-
1
-
-
0024821263
-
Molecular mechanics: The MM3 force field for hydrocarbons. 1
-
Allinger N.L., Yuh Y.H., and Lii J.-H. Molecular mechanics: The MM3 force field for hydrocarbons. 1. J. Am. Chem. Soc. 111 (1989) 8551-8566
-
(1989)
J. Am. Chem. Soc.
, vol.111
, pp. 8551-8566
-
-
Allinger, N.L.1
Yuh, Y.H.2
Lii, J.-H.3
-
2
-
-
0242338386
-
-
Pacific Northwest National Laboratory, Richland, Washington
-
Aprà E., Windus T.L., Straatsma T.P., Bylaska E.J., de Jong W., Hirata S., Valiev M., Hackler M., Pollack L., Kowalski K., Harrison R., Dupuis M., Smith D.M.A., Nieplocha J., Tipparaju V., Krishnan M., Auer A.A., Brown E., Cisneros G., Fann G., Früchtl H., Garza J., Hirao K., Kendall R., Nichols J., Tsemekhman K., Wolinski K., Anchell J., Bernholdt D., Borowski P., Clark T., Clerc D., Dachsel H., Deegan M., Dyall K., Elwood D., Glending E., Gutowski M., Hess A., Jaffe J., Johnson B., Ju J., Kobayashi R., Kutteh R., Lin Z., Littlefield R., Long X., Meng B., Nakajima T., Niu S., Rosing M., Sandrone G., Stave M., Taylor H., Thomas G., van Lenthe J., Wong A., and Zhang Z. NWChem, A computational chemistry package for parallel computers, version 4.6. (2004), Pacific Northwest National Laboratory, Richland, Washington
-
(2004)
NWChem, A computational chemistry package for parallel computers, version 4.6.
-
-
Aprà, E.1
Windus, T.L.2
Straatsma, T.P.3
Bylaska, E.J.4
de Jong, W.5
Hirata, S.6
Valiev, M.7
Hackler, M.8
Pollack, L.9
Kowalski, K.10
Harrison, R.11
Dupuis, M.12
Smith, D.M.A.13
Nieplocha, J.14
Tipparaju, V.15
Krishnan, M.16
Auer, A.A.17
Brown, E.18
Cisneros, G.19
Fann, G.20
Früchtl, H.21
Garza, J.22
Hirao, K.23
Kendall, R.24
Nichols, J.25
Tsemekhman, K.26
Wolinski, K.27
Anchell, J.28
Bernholdt, D.29
Borowski, P.30
Clark, T.31
Clerc, D.32
Dachsel, H.33
Deegan, M.34
Dyall, K.35
Elwood, D.36
Glending, E.37
Gutowski, M.38
Hess, A.39
Jaffe, J.40
Johnson, B.41
Ju, J.42
Kobayashi, R.43
Kutteh, R.44
Lin, Z.45
Littlefield, R.46
Long, X.47
Meng, B.48
Nakajima, T.49
Niu, S.50
Rosing, M.51
Sandrone, G.52
Stave, M.53
Taylor, H.54
Thomas, G.55
van Lenthe, J.56
Wong, A.57
Zhang, Z.58
more..
-
4
-
-
0037954108
-
Prudent modeling of core polar residues in computational protein design
-
Bolon D.N., Marcus J.S., Ross S.A., and Mayo S.L. Prudent modeling of core polar residues in computational protein design. J. Mol. Biol. 329 (2003) 611-622
-
(2003)
J. Mol. Biol.
, vol.329
, pp. 611-622
-
-
Bolon, D.N.1
Marcus, J.S.2
Ross, S.A.3
Mayo, S.L.4
-
5
-
-
84890021933
-
Calculation of small molecular interactions by differences of separate total energies: Some procedures with reduced errors
-
Boys S.F., and Bernardi F. Calculation of small molecular interactions by differences of separate total energies: Some procedures with reduced errors. Mol. Phys. 19 (1970) 553-566
-
(1970)
Mol. Phys.
, vol.19
, pp. 553-566
-
-
Boys, S.F.1
Bernardi, F.2
-
6
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4 (1983) 187-217
-
(1983)
J. Comp. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
7
-
-
0035829905
-
Hydrogen bond energetics: A simulation and statistical analysis of N-methyl acetamide (NMA), water, and human lysozyme
-
Buck M., and Karplus M. Hydrogen bond energetics: A simulation and statistical analysis of N-methyl acetamide (NMA), water, and human lysozyme. J. Phys. Chem. B 105 (2001) 11000-11015
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 11000-11015
-
-
Buck, M.1
Karplus, M.2
-
8
-
-
0036468396
-
Protein-protein association kinetics and protein docking
-
Camacho C.J., and Vajda S. Protein-protein association kinetics and protein docking. Curr. Opin. Struct. Biol. 12 (2002) 36-40
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 36-40
-
-
Camacho, C.J.1
Vajda, S.2
-
9
-
-
4944226552
-
A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys
-
Chen Y., Kortemme T., Robertson T., Baker D., and Varani G. A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res. 32 (2004) 5147-5162
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5147-5162
-
-
Chen, Y.1
Kortemme, T.2
Robertson, T.3
Baker, D.4
Varani, G.5
-
10
-
-
0036810246
-
Design, activity, and structure of a highly specific artificial endonuclease
-
Chevalier B.S., Kortemme T., Chadsey M.S., Baker D., Monnat R.J.J., and Stoddard B.L. Design, activity, and structure of a highly specific artificial endonuclease. Mol. Cell 10 (2002) 895-905
-
(2002)
Mol. Cell
, vol.10
, pp. 895-905
-
-
Chevalier, B.S.1
Kortemme, T.2
Chadsey, M.S.3
Baker, D.4
Monnat, R.J.J.5
Stoddard, B.L.6
-
11
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., and Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
12
-
-
0030793767
-
De novo protein design: Fully automated sequence selection
-
Dahiyat B.I., and Mayo S.L. De novo protein design: Fully automated sequence selection. Science 278 (1997) 82-87
-
(1997)
Science
, vol.278
, pp. 82-87
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
13
-
-
3042655537
-
Computational design of a biologically active enzyme
-
Dwyer M.A., Looger L.L., and Hellinga H.W. Computational design of a biologically active enzyme. Science 304 (2004) 1967-1971
-
(2004)
Science
, vol.304
, pp. 1967-1971
-
-
Dwyer, M.A.1
Looger, L.L.2
Hellinga, H.W.3
-
14
-
-
0041746814
-
Electrostatic interaction potentials in molecular force fields
-
Dykstra C.E. Electrostatic interaction potentials in molecular force fields. Chem. Rev. 93 (1993) 2339-2353
-
(1993)
Chem. Rev.
, vol.93
, pp. 2339-2353
-
-
Dykstra, C.E.1
-
15
-
-
0036100338
-
An improved hydrogen bond potential: Impact on medium resolution protein structures
-
Fabiola F., Bertram R., Korostelev A., and Chapman M.S. An improved hydrogen bond potential: Impact on medium resolution protein structures. Protein Sci. 11 (2002) 1415-1423
-
(2002)
Protein Sci.
, vol.11
, pp. 1415-1423
-
-
Fabiola, F.1
Bertram, R.2
Korostelev, A.3
Chapman, M.S.4
-
16
-
-
0347007668
-
Application of systematic sequences of wave-functions to the water dimer
-
Feller D. Application of systematic sequences of wave-functions to the water dimer. J. Chem. Phys. 96 (1992) 6104-6114
-
(1992)
J. Chem. Phys.
, vol.96
, pp. 6104-6114
-
-
Feller, D.1
-
17
-
-
84961974890
-
Hybrid ab initio QM/MM simulation of N-methylacetamide in aqueous solution
-
Gao J., and Freindorf M. Hybrid ab initio QM/MM simulation of N-methylacetamide in aqueous solution. J. Phys. Chem. A 101 (1997) 3182-3188
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 3182-3188
-
-
Gao, J.1
Freindorf, M.2
-
18
-
-
0006248511
-
Geometry of the intermolecular X-H... .Y (X, Y = N, O) hydrogen bond and the calibration of empirical hydrogen-bond potentials
-
Gavezzotti A., and Filippini G. Geometry of the intermolecular X-H... .Y (X, Y = N, O) hydrogen bond and the calibration of empirical hydrogen-bond potentials. J. Phys. Chem. 98 (1994) 4831-4837
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 4831-4837
-
-
Gavezzotti, A.1
Filippini, G.2
-
20
-
-
0038697805
-
Protein-protein docking predictions for the CAPRI experiment
-
Gray J.J., Moughon S., Kortemme T., Schueler-Furman O., Misura K.M.S., Morozov A.V., and Baker D. Protein-protein docking predictions for the CAPRI experiment. Proteins Struct. Funct. Gen. 52 (2003) 118-122
-
(2003)
Proteins Struct. Funct. Gen.
, vol.52
, pp. 118-122
-
-
Gray, J.J.1
Moughon, S.2
Kortemme, T.3
Schueler-Furman, O.4
Misura, K.M.S.5
Morozov, A.V.6
Baker, D.7
-
21
-
-
0038161052
-
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
-
Gray J.J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C.A., and Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331 (2003) 281-299
-
(2003)
J. Mol. Biol.
, vol.331
, pp. 281-299
-
-
Gray, J.J.1
Moughon, S.2
Wang, C.3
Schueler-Furman, O.4
Kuhlman, B.5
Rohl, C.A.6
Baker, D.7
-
22
-
-
2942565710
-
An empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation
-
Grishaev A., and Bax A. An empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation. J. Am. Chem. Soc. 126 (2004) 7281-7292
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 7281-7292
-
-
Grishaev, A.1
Bax, A.2
-
23
-
-
0034248140
-
Development of a knowledge-based potential for crystals of small organic molecules: Calculation of energy surfaces for C=0⋯H-N hydrogen bonds
-
Grzybowski B.A., Ishchenko A.V., DeWitte R.S., Whitesides G.M., and Shakhnovich E.I. Development of a knowledge-based potential for crystals of small organic molecules: Calculation of energy surfaces for C=0⋯H-N hydrogen bonds. J. Phys. Chem. B 104 (2000) 7293-7298
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 7293-7298
-
-
Grzybowski, B.A.1
Ishchenko, A.V.2
DeWitte, R.S.3
Whitesides, G.M.4
Shakhnovich, E.I.5
-
24
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois R., Nielsen J.E., and Serrano L. Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. J. Mol. Biol. 320 (2002) 369-387
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
25
-
-
33644930396
-
Ab initio studies of hydrogen bonding of N-methylacetamide: Structure, cooperativity, and internal rotational barriers
-
Guo H., and Karplus M. Ab initio studies of hydrogen bonding of N-methylacetamide: Structure, cooperativity, and internal rotational barriers. J. Phys. Chem. 96 (1992) 7273-7287
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 7273-7287
-
-
Guo, H.1
Karplus, M.2
-
26
-
-
0000724150
-
Solvent influence on the stability of the peptide hydrogen bond: A supramolecular cooperative effect
-
Guo H., and Karplus M. Solvent influence on the stability of the peptide hydrogen bond: A supramolecular cooperative effect. J. Phys. Chem. 98 (1994) 7104-7105
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 7104-7105
-
-
Guo, H.1
Karplus, M.2
-
27
-
-
0016399124
-
Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals
-
Hagler A.T., Huler E., and Lifson S. 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 (1974) 5319-5327
-
(1974)
J. Am. Chem. Soc.
, vol.96
, pp. 5319-5327
-
-
Hagler, A.T.1
Huler, E.2
Lifson, S.3
-
28
-
-
0016399126
-
Energy functions for peptides and proteins. II. Amide hydrogen bond and calculation of amide crystal properties
-
Hagler A.T., and Lifson S. Energy functions for peptides and proteins. II. Amide hydrogen bond and calculation of amide crystal properties. J. Am. Chem. Soc. 96 (1974) 5327-5335
-
(1974)
J. Am. Chem. Soc.
, vol.96
, pp. 5327-5335
-
-
Hagler, A.T.1
Lifson, S.2
-
30
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin I., Ma B., Wolfson H., and Nussinov R. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins Struct. Funct. Gen. 47 (2002) 409-443
-
(2002)
Proteins Struct. Funct. Gen.
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
33
-
-
0034228977
-
Characterization of hydrogen bonding in a continuum solvent model
-
Hassan S.A., Guarnieri F., and Mehler E.L. Characterization of hydrogen bonding in a continuum solvent model. J. Phys. Chem. B 104 (2000) 6490-6498
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 6490-6498
-
-
Hassan, S.A.1
Guarnieri, F.2
Mehler, E.L.3
-
34
-
-
0037217406
-
Automated design of specificity in molecular recognition
-
Havranek J.J., and Harbury P.B. Automated design of specificity in molecular recognition. Nature Struct. Biol. 10 (2003) 45-52
-
(2003)
Nature Struct. Biol.
, vol.10
, pp. 45-52
-
-
Havranek, J.J.1
Harbury, P.B.2
-
35
-
-
0037434686
-
Density functional theory study of the cooperativity of hydrogen bonds in finite and infinite α-helices
-
Ireta J., Neugebauer J., Scheffler M., Rojo A., and Galvan M. Density functional theory study of the cooperativity of hydrogen bonds in finite and infinite α-helices. J. Phys. Chem. B 107 (2003) 1432-1437
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 1432-1437
-
-
Ireta, J.1
Neugebauer, J.2
Scheffler, M.3
Rojo, A.4
Galvan, M.5
-
36
-
-
0001087855
-
Covalency of the hydrogen bond in ice: A direct X-ray measurement
-
Isaacs E.D., Shukla A., Platzman P.M., Hamann D.R., Barbiellini B., and Tulk C.A. Covalency of the hydrogen bond in ice: A direct X-ray measurement. Phys. Rev. Lett. 82 (1999) 600-603
-
(1999)
Phys. Rev. Lett.
, vol.82
, pp. 600-603
-
-
Isaacs, E.D.1
Shukla, A.2
Platzman, P.M.3
Hamann, D.R.4
Barbiellini, B.5
Tulk, C.A.6
-
37
-
-
0029942661
-
Structure-derived potentials and protein simulations
-
Jernigan R.L., and Bahar I. Structure-derived potentials and protein simulations. Curr. Opin. Struct. Biol. 6 (1996) 195-209
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, pp. 195-209
-
-
Jernigan, R.L.1
Bahar, I.2
-
38
-
-
33645941402
-
The OPLS potential functions for proteins: Energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen W.L., and Tirado-Rives J. The OPLS potential functions for proteins: Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110 (1988) 1657-1666
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
39
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen W.L., Maxwell D.S., and Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118 (1996) 11225-11236
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
40
-
-
0000337925
-
Density functional theory and biomolecules: A study of glycine, alanine, and their oligopeptides
-
Kaschner R., and Hohl D. Density functional theory and biomolecules: A study of glycine, alanine, and their oligopeptides. J. Phys. Chem. A 102 (1998) 5111-5116
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 5111-5116
-
-
Kaschner, R.1
Hohl, D.2
-
41
-
-
0347578256
-
Cooperativity in amide hydrogen bonding chains: Relation between energy, position, and H-bond chain length in peptide and protein folding models
-
Kobko N., and Dannenberg J.J. Cooperativity in amide hydrogen bonding chains: Relation between energy, position, and H-bond chain length in peptide and protein folding models. J. Phys. Chem. A 107 (2003) 10389-10395
-
(2003)
J. Phys. Chem. A
, vol.107
, pp. 10389-10395
-
-
Kobko, N.1
Dannenberg, J.J.2
-
42
-
-
0000455490
-
Noncovalent interactions
-
Kollman P.A. Noncovalent interactions. Accounts Chem. Res. 10 (1977) 365-371
-
(1977)
Accounts Chem. Res.
, vol.10
, pp. 365-371
-
-
Kollman, P.A.1
-
43
-
-
0037195144
-
A simple physical model for binding energy hot spots in protein-protein complexes
-
Kortemme T., and Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. USA 99 (2002) 14116-14121
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 14116-14121
-
-
Kortemme, T.1
Baker, D.2
-
44
-
-
1042298843
-
Computational design of protein-protein interactions
-
Kortemme T., and Baker D. Computational design of protein-protein interactions. Curr. Opin. Chem. Biol. 8 (2004) 91-97
-
(2004)
Curr. Opin. Chem. Biol.
, vol.8
, pp. 91-97
-
-
Kortemme, T.1
Baker, D.2
-
45
-
-
1842577654
-
Computational redesign of protein-protein interaction specificity
-
Kortemme T., Joachimiak L.A., Bullock A.N., Schuler A.D., Stoddard B.L., and Baker D. Computational redesign of protein-protein interaction specificity. Nature Struct. Mol. Biol. 11 (2004) 371-379
-
(2004)
Nature Struct. Mol. Biol.
, vol.11
, pp. 371-379
-
-
Kortemme, T.1
Joachimiak, L.A.2
Bullock, A.N.3
Schuler, A.D.4
Stoddard, B.L.5
Baker, D.6
-
46
-
-
0037470581
-
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
-
Kortemme T., Morozov A.V., and Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol. 326 (2003) 1239-1259
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
Baker, D.3
-
47
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
Kuhlman B., and Baker D. Native protein sequences are close to optimal for their structures. Proc. Natl. Acad. Sci. USA 97 (2000) 10383-10388
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
-
48
-
-
0027772959
-
Shape complementarity at protein/protein interfaces
-
Lawrence M.C., and Colman P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234 (1993) 946-950
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 946-950
-
-
Lawrence, M.C.1
Colman, P.M.2
-
49
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
Lazaridis T., and Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J. Mol. Biol. 288 (1998) 477-487
-
(1998)
J. Mol. Biol.
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
50
-
-
0034031680
-
Effective energy functions for protein structure prediction
-
Lazaridis T., and Karplus M. Effective energy functions for protein structure prediction. Curr. Opin. Struct. Biol. 10 (2000) 139-145
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 139-145
-
-
Lazaridis, T.1
Karplus, M.2
-
51
-
-
0035914481
-
Molecular dynamics in the endgame of protein structure prediction
-
Lee M.R., Tsai J., Baker D., and Kollman P.A. Molecular dynamics in the endgame of protein structure prediction. J. Mol. Biol. 313 (2001) 417-430
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 417-430
-
-
Lee, M.R.1
Tsai, J.2
Baker, D.3
Kollman, P.A.4
-
52
-
-
84985450740
-
Directional hydrogen bonding in the MM3 force field. I
-
Lii J.-H., and Allinger N.L. Directional hydrogen bonding in the MM3 force field. I. J. Phys. Org. Chem. 7 (1994) 591-609
-
(1994)
J. Phys. Org. Chem.
, vol.7
, pp. 591-609
-
-
Lii, J.-H.1
Allinger, N.L.2
-
53
-
-
0000837770
-
Directional hydrogen bonding in the MM3 force field: II
-
Lii J.-H., and Allinger N.L. Directional hydrogen bonding in the MM3 force field: II. J. Comp. Chem. 19 (1998) 1001-1016
-
(1998)
J. Comp. Chem.
, vol.19
, pp. 1001-1016
-
-
Lii, J.-H.1
Allinger, N.L.2
-
54
-
-
0037019550
-
Hydrogen bonding in high-resolution protein structures: A new method to assess NMR protein geometry
-
Lipsitz R.S., Sharma Y., Brooks B.R., and Tjandra N. Hydrogen bonding in high-resolution protein structures: A new method to assess NMR protein geometry. J. Am. Chem. Soc. 124 (2002) 10621-10626
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 10621-10626
-
-
Lipsitz, R.S.1
Sharma, Y.2
Brooks, B.R.3
Tjandra, N.4
-
55
-
-
0038752617
-
Computational design of receptor and sensor proteins with novel functions
-
Looger L.L., Dwyer M.A., Smith J.J., and Hellinga H.W. Computational design of receptor and sensor proteins with novel functions. Nature 423 (2003) 185-190
-
(2003)
Nature
, vol.423
, pp. 185-190
-
-
Looger, L.L.1
Dwyer, M.A.2
Smith, J.J.3
Hellinga, H.W.4
-
56
-
-
0029008590
-
A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil
-
Lumb K.J., and Kim P.S. A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil. Biochemistry 34 (1995) 8642-8648
-
(1995)
Biochemistry
, vol.34
, pp. 8642-8648
-
-
Lumb, K.J.1
Kim, P.S.2
-
57
-
-
0000543010
-
Molecular polarizabilities and induced dipole moments in molecular mechanics
-
Ma B., Lii J.-H., and Allinger N.L. Molecular polarizabilities and induced dipole moments in molecular mechanics. J. Comp. Chem. 21 (2000) 813-825
-
(2000)
J. Comp. Chem.
, vol.21
, pp. 813-825
-
-
Ma, B.1
Lii, J.-H.2
Allinger, N.L.3
-
58
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerrell Jr. A.D., Bashford D., Bellott M., Dunbrack Jr. R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Reiher W.E., Roux III B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Yin D., and Karplus M.M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102 (1998) 3586-3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerrell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux III, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.M.29
more..
-
59
-
-
9144240095
-
DREIDING: A generic force field for molecular simulations
-
Mayo S.L., Olafson B.D., and Goddard III W.A. DREIDING: A generic force field for molecular simulations. J. Phys. Chem. 94 (1990) 8897-8909
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8897-8909
-
-
Mayo, S.L.1
Olafson, B.D.2
Goddard III, W.A.3
-
60
-
-
0028304962
-
Satisfying hydrogen bonding potential in proteins
-
McDonald I.K., and Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238 (1994) 777-793
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 777-793
-
-
McDonald, I.K.1
Thornton, J.M.2
-
61
-
-
0015492519
-
Energy parameters in polypeptides. V. Empirical hydrogen bond potential function based on molecular orbital calculations
-
McGuire R.F., Momany F.A., and Scheraga H.A. Energy parameters in polypeptides. V. Empirical hydrogen bond potential function based on molecular orbital calculations. J. Phys. Chem. 76 (1972) 375-393
-
(1972)
J. Phys. Chem.
, vol.76
, pp. 375-393
-
-
McGuire, R.F.1
Momany, F.A.2
Scheraga, H.A.3
-
62
-
-
0037422359
-
Evaluation of models of electrostatic interactions in proteins
-
Morozov A.V., Kortemme T., and Baker D. Evaluation of models of electrostatic interactions in proteins. J. Phys. Chem. B 107 (2003) 2075-2090
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 2075-2090
-
-
Morozov, A.V.1
Kortemme, T.2
Baker, D.3
-
63
-
-
2342593131
-
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
-
Morozov A.V., Kortemme T., Tsemekhman K., and Baker D. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc. Natl. Acad. Sci. USA 101 (2004) 6946-6951
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 6946-6951
-
-
Morozov, A.V.1
Kortemme, T.2
Tsemekhman, K.3
Baker, D.4
-
66
-
-
0000036869
-
Simulation of activation free energies in molecular systems
-
Neria E., Fischer S., and Karplus M. Simulation of activation free energies in molecular systems. J. Chem. Phys. 105 (1996) 1902-1921
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 1902-1921
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
67
-
-
0011498404
-
A simple functional representation of angular-dependent hydrogen-bonded systems. 1. Amide, carboxylic acid, and amide-carboxylic acid pairs
-
No K.T., Kwon O.Y., Kim S.Y., Jhon M.S., and Scheraga H.A. A simple functional representation of angular-dependent hydrogen-bonded systems. 1. Amide, carboxylic acid, and amide-carboxylic acid pairs. J. Phys. Chem. 99 (1995) 3478-3486
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 3478-3486
-
-
No, K.T.1
Kwon, O.Y.2
Kim, S.Y.3
Jhon, M.S.4
Scheraga, H.A.5
-
68
-
-
0034250726
-
Stabilization of α-helices by dipole-dipole interactions within α-helices
-
Park C., and Goddard III W.A. Stabilization of α-helices by dipole-dipole interactions within α-helices. J. Phys. Chem. B 104 (2000) 7784-7789
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 7784-7789
-
-
Park, C.1
Goddard III, W.A.2
-
70
-
-
0000573263
-
Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets
-
Pauling L., and Corey R.B. Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets. Proc. Natl. Acad. Sci. USA 37 (1951) 729-740
-
(1951)
Proc. Natl. Acad. Sci. USA
, vol.37
, pp. 729-740
-
-
Pauling, L.1
Corey, R.B.2
-
71
-
-
4243943295
-
Generalized gradient approximation made simple
-
Perdew J., Burke K., and Ernzerhof M. Generalized gradient approximation made simple. Phys. Rev. Lett. 77 (1996) 3865-3868
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 3865-3868
-
-
Perdew, J.1
Burke, K.2
Ernzerhof, M.3
-
72
-
-
0035829446
-
Evaluation of docking functions for protein-ligand docking
-
Perez C., and Ortiz A.R. Evaluation of docking functions for protein-ligand docking. J. Med. Chem. 44 (2001) 3768-3785
-
(2001)
J. Med. Chem.
, vol.44
, pp. 3768-3785
-
-
Perez, C.1
Ortiz, A.R.2
-
73
-
-
0034486196
-
Free energy determinants of tertiary structure and the evaluation of protein models
-
Petrey D., and Honig B. Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci. 9 (2000) 2181-2191
-
(2000)
Protein Sci.
, vol.9
, pp. 2181-2191
-
-
Petrey, D.1
Honig, B.2
-
74
-
-
0035782661
-
Review: Protein design-Where we were, where we are, where we're going
-
Pokala N., and Handel T.M. Review: Protein design-Where we were, where we are, where we're going. J. Struct. Biol. 134 (2001) 269-281
-
(2001)
J. Struct. Biol.
, vol.134
, pp. 269-281
-
-
Pokala, N.1
Handel, T.M.2
-
75
-
-
0242443693
-
Force fields for protein simulations
-
Ponder J.W., and Case D.A. Force fields for protein simulations. Adv. Protein Chem. 66 (2003) 27-85
-
(2003)
Adv. Protein Chem.
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
76
-
-
0000160240
-
A spectroscopically effective molecular mechanics model for the intermolecular interactions of the hydrogen-bonded N-methylacetamide dimer
-
Qian W., Mirkin N.G., and Krimm S. A spectroscopically effective molecular mechanics model for the intermolecular interactions of the hydrogen-bonded N-methylacetamide dimer. Chem. Phys. Lett. 315 (1999) 125-129
-
(1999)
Chem. Phys. Lett.
, vol.315
, pp. 125-129
-
-
Qian, W.1
Mirkin, N.G.2
Krimm, S.3
-
77
-
-
0035967864
-
Crystal structure of lactose synthase reveals a large conformational change in its catalytic component, the beta1, 4-galactosyltransferase-I
-
Ramakrishnan B., and Qasba P.K. Crystal structure of lactose synthase reveals a large conformational change in its catalytic component, the beta1, 4-galactosyltransferase-I. J. Mol. Biol. 310 (2001) 205-218
-
(2001)
J. Mol. Biol.
, vol.310
, pp. 205-218
-
-
Ramakrishnan, B.1
Qasba, P.K.2
-
79
-
-
0036315558
-
Computer-aided design of a PDZ domain to recognize new target sequences
-
Reina J., Lacroix E., Hobson S.D., Fernandez-Ballester G., Rybin V., Schwab M.S., Serrano L., and Gonzalez C. Computer-aided design of a PDZ domain to recognize new target sequences. Nature Struct. Biol. 9 (2002) 621-627
-
(2002)
Nature Struct. Biol.
, vol.9
, pp. 621-627
-
-
Reina, J.1
Lacroix, E.2
Hobson, S.D.3
Fernandez-Ballester, G.4
Rybin, V.5
Schwab, M.S.6
Serrano, L.7
Gonzalez, C.8
-
82
-
-
36549100963
-
A water dimer potential based on ab initio calculations using Morokuma component analyses
-
Singh U.C., and Kollman P.A. A water dimer potential based on ab initio calculations using Morokuma component analyses. J. Chem. Phys. 83 (1985) 4033-4040
-
(1985)
J. Chem. Phys.
, vol.83
, pp. 4033-4040
-
-
Singh, U.C.1
Kollman, P.A.2
-
83
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith G.R., and Sternberg M.J.E. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 12 (2002) 28-35
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.E.2
-
85
-
-
0029909384
-
An iterative method for extracting energy-like quantities from protein structures
-
Thomas P.D., and Dill K.A. An iterative method for extracting energy-like quantities from protein structures. Proc. Natl. Acad. Sci. 93 (1996) 11628-11633
-
(1996)
Proc. Natl. Acad. Sci.
, vol.93
, pp. 11628-11633
-
-
Thomas, P.D.1
Dill, K.A.2
-
86
-
-
0001298538
-
Can contemporary density functional theory yield accurate thermodynamics for hydrogen bonding?
-
Topol I.A., Burt S.K., and Rashin A.A. Can contemporary density functional theory yield accurate thermodynamics for hydrogen bonding?. Chem. Phys. Lett. 247 (1995) 112-119
-
(1995)
Chem. Phys. Lett.
, vol.247
, pp. 112-119
-
-
Topol, I.A.1
Burt, S.K.2
Rashin, A.A.3
-
87
-
-
0031648837
-
Effects of intermolecular hydrogen-bonding interactions on the amide I mode of N-methylacetamide: Matrix-isolation infrared studies and ab initio molecular orbital calculations
-
Torii H., Tatsumi T., Kanazawa T., and Tasumi M. Effects of intermolecular hydrogen-bonding interactions on the amide I mode of N-methylacetamide: Matrix-isolation infrared studies and ab initio molecular orbital calculations. J. Phys. Chem. B 102 (1998) 309-314
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 309-314
-
-
Torii, H.1
Tatsumi, T.2
Kanazawa, T.3
Tasumi, M.4
-
88
-
-
0033056708
-
Folding funnels, binding funnels, and protein function
-
Tsai C.J., Kumar S., Ma B., and Nussinov R. Folding funnels, binding funnels, and protein function. Protein Sci. 8 (1999) 1181-1190
-
(1999)
Protein Sci.
, vol.8
, pp. 1181-1190
-
-
Tsai, C.J.1
Kumar, S.2
Ma, B.3
Nussinov, R.4
-
89
-
-
0033199846
-
Predicting the binding energies of H-bonded complexes: A comparative DFT study
-
Tuma C., Boese A.D., and Handy N.C. Predicting the binding energies of H-bonded complexes: A comparative DFT study. Phys. Chem. Chem. Phys. 1 (1999) 3939-3947
-
(1999)
Phys. Chem. Chem. Phys.
, vol.1
, pp. 3939-3947
-
-
Tuma, C.1
Boese, A.D.2
Handy, N.C.3
-
90
-
-
33847088301
-
The origin of hydrogen bonding: An energy decomposition study
-
Umeyana H., and Morokuma K.J. The origin of hydrogen bonding: An energy decomposition study. J. Am. Chem. Soc. 99 (1977) 1316-1332
-
(1977)
J. Am. Chem. Soc.
, vol.99
, pp. 1316-1332
-
-
Umeyana, H.1
Morokuma, K.J.2
-
91
-
-
1242270553
-
Protein-protein docking: Is the glass half-full or half-empty?
-
Vajda S., and Camacho C.J. Protein-protein docking: Is the glass half-full or half-empty?. Trends Biotech. 22 (2004) 110-116
-
(2004)
Trends Biotech.
, vol.22
, pp. 110-116
-
-
Vajda, S.1
Camacho, C.J.2
-
92
-
-
0035942888
-
Strength of the N{single bond}H⋯O{double bond, long}C and C{single bond}H⋯O{double bond, long}C bonds in formamide and N-methylacetamide dimers
-
Vargas R., Garza J., Friesner R.A., Stern H., Hay B.P., and Dixon D.A. Strength of the N{single bond}H⋯O{double bond, long}C and C{single bond}H⋯O{double bond, long}C bonds in formamide and N-methylacetamide dimers. J. Phys. Chem. A 105 (2001) 4963-4968
-
(2001)
J. Phys. Chem. A
, vol.105
, pp. 4963-4968
-
-
Vargas, R.1
Garza, J.2
Friesner, R.A.3
Stern, H.4
Hay, B.P.5
Dixon, D.A.6
-
93
-
-
0031872292
-
Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
-
Vorobjev Y.N., Almagro J.C., and Hermans J. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins Struct. Funct. Gen. 32 (1998) 399-413
-
(1998)
Proteins Struct. Funct. Gen.
, vol.32
, pp. 399-413
-
-
Vorobjev, Y.N.1
Almagro, J.C.2
Hermans, J.3
-
94
-
-
0033003955
-
ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
-
Vorobjev Y.N., and Hermans J. ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model. Biophys. Chem. 78 (1999) 195-205
-
(1999)
Biophys. Chem.
, vol.78
, pp. 195-205
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
95
-
-
0037194966
-
Density functional theory vibrational frequencies of amides and amide dimers
-
Watson T.M., and Hirst J.D. Density functional theory vibrational frequencies of amides and amide dimers. J. Phys. Chem. A 106 (2002) 7858-7867
-
(2002)
J. Phys. Chem. A
, vol.106
, pp. 7858-7867
-
-
Watson, T.M.1
Hirst, J.D.2
-
96
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner S.J., Kollman P.A., Case D.A., Singh U.C., Ghio C., Alagona G., Profeta Jr. S., and Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106 (1984) 765-784
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta Jr., S.7
Weiner, P.8
-
97
-
-
0038682661
-
H-bonding cooperativity and energetics of α-helix formation of five 17-amino acid peptides
-
Wieczorek R., and Dannenberg J.J. H-bonding cooperativity and energetics of α-helix formation of five 17-amino acid peptides. J. Am. Chem. Soc. 125 (2003) 8124-8129
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 8124-8129
-
-
Wieczorek, R.1
Dannenberg, J.J.2
-
99
-
-
0036428782
-
Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing
-
Zagrovic B., Snow C.D., Shirts M.R., and Pande V.S. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 323 (2002) 927-937
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 927-937
-
-
Zagrovic, B.1
Snow, C.D.2
Shirts, M.R.3
Pande, V.S.4
-
100
-
-
17144383951
-
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
-
Zhang C., Liu S., Zhu Q., and Zhou Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J. Med. Chem. 48 (2005) 2325-2335
-
(2005)
J. Med. Chem.
, vol.48
, pp. 2325-2335
-
-
Zhang, C.1
Liu, S.2
Zhu, Q.3
Zhou, Y.4
-
101
-
-
0037181045
-
A theoretical study of β-sheet models: Is the formation of hydrogen-bond networks cooperative?
-
Zhao Y., and Wu Y. A theoretical study of β-sheet models: Is the formation of hydrogen-bond networks cooperative?. J. Am. Chem. Soc. 124 (2002) 1570-1571
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 1570-1571
-
-
Zhao, Y.1
Wu, Y.2
|