–787
73. García AE, Sanbonmatsu KY (2001) Exploring the energy landscape of a ß hairpin in
explicit solvent. Proteins: Struct, Funct, Bioinf 42(3):345–354
74. Mitsutake A, Sugita Y, Okamoto Y (2001) Generalized-ensemble algorithms for molecular
simulations of biopolymers. Pept Sci 60(2):96–123
75. García AE, Sanbonmatsu KY (2002) a-Helical stabilization by side chain shielding of
backbone hydrogen bonds. Proc Natl Acad Sci 99(5):2782–2787
76. Simmerling C, Strockbine B, Roitberg AE (2002) All-atom structure prediction and folding
simulations of a stable protein. J Am Chem Soc 124(38):11258–11259
77. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan SA, Karplus M (1983)
CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4(2):187–217
298
D. Velmurugan et al.
of protein ligands from three-dimensional models: application to peptide binding to class I
major histocompatibility proteins. J Med Chem 42(22):4650–4658
58. Wang R, Lai L, Wang S (2002) Further development and validation of empirical scoring
functions for structure-based binding affinity prediction. J Comput Aided Mol Des 16(1):
11–26
59. Muegge I (2000) A knowledge-based scoring function for protein-ligand interactions:
probing the reference state. Perspect Drug Discov Des 20(1):99–114
60. Muegge I (2001) Effect of ligand volume correction on PMF scoring. J Comput Chem 22(4):
418–425
61. Muegge I, Martin YC (1999) A general and fast scoring function for protein-ligand
interactions: a simplified potential approach. J Med Chem 42(5):791–804
62. Gohlke H, Hendlich M, Klebe G (2000) Knowledge-based scoring function to predict
protein-ligand interactions. J Mol Biol 295(2):337–356
63. DeWitte RS, Shakhnovich EI (1996) SMoG: de novo design method based on simple, fast,
and accurate free energy estimates. 1. Methodology and supporting evidence. J Am Chem
Soc 118(47):11733–11744
64. Momany FA, McGuire RF, Burgess AW, Scheraga HA (1975) Energy parameters in
polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions,
hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring
amino acids. The J Phys Chem 79(22):2361–2381
65. Nemethy G, Pottle MS, Scheraga HA (1983) Energy parameters in polypeptides. 9.
Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. The J Phys Chem 87(11):1883–1887
66. Lifson S, Warshel A (1968) Consistent force field for calculations of conformations,
vibrational spectra, and enthalpies of cycloalkane and n-alkane molecules. J Chem Phys 49
(11):5116–5129
67. Hagler AT, Huler E, Lifson S (1974) Energy functions for peptides and proteins.
I. Derivation of a consistent force field including the hydrogen bond from amide crystals.
J Am Chem Soc 96(17):5319–5327
68. Hagler AT, Lifson S (1974) Energy functions for peptides and proteins. II. Amide hydrogen
bond and calculation of amide crystal properties. J Am Chem Soc 96(17):5327–5335
69. Jorgensen WL (1981) Quantum and statistical mechanical studies of liquids. 10.
Transferable intermolecular potential functions for water, alcohols, and ethers. Application
to liquid water. J Am Chem Soc 103(2):335–340
70. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S, Weiner P
(1984) A new force field for molecular mechanical simulation of nucleic acids and proteins.
J Am Chem Soc 106(3):765–784
71. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC,
Fox T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation
of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117(19):5179–5197
72. Damm W, van Gunsteren WF (2000) Reversible peptide folding: dependence on molecular
force field used. J Comput Chem 21(9):774–787
73. García AE, Sanbonmatsu KY (2001) Exploring the energy landscape of a ß hairpin in
explicit solvent. Proteins: Struct, Funct, Bioinf 42(3):345–354
74. Mitsutake A, Sugita Y, Okamoto Y (2001) Generalized-ensemble algorithms for molecular
simulations of biopolymers. Pept Sci 60(2):96–123
75. García AE, Sanbonmatsu KY (2002) a-Helical stabilization by side chain shielding of
backbone hydrogen bonds. Proc Natl Acad Sci 99(5):2782–2787
76. Simmerling C, Strockbine B, Roitberg AE (2002) All-atom structure prediction and folding
simulations of a stable protein. J Am Chem Soc 124(38):11258–11259
77. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan SA, Karplus M (1983)
CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4(2):187–217
298
D. Velmurugan et al.