-
1
-
-
0008874240
-
Structure and function in myoglobin and other proteins
-
Kendrew, J. C. Structure and function in myoglobin and other proteins Fed. Proc. 1959, 18 (2, Part 1) 740-751
-
(1959)
Fed. Proc.
, vol.18
, Issue.2 PART 1
, pp. 740-751
-
-
Kendrew, J.C.1
-
2
-
-
36949066642
-
Structure of haemoglobin: A three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis
-
Perutz, M. F.; Rossmann, M. G.; Cullis, A. F.; Muirhead, H.; Will, G.; North, A. C. Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis Nature 1960, 185 (4711) 416-422
-
(1960)
Nature
, vol.185
, Issue.4711
, pp. 416-422
-
-
Perutz, M.F.1
Rossmann, M.G.2
Cullis, A.F.3
Muirhead, H.4
Will, G.5
North, A.C.6
-
3
-
-
0021683974
-
The crystal structure of human deoxyhaemoglobin at 1.74 A resolution
-
Fermi, G.; Perutz, M. F.; Shaanan, B.; Fourme, R. The crystal structure of human deoxyhaemoglobin at 1.74 A resolution J. Mol. Biol. 1984, 175 (2) 159-174
-
(1984)
J. Mol. Biol.
, vol.175
, Issue.2
, pp. 159-174
-
-
Fermi, G.1
Perutz, M.F.2
Shaanan, B.3
Fourme, R.4
-
4
-
-
0018780591
-
Side-chain torsional potentials: Effect of dipeptide, protein, and solvent environment
-
Gelin, B. R.; Karplus, M. Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment Biochemistry (Mosc) 1979, 18 (7) 1256-1268
-
(1979)
Biochemistry (Mosc)
, vol.18
, Issue.7
, pp. 1256-1268
-
-
Gelin, B.R.1
Karplus, M.2
-
5
-
-
0035812625
-
The energetics of off-rotamer protein side-chain conformations
-
Petrella, R. J.; Karplus, M. The energetics of off-rotamer protein side-chain conformations J. Mol. Biol. 2001, 312 (5) 1161-1175
-
(2001)
J. Mol. Biol.
, vol.312
, Issue.5
, pp. 1161-1175
-
-
Petrella, R.J.1
Karplus, M.2
-
6
-
-
0344413597
-
Boltzmann-type distribution of side-chain conformation in proteins
-
Butterfoss, G. L.; Hermans, J. Boltzmann-type distribution of side-chain conformation in proteins Protein Sci. 2003, 12 (12) 2719-2731
-
(2003)
Protein Sci.
, vol.12
, Issue.12
, pp. 2719-2731
-
-
Butterfoss, G.L.1
Hermans, J.2
-
7
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28 (1) 235-242
-
(2000)
Nucleic Acids Res.
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
8
-
-
77953513118
-
Improved side-chain torsion potentials for the Amber ff99SB protein force field
-
Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Improved side-chain torsion potentials for the Amber ff99SB protein force field Proteins 2010, 78 (8) 1950-1958
-
(2010)
Proteins
, vol.78
, Issue.8
, pp. 1950-1958
-
-
Lindorff-Larsen, K.1
Piana, S.2
Palmo, K.3
Maragakis, P.4
Klepeis, J.L.5
Dror, R.O.6
Shaw, D.E.7
-
9
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 2001, 105 (28) 6474-6487
-
(2001)
J. Phys. Chem. B
, vol.105
, Issue.28
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
10
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
Brooks, B. R.; Brooks, C. L., 3rd; MacKerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: The biomolecular simulation program J. Comput. Chem. 2009, 30 (10) 1545-1614
-
(2009)
J. Comput. Chem.
, vol.30
, Issue.10
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks III, B.R.2
Mackerell Jr., A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
11
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, 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, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 1998, 102 (18) 3586-3616
-
(1998)
J. Phys. Chem. B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, 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, 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.29
more..
-
12
-
-
3142714765
-
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
-
MacKerell, A. D.; Feig, M.; Brooks, C. L. 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. 2004, 25 (11) 1400-1415
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.11
, pp. 1400-1415
-
-
MacKerell, A.D.1
Feig, M.2
Brooks, C.L.3
-
13
-
-
0000179199
-
Knowledge based modelling of homologous proteins, Part II: Rules for the conformations of substituted sidechains
-
Sutcliffe, M. J.; Hayes, F. R.; Blundell, T. L. Knowledge based modelling of homologous proteins, Part II: Rules for the conformations of substituted sidechains Protein Eng. 1987, 1 (5) 385-392
-
(1987)
Protein Eng.
, vol.1
, Issue.5
, pp. 385-392
-
-
Sutcliffe, M.J.1
Hayes, F.R.2
Blundell, T.L.3
-
14
-
-
0038626673
-
-
Revision C.02; Gaussian, Inc. Wallingford CT.
-
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision C.02; Gaussian, Inc.: Wallingford CT, 2004.
-
(2004)
Gaussian 03
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Montgomery Jr., J.A.7
Vreven, T.8
Kudin, K.N.9
Burant, J.C.10
Millam, J.M.11
Iyengar, S.S.12
Tomasi, J.13
Barone, V.14
Mennucci, B.15
Cossi, M.16
Scalmani, G.17
Rega, N.18
Petersson, G.A.19
Nakatsuji, H.20
Hada, M.21
Ehara, M.22
Toyota, K.23
Fukuda, R.24
Hasegawa, J.25
Ishida, M.26
Nakajima, T.27
Honda, Y.28
Kitao, O.29
Nakai, H.30
Klene, M.31
Li, X.32
Knox, J.E.33
Hratchian, H.P.34
Cross, J.B.35
Bakken, V.36
Adamo, C.37
Jaramillo, J.38
Gomperts, R.39
Stratmann, R.E.40
Yazyev, O.41
Austin, A.J.42
Cammi, R.43
Pomelli, C.44
Ochterski, J.W.45
Ayala, P.Y.46
Morokuma, K.47
Voth, G.A.48
Salvador, P.49
Dannenberg, J.J.50
Zakrzewski, V.G.51
Dapprich, S.52
Daniels, A.D.53
Strain, M.C.54
Farkas, O.55
Malick, D.K.56
Rabuck, A.D.57
Raghavachari, K.58
Foresman, J.B.59
Ortiz, J.V.60
Cui, Q.61
Baboul, A.G.62
Clifford, S.63
Cioslowski, J.64
Stefanov, B.B.65
Liu, G.66
Liashenko, A.67
Piskorz, P.68
Komaromi, I.69
Martin, R.L.70
Fox, D.J.71
Keith, T.72
Al-Laham, M.A.73
Peng, C.Y.74
Nanayakkara, A.75
Challacombe, M.76
Gill, P.M.W.77
Johnson, B.78
Chen, W.79
Wong, M.W.80
Gonzalez, C.81
Pople, J.A.82
more..
-
15
-
-
0347170005
-
-
Hehre, W. J.; Ditchfield, R.; Pople, J. A. J. Chem. Phys. 1972, 56, 2257
-
(1972)
J. Chem. Phys.
, vol.56
, pp. 2257
-
-
Hehre, W.J.1
Ditchfield, R.2
Pople, J.A.3
-
16
-
-
33748545144
-
The influence of polarization functions on molecular orbital hydrogenation energies
-
Hariharan, P. C.; Pople, J. A. The influence of polarization functions on molecular orbital hydrogenation energies Theor. Chim. Acta (Berlin) 1973, 28, 213-222
-
(1973)
Theor. Chim. Acta (Berlin)
, vol.28
, pp. 213-222
-
-
Hariharan, P.C.1
Pople, J.A.2
-
17
-
-
6944251055
-
Note on an approximation treatment for many-electron systems
-
Møller, C.; Plesset, M. S. Note on an approximation treatment for many-electron systems Phys. Rev. 1934, 46, 618-622
-
(1934)
Phys. Rev.
, vol.46
, pp. 618-622
-
-
Møller, C.1
Plesset, M.S.2
-
18
-
-
33746563448
-
Advances in methods and algorithms in a modern quantum chemistry program package
-
Shao, Y.; Molnar, L. F.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.; Brown, S. T.; Gilbert, A. T.; Slipchenko, L. V.; Levchenko, S. V.; O'Neill, D. P.; DiStasio, R. A., Jr.; Lochan, R. C.; Wang, T.; Beran, G. J.; Besley, N. A.; Herbert, J. M.; Lin, C. Y.; Van Voorhis, T.; Chien, S. H.; Sodt, A.; Steele, R. P.; Rassolov, V. A.; Maslen, P. E.; Korambath, P. P.; Adamson, R. D.; Austin, B.; Baker, J.; Byrd, E. F.; Dachsel, H.; Doerksen, R. J.; Dreuw, A.; Dunietz, B. D.; Dutoi, A. D.; Furlani, T. R.; Gwaltney, S. R.; Heyden, A.; Hirata, S.; Hsu, C. P.; Kedziora, G.; Khalliulin, R. Z.; Klunzinger, P.; Lee, A. M.; Lee, M. S.; Liang, W.; Lotan, I.; Nair, N.; Peters, B.; Proynov, E. I.; Pieniazek, P. A.; Rhee, Y. M.; Ritchie, J.; Rosta, E.; Sherrill, C. D.; Simmonett, A. C.; Subotnik, J. E.; Woodcock, H. L., 3rd; Zhang, W.; Bell, A. T.; Chakraborty, A. K.; Chipman, D. M.; Keil, F. J.; Warshel, A.; Hehre, W. J.; Schaefer, H. F., 3rd; Kong, J.; Krylov, A. I.; Gill, P. M.; Head-Gordon, M. Advances in methods and algorithms in a modern quantum chemistry program package Phys. Chem. Chem. Phys. 2006, 8 (27) 3172-3191
-
(2006)
Phys. Chem. Chem. Phys.
, vol.8
, Issue.27
, pp. 3172-3191
-
-
Shao, Y.1
Molnar, L.F.2
Jung, Y.3
Kussmann, J.4
Ochsenfeld, C.5
Brown, S.T.6
Gilbert, A.T.7
Slipchenko, L.V.8
Levchenko, S.V.9
O'Neill, D.P.10
Distasio Jr., R.A.11
Lochan, R.C.12
Wang, T.13
Beran, G.J.14
Besley, N.A.15
Herbert, J.M.16
Lin, C.Y.17
Van Voorhis, T.18
Chien, S.H.19
Sodt, A.20
Steele, R.P.21
Rassolov, V.A.22
Maslen, P.E.23
Korambath, P.P.24
Adamson, R.D.25
Austin, B.26
Baker, J.27
Byrd, E.F.28
Dachsel, H.29
Doerksen, R.J.30
Dreuw, A.31
Dunietz, B.D.32
Dutoi, A.D.33
Furlani, T.R.34
Gwaltney, S.R.35
Heyden, A.36
Hirata, S.37
Hsu, C.P.38
Kedziora, G.39
Khalliulin, R.Z.40
Klunzinger, P.41
Lee, A.M.42
Lee, M.S.43
Liang, W.44
Lotan, I.45
Nair, N.46
Peters, B.47
Proynov, E.I.48
Pieniazek, P.A.49
Rhee, Y.M.50
Ritchie, J.51
Rosta, E.52
Sherrill, C.D.53
Simmonett, A.C.54
Subotnik, J.E.55
Zhang, H.L.56
Zhang, W.57
Bell, A.T.58
Chakraborty, A.K.59
Chipman, D.M.60
Keil, F.J.61
Warshel, A.62
Hehre, W.J.63
Kong III, H.L.64
Kong, J.65
Krylov, A.I.66
Gill, P.M.67
Head-Gordon, M.68
more..
-
19
-
-
36449006587
-
Gaussian-basis sets for use in correlated molecular calculations 0.5. Core-valence basis-sets for boron through neon
-
Woon, D. E.; Dunning, T. H. Gaussian-basis sets for use in correlated molecular calculations 0.5. Core-valence basis-sets for boron through neon J. Chem. Phys. 1995, 103 (11) 4572-4585
-
(1995)
J. Chem. Phys.
, vol.103
, Issue.11
, pp. 4572-4585
-
-
Woon, D.E.1
Dunning, T.H.2
-
20
-
-
0031285839
-
RI-MP2: First derivatives and global consistency
-
Weigend, F.; Häser, M. RI-MP2: First derivatives and global consistency Theor. Chem. Acc.: Theory, Comput., Model. (Theor. Chim. Acta) 1997, 97 (1) 331-340
-
(1997)
Theor. Chem. Acc.: Theory, Comput., Model. (Theor. Chim. Acta)
, vol.97
, Issue.1
, pp. 331-340
-
-
Weigend, F.1
Häser, M.2
-
21
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F.; Gish, W.; Miller, W.; Myers, E. W.; Lipman, D. J. Basic local alignment search tool J. Mol. Biol. 1990, 215 (3) 403-410
-
(1990)
J. Mol. Biol.
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
22
-
-
3242887525
-
STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins
-
Web Server Issue
-
Heinig, M.; Frishman, D. STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins Nucleic Acids Res. 2004, 32 (Web Server issue) W500-W502
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Heinig, M.1
Frishman, D.2
-
23
-
-
0034663722
-
The penultimate rotamer library
-
Lovell, S. C.; Word, J. M.; Richardson, J. S.; Richardson, D. C. The penultimate rotamer library Proteins 2000, 40 (3) 389-408
-
(2000)
Proteins
, vol.40
, Issue.3
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
24
-
-
0027418205
-
Measurement of co-localization of objects in dual-colour confocal images
-
Manders, E. M. M.; Verbeek, F. J.; Aten, J. A. Measurement of co-localization of objects in dual-colour confocal images J. Microsc. 1993, 169, 375-382
-
(1993)
J. Microsc.
, vol.169
, pp. 375-382
-
-
Manders, E.M.M.1
Verbeek, F.J.2
Aten, J.A.3
-
25
-
-
34247189120
-
Quantitative conformationally sampled pharmacophore for delta opioid ligands: Reevaluation of hydrophobic moieties essential for biological activity
-
Bernard, D.; Coop, A.; MacKerell, A. D., Jr. Quantitative conformationally sampled pharmacophore for delta opioid ligands: reevaluation of hydrophobic moieties essential for biological activity J. Med. Chem. 2007, 50 (8) 1799-1809
-
(2007)
J. Med. Chem.
, vol.50
, Issue.8
, pp. 1799-1809
-
-
Bernard, D.1
Coop, A.2
Mackerell Jr., A.D.3
-
26
-
-
77953752095
-
Molecular switch controlling the binding of anionic bile acid conjugates to human apical sodium-dependent bile acid transporter
-
Rais, R.; Acharya, C.; Tririya, G.; MacKerell, A. D.; Polli, J. E. Molecular switch controlling the binding of anionic bile acid conjugates to human apical sodium-dependent bile acid transporter J. Med. Chem. 2010, 53 (12) 4749-4760
-
(2010)
J. Med. Chem.
, vol.53
, Issue.12
, pp. 4749-4760
-
-
Rais, R.1
Acharya, C.2
Tririya, G.3
MacKerell, A.D.4
Polli, J.E.5
-
27
-
-
78649971657
-
Structural determinants for transport across the intestinal bile acid transporter using C-24 bile acid conjugates
-
Rais, R.; Acharya, C.; MacKerell, A. D.; Polli, J. E. Structural determinants for transport across the intestinal bile acid transporter using C-24 bile acid conjugates Mol. Pharmaceutics 2010, 7 (6) 2240-2254
-
(2010)
Mol. Pharmaceutics
, vol.7
, Issue.6
, pp. 2240-2254
-
-
Rais, R.1
Acharya, C.2
MacKerell, A.D.3
Polli, J.E.4
-
28
-
-
78951480525
-
Recent advances in ligand-based drug design: Relevance and utility of the conformationally sampled pharmacophore approach
-
Acharya, C.; Coop, A.; Polli, J. E.; MacKerell, A. D., Jr. Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach Curr. Comput.-Aided Drug Des. 2011, 7 (1) 10-22
-
(2011)
Curr. Comput.-Aided Drug Des.
, vol.7
, Issue.1
, pp. 10-22
-
-
Acharya, C.1
Coop, A.2
Polli, J.E.3
Mackerell Jr., A.D.4
-
29
-
-
0036136694
-
Composites of local structure propensities: Evidence for local encoding of long-range structure
-
Shortle, D. Composites of local structure propensities: Evidence for local encoding of long-range structure Protein Sci. 2002, 11 (1) 18-26
-
(2002)
Protein Sci.
, vol.11
, Issue.1
, pp. 18-26
-
-
Shortle, D.1
-
30
-
-
79952748270
-
The amino acid dipeptide: Small but still influential after 50 years
-
Hermans, J. The amino acid dipeptide: small but still influential after 50 years Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (8) 3095-3096
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, Issue.8
, pp. 3095-3096
-
-
Hermans, J.1
-
31
-
-
0242443693
-
Force fields for protein simulations
-
Ponder, J. W.; Case, D. A. Force fields for protein simulations Adv. Protein Chem. 2003, 66, 27-85
-
(2003)
Adv. Protein Chem.
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
32
-
-
0020685129
-
Structure and refinement of penicillopepsin at 1.8 Å resolution
-
James, M. N.; Sielecki, A. R. Structure and refinement of penicillopepsin at 1.8 Å resolution J. Mol. Biol. 1983, 163 (2) 299-361
-
(1983)
J. Mol. Biol.
, vol.163
, Issue.2
, pp. 299-361
-
-
James, M.N.1
Sielecki, A.R.2
-
33
-
-
0014885326
-
Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins
-
Chandrasekaran, R.; Ramachandran, G. N. Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins Int. J. Protein Res. 1970, 2 (4) 223-233
-
(1970)
Int. J. Protein Res.
, vol.2
, Issue.4
, pp. 223-233
-
-
Chandrasekaran, R.1
Ramachandran, G.N.2
-
34
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack, R. L., Jr.; Cohen, F. E. Bayesian statistical analysis of protein side-chain rotamer preferences Protein Sci. 1997, 6 (8) 1661-1681
-
(1997)
Protein Sci.
, vol.6
, Issue.8
, pp. 1661-1681
-
-
Dunbrack Jr., R.L.1
Cohen, F.E.2
-
35
-
-
79958079887
-
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions
-
Shapovalov, M. V.; Dunbrack, R. L., Jr. A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions Structure 2011, 19 (6) 844-858
-
(2011)
Structure
, vol.19
, Issue.6
, pp. 844-858
-
-
Shapovalov, M.V.1
Dunbrack Jr., R.L.2
-
36
-
-
0029002720
-
The hydrophobic effect in protein folding
-
Lins, L.; Brasseur, R. The hydrophobic effect in protein folding FASEB J. 1995, 9 (7) 535-540
-
(1995)
FASEB J.
, vol.9
, Issue.7
, pp. 535-540
-
-
Lins, L.1
Brasseur, R.2
-
37
-
-
0024538543
-
How do serine proteases really work?
-
Warshel, A.; Naray-Szabo, G.; Sussman, F.; Hwang, J. K. How do serine proteases really work? Biochemistry (Mosc.) 1989, 28 (9) 3629-3637
-
(1989)
Biochemistry (Mosc.)
, vol.28
, Issue.9
, pp. 3629-3637
-
-
Warshel, A.1
Naray-Szabo, G.2
Sussman, F.3
Hwang, J.K.4
-
38
-
-
68849086984
-
Highly Conserved Histidine Plays a Dual Catalytic Role in Protein Splicing: A pKa Shift Mechanism
-
Du, Z.; Shemella, P. T.; Liu, Y.; McCallum, S. A.; Pereira, B.; Nayak, S. K.; Belfort, G.; Belfort, M.; Wang, C. Highly Conserved Histidine Plays a Dual Catalytic Role in Protein Splicing: A pKa Shift Mechanism J. Am. Chem. Soc. 2009, 131 (32) 11581-11589
-
(2009)
J. Am. Chem. Soc.
, vol.131
, Issue.32
, pp. 11581-11589
-
-
Du, Z.1
Shemella, P.T.2
Liu, Y.3
McCallum, S.A.4
Pereira, B.5
Nayak, S.K.6
Belfort, G.7
Belfort, M.8
Wang, C.9
-
40
-
-
4644355809
-
The architecture of metal coordination groups in proteins
-
Harding, M. M. The architecture of metal coordination groups in proteins Acta Crystallogr. Sect. D. Biol. Crystallogr. 2004, 60 (Pt 5) 849-859
-
(2004)
Acta Crystallogr. Sect. D. Biol. Crystallogr.
, vol.60
, Issue.PART 5
, pp. 849-859
-
-
Harding, M.M.1
-
41
-
-
0036180616
-
The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain
-
Frank, B. S.; Vardar, D.; Buckley, D. A.; McKnight, C. J. The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain Protein Sci. 2002, 11 (3) 680-687
-
(2002)
Protein Sci.
, vol.11
, Issue.3
, pp. 680-687
-
-
Frank, B.S.1
Vardar, D.2
Buckley, D.A.3
McKnight, C.J.4
-
42
-
-
82955240563
-
Slow motions in the hydrophobic core of chicken villin headpiece subdomain and their contributions to configurational entropy and heat capacity from solid-state deuteron NMR measurements
-
Vugmeyster, L.; Ostrovsky, D.; Khadjinova, A.; Ellden, J.; Hoatson, G. L.; Vold, R. L. Slow motions in the hydrophobic core of chicken villin headpiece subdomain and their contributions to configurational entropy and heat capacity from solid-state deuteron NMR measurements Biochemistry (Mosc.) 2011, 50 (49) 10637-10646
-
(2011)
Biochemistry (Mosc.)
, vol.50
, Issue.49
, pp. 10637-10646
-
-
Vugmeyster, L.1
Ostrovsky, D.2
Khadjinova, A.3
Ellden, J.4
Hoatson, G.L.5
Vold, R.L.6
-
43
-
-
0027208112
-
Rotamers: To be or not to be? An analysis of amino acid side-chain conformations in globular proteins
-
Schrauber, H.; Eisenhaber, F.; Argos, P. Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins J. Mol. Biol. 1993, 230 (2) 592-612
-
(1993)
J. Mol. Biol.
, vol.230
, Issue.2
, pp. 592-612
-
-
Schrauber, H.1
Eisenhaber, F.2
Argos, P.3
-
44
-
-
0028429178
-
Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains
-
Dunbrack, R. L., Jr.; Karplus, M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains Nat. Struct. Biol. 1994, 1 (5) 334-340
-
(1994)
Nat. Struct. Biol.
, vol.1
, Issue.5
, pp. 334-340
-
-
Dunbrack Jr., R.L.1
Karplus, M.2
-
45
-
-
1542346466
-
The role of carbon-donor hydrogen bonds in stabilizing tryptophan conformations
-
Petrella, R. J.; Karplus, M. The role of carbon-donor hydrogen bonds in stabilizing tryptophan conformations Proteins 2004, 54 (4) 716-726
-
(2004)
Proteins
, vol.54
, Issue.4
, pp. 716-726
-
-
Petrella, R.J.1
Karplus, M.2
-
46
-
-
0035782925
-
Review: Protein secondary structure prediction continues to rise
-
Burkhard, R. Review: Protein secondary structure prediction continues to rise J. Struct. Biol. 2001, 134 (2-3) 204-218
-
(2001)
J. Struct. Biol.
, vol.134
, Issue.2-3
, pp. 204-218
-
-
Burkhard, R.1
-
47
-
-
0000262018
-
The dependence of the conformations of synthetic polypeptides on amino acid composition
-
Blout, E. R.; Lozé, C. d.; Bloom, S. M.; Fasman, G. D. The dependence of the conformations of synthetic polypeptides on amino acid composition J. Am. Chem. Soc. 1960, 82, 3787-3789
-
(1960)
J. Am. Chem. Soc.
, vol.82
, pp. 3787-3789
-
-
Blout, E.R.1
Bloom, S.M.2
Fasman, G.D.3
-
48
-
-
0040095109
-
Prediction of secondary structure from the amino acid sequence
-
In; Cantor, C. R. Springer-Verlag: New York.
-
Schulz, G. E.; Schirmer, R. H. Prediction of secondary structure from the amino acid sequence. In Principles of Protein Structure; Cantor, C. R., Ed.; Springer-Verlag: New York, 1979.
-
(1979)
Principles of Protein Structure
-
-
Schulz, G.E.1
Schirmer, R.H.2
-
49
-
-
31944437630
-
Intrinsic backbone preferences are fully present in blocked amino acids
-
Avbelj, F.; Grdadolnik, S. G.; Grdadolnik, J.; Baldwin, R. L. Intrinsic backbone preferences are fully present in blocked amino acids Proc. Natl. Acad. Sci. U. S. A. 2006, 103 (5) 1272-1277
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, Issue.5
, pp. 1272-1277
-
-
Avbelj, F.1
Grdadolnik, S.G.2
Grdadolnik, J.3
Baldwin, R.L.4
-
50
-
-
14644390842
-
A survey of left-handed helices in protein structures
-
Novotny, M.; Kleywegt, G. J. A survey of left-handed helices in protein structures J. Mol. Biol. 2005, 347 (2) 231-241
-
(2005)
J. Mol. Biol.
, vol.347
, Issue.2
, pp. 231-241
-
-
Novotny, M.1
Kleywegt, G.J.2
-
51
-
-
3342969223
-
Origin of the neighboring residue effect on peptide backbone conformation
-
Avbelj, F.; Baldwin, R. L. Origin of the neighboring residue effect on peptide backbone conformation Proc. Natl. Acad. Sci. U. S. A. 2004, 101 (30) 10967-10972
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, Issue.30
, pp. 10967-10972
-
-
Avbelj, F.1
Baldwin, R.L.2
-
52
-
-
0033614004
-
Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
-
Word, J. M.; Lovell, S. C.; Richardson, J. S.; Richardson, D. C. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 1999, 285 (4) 1735-1747
-
(1999)
J. Mol. Biol.
, vol.285
, Issue.4
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
53
-
-
79958185452
-
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
-
Michaud-Agrawal, N.; Denning, E. J.; Woolf, T. B.; Beckstein, O. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations J. Comput. Chem. 2011, 32 (10) 2319-2327
-
(2011)
J. Comput. Chem.
, vol.32
, Issue.10
, pp. 2319-2327
-
-
Michaud-Agrawal, N.1
Denning, E.J.2
Woolf, T.B.3
Beckstein, O.4
|