-
4
-
-
0001502420
-
The role of dipole interactions in determining polypeptide configurations
-
Brant D A and Flory P J 1965 The role of dipole interactions in determining polypeptide configurations J. Am. Chem. Soc. 87 663-4
-
(1965)
J. Am. Chem. Soc.
, vol.87
, Issue.3
, pp. 663-664
-
-
Brant, D.A.1
And Flory, P.J.2
-
5
-
-
3042750640
-
Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine-based (AXA) tripeptides in aqueous solution
-
DOI 10.1073/pnas.0402623101
-
Eker F, Griebenow K, Cao X, Nafie L A and Schweitzer-Stenner R 2004 Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine-based (AXA) tripeptides in aqueous solution Proc. Natl. Acad. Sci. USA 101 10054-59 (Pubitemid 38891193)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.27
, pp. 10054-10059
-
-
Eker, F.1
Griebenow, K.2
Cao, X.3
Nafie, L.A.4
Schweitzer-Stenner, R.5
-
6
-
-
33749572252
-
Minimalist Representations and the Importance of Nearest Neighbor Effects in Protein Folding Simulations
-
DOI 10.1016/j.jmb.2006.08.035, PII S002228360601062X
-
Colubri A, Jha A K, Shen M Y, Sali A, Berry R S, Sosnick T R and Freed K F 2006 Minimalist representations and the importance of nearest neighbor effects in protein folding simulations J. Mol. Biol. 363 835-57 (Pubitemid 44537288)
-
(2006)
Journal of Molecular Biology
, vol.363
, Issue.4
, pp. 835-857
-
-
Colubri, A.1
Jha, A.K.2
Shen, M.Y.3
Sali, A.4
Berry, R.S.5
Sosnick, T.R.6
Freed, K.F.7
-
9
-
-
22244458915
-
Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library
-
DOI 10.1021/bi0474822
-
Jha A K, Colubri A, Zaman M H, Koide S, Sosnick T R and Freed K F 2005 Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library Biochemistry 44 9691-702 (Pubitemid 40994363)
-
(2005)
Biochemistry
, vol.44
, Issue.28
, pp. 9691-9702
-
-
Jha, A.K.1
Colubri, A.2
Zaman, M.H.3
Koide, S.4
Sosnick, T.R.5
Freed, K.F.6
-
10
-
-
0345564821
-
Exploring Flory's isolated-pair hypothesis: Statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A
-
DOI 10.1073/pnas.2334257100
-
Ohkubo Y Z and Brooks C L 2003 3rd Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A Proc. Natl. Acad. Sci. USA 100 13916-21 (Pubitemid 37499166)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.SUPPL. 2
, pp. 13916-13921
-
-
Ohkubo, Y.Z.1
Brooks Iii, C.L.2
-
11
-
-
0033730431
-
The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding
-
Pappu R V, Srinivasan R and Rose G D 2000 The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding Proc. Natl. Acad. Sci. USA 97 12565-70
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, Issue.23
, pp. 12565-12570
-
-
Pappu, R.V.1
Srinivasan, R.2
Rose, G.D.3
-
12
-
-
0042701995
-
Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the flory isolated-pair hypothesis for peptides
-
DOI 10.1016/S0022-2836(03)00765-4
-
Zaman M H, Shen M Y, Berry R S, Freed K F and Sosnick T R 2003 Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides J. Mol. Biol. 331 693-711 (Pubitemid 36939184)
-
(2003)
Journal of Molecular Biology
, vol.331
, Issue.3
, pp. 693-711
-
-
Zaman, M.H.1
Shen, M.-Y.2
Berry, R.S.3
Freed, K.F.4
Sosnick, T.R.5
-
13
-
-
2542560465
-
Relationships between amino acid sequence and backbone torsion angle preferences
-
DOI 10.1002/prot.20100
-
Keskin O, Yuret D, Gursoy A, Turkay M and Erman B 2004 Relationships between amino acid sequence and backbone torsion angle preferences Proteins 55 992-8 (Pubitemid 38702955)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.55
, Issue.4
, pp. 992-998
-
-
Keskin, O.1
Yuret, D.2
Gursoy, A.3
Turkay, M.4
Erman, B.5
-
14
-
-
0037441479
-
Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine dipeptides (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
-
DOI 10.1002/prot.10279
-
Hu H, Elstner M and Hermans J 2003 Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine 'dipeptides' (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution Proteins 50 451-63 (Pubitemid 36158458)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.50
, Issue.3
, pp. 451-463
-
-
Hu, H.1
Elstner, M.2
Hermans, J.3
-
15
-
-
0025881751
-
Influence of the local amino acid sequence upon the zones of the torsional angles and ψ adopted by residues in proteins
-
Gibrat J F, Robson B and Garnier J 1991 Influence of the local amino acid sequence upon the zones of the torsional angles and ψ adopted by residues in proteins Biochemistry 30 1578-86
-
(1991)
Biochemistry
, vol.30
, Issue.6
, pp. 1578-1586
-
-
Gibrat, J.F.1
Robson, B.2
Garnier, J.3
-
16
-
-
0034062925
-
Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures
-
Eswar N and Ramakrishnan C 2000 Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures Protein Eng. 13 227-38 (Pubitemid 30258956)
-
(2000)
Protein Engineering
, vol.13
, Issue.4
, pp. 227-238
-
-
Eswar, N.1
Ramakrishnan, C.2
-
17
-
-
84929948529
-
-
Spoel D B, Apol A R, Meulenhoff E, Tieleman D P, Sijbers A, Hess B, Feenstra K, Lindahl E, Drunen R and Berendsen H 2002 Gromos User Manual version 3.3.1 www.gromacs.org
-
(2002)
-
-
Spoel, D.B.1
Apol, A.R.2
Meulenhoff, E.3
Tieleman, D.P.4
Sijbers, A.5
Hess, B.6
Feenstra, K.7
Lindahl, E.8
Drunen, R.9
Berendsen, H.10
-
18
-
-
4444282928
-
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
-
Oostenbrink C, Villa A, Mark A and Gunsteren W F 2004 A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem 25 1656-76
-
(2004)
J. Comput. Chem
, vol.25
, Issue.13
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.3
Gunsteren, W.F.4
-
20
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen H J C, Postma J P, van Gunsteren W F, DiNola A and Haak J R 1984 Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 3684-90
-
(1984)
J. Chem. Phys.
, vol.81
, Issue.8
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
21
-
-
33846823909
-
Particle mesh Ewald: An N log (N) method for Ewald sums in large systems
-
Darden T A, York D M and Pedersen L G 1993 Particle mesh Ewald: an N log (N) method for Ewald sums in large systems J. Chem. Phys. 98 10089-92
-
(1993)
J. Chem. Phys.
, vol.98
, Issue.12
, pp. 10089-10092
-
-
Darden, T.A.1
York, D.M.2
Pedersen, L.G.3
-
23
-
-
0030832809
-
Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
-
DOI 10.1002/(SICI)1097-0134(199711)29:3<292::AID-PROT4>3.0.CO;2-D
-
Bahar I, Kaplan M and Jernigan R L 1997 Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches Proteins: Struct. Funct. Genet. 29 292-308 (Pubitemid 27484221)
-
(1997)
Proteins: Structure, Function and Genetics
, vol.29
, Issue.3
, pp. 292-308
-
-
Bahar, I.1
Kaplan, M.2
Jernigan, R.L.3
-
24
-
-
33845675698
-
Computational basis of knowledge-based conformational probabilities derived from local- and long-range interactions in proteins
-
Ormeci L, Gursoy A, Tunca G and Erman B 2007 Computational basis of knowledge-based conformational probabilities derived from local- and long-range interactions in proteins Proteins 66 29-40
-
(2007)
Proteins
, vol.66
, Issue.1
, pp. 29-40
-
-
Ormeci, L.1
Gursoy, A.2
Tunca, G.3
Erman, B.4
-
25
-
-
1542618345
-
Water in structure prediction
-
Papoian A G, Ulander J, Eastwood M, Schulten Z L and Wolynes P G 2004 Water in structure prediction Proc. Natl. Acad. Sci. 101 3352-7
-
(2004)
Proc. Natl. Acad. Sci.
, vol.101
, Issue.10
, pp. 3352-3357
-
-
Papoian, A.G.1
Ulander, J.2
Eastwood, M.3
Schulten, Z.L.4
Wolynes, P.G.5
-
26
-
-
0001312299
-
The γ-turn, a possible folded conformation of the polypeptide chain. Comparison with β-turn
-
Némethy G and Printz M P 1972 The γ-turn, a possible folded conformation of the polypeptide chain. Comparison with β-turn Macromolecules 5 755-8
-
(1972)
Macromolecules
, vol.5
, Issue.6
, pp. 755-758
-
-
Némethy And Printz G, M.P.1
|