-
1
-
-
0025197061
-
as of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
-
as of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry. 29:1990;10219-10225.
-
(1990)
Biochemistry
, vol.29
, pp. 10219-10225
-
-
Bashford, D.1
Karplus, M.2
-
4
-
-
0030852818
-
Thermodynamic of a reverse turn motif. Solvent effects and side-chain packing
-
Demchuk E., Bashford D., Gippert G. P., Case D. A. Thermodynamic of a reverse turn motif. Solvent effects and side-chain packing. J. Mol. Biol. 270:1997a;305-317.
-
(1997)
J. Mol. Biol.
, vol.270
, pp. 305-317
-
-
Demchuk, E.1
Bashford, D.2
Gippert, G.P.3
Case, D.A.4
-
5
-
-
0030627746
-
Dynamic of a type VI reverse turn in a linear peptide in aqueous solution
-
Demchuk E., Bashford D., Case D. A. Dynamic of a type VI reverse turn in a linear peptide in aqueous solution. Folding Des. 2:1997b;35-46.
-
(1997)
Folding Des.
, vol.2
, pp. 35-46
-
-
Demchuk, E.1
Bashford, D.2
Case, D.A.3
-
6
-
-
0024278597
-
Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn
-
Dyson H. J., Rance M., Houghten R. A., Lerner R. A., Wright P. E. Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn. J. Mol. Biol. 201:1988;161-200.
-
(1988)
J. Mol. Biol.
, vol.201
, pp. 161-200
-
-
Dyson, H.J.1
Rance, M.2
Houghten, R.A.3
Lerner, R.A.4
Wright, P.E.5
-
8
-
-
0020949717
-
Algorithm 611. Subroutines for unconstrained minimization using a model/trust-region approach
-
Gay D. M. Algorithm 611. Subroutines for unconstrained minimization using a model/trust-region approach. ACM Trans. Math. Software. 9:1983;503-524.
-
(1983)
ACM Trans. Math. Software
, vol.9
, pp. 503-524
-
-
Gay, D.M.1
-
9
-
-
0027477251
-
Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins
-
Gilson M. K. Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins: Struct. Funct. Genet. 15:1993;266-282.
-
(1993)
Proteins: Struct. Funct. Genet.
, vol.15
, pp. 266-282
-
-
Gilson, M.K.1
-
10
-
-
51149216498
-
Analysis of the contribution of internal vibrations to the statistical weights of equilibrium conformations of macromolecules
-
G o N., Scheraga H. A. Analysis of the contribution of internal vibrations to the statistical weights of equilibrium conformations of macromolecules. J. Chem. Phys. 51:1969;4751-4767.
-
(1969)
J. Chem. Phys.
, vol.51
, pp. 4751-4767
-
-
Go, N.1
Scheraga, H.A.2
-
11
-
-
0017189603
-
The X-Pro peptide bond as an NMR probe for conformational studies of flexible linear peptides
-
Grathwohl C., Wüthrich K. The X-Pro peptide bond as an NMR probe for conformational studies of flexible linear peptides. Biopolymers. 15:1976;2025-2041.
-
(1976)
Biopolymers
, vol.15
, pp. 2025-2041
-
-
Grathwohl, C.1
Wüthrich, K.2
-
12
-
-
33745356391
-
Contact electron-spin coupling of nuclear magnetic moments
-
Karplus M. Contact electron-spin coupling of nuclear magnetic moments. J. Chem. Phys. 30:1959;11-15.
-
(1959)
J. Chem. Phys.
, vol.30
, pp. 11-15
-
-
Karplus, M.1
-
13
-
-
12244297937
-
Vicinal proton coupling in nuclear magnetic resonance
-
Karplus M. Vicinal proton coupling in nuclear magnetic resonance. J. Am. Chem. Soc. 85:1963;2870-2871.
-
(1963)
J. Am. Chem. Soc.
, vol.85
, pp. 2870-2871
-
-
Karplus, M.1
-
14
-
-
0030010605
-
Experimentally observed conformation-dependent geometry and hidden strain in proteins
-
Karplus P. A. Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci. 5:1996;1406-1420.
-
(1996)
Protein Sci.
, vol.5
, pp. 1406-1420
-
-
Karplus, P.A.1
-
15
-
-
33947455928
-
Thermodynamic considerations of protein reactions. I. Modified reactivity of polar groups
-
Laskowski M. Jr, Scheraga H. A. Thermodynamic considerations of protein reactions. I. Modified reactivity of polar groups. J. Am. Chem. Soc. 76:1954;6305-6319.
-
(1954)
J. Am. Chem. Soc.
, vol.76
, pp. 6305-6319
-
-
Laskowski M., Jr.1
Scheraga, H.A.2
-
17
-
-
0031587288
-
Kinetics of peptide folding: Computer simulations of SYPFDV and peptide variants in water
-
Mohanty D., Elber R., Thirumalai D., Beglov D., Roux B. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J. Mol. Biol. 272:1997;423-442.
-
(1997)
J. Mol. Biol.
, vol.272
, pp. 423-442
-
-
Mohanty, D.1
Elber, R.2
Thirumalai, D.3
Beglov, D.4
Roux, B.5
-
18
-
-
5944250450
-
Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, non-bonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino-acids
-
Momany F. A., McGuire R. F., Burgess A. W., Scheraga H. A. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, non-bonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino-acids. J. Phys. Chem. 79:1975;2361-2381.
-
(1975)
J. Phys. Chem.
, vol.79
, pp. 2361-2381
-
-
Momany, F.A.1
McGuire, R.F.2
Burgess, A.W.3
Scheraga, H.A.4
-
19
-
-
33845550595
-
Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids
-
Némethy G., Pottle M. S., Scheraga H. A. Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87:1983;1883-1887.
-
(1983)
J. Phys. Chem.
, vol.87
, pp. 1883-1887
-
-
Némethy, G.1
Pottle, M.S.2
Scheraga, H.A.3
-
20
-
-
0001731773
-
Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm with application to proline-containing peptides
-
Némethy G., Gibson K. D., Palmer K. A., Yoon C. N., Paterlini G., Zagari A., Rumsey S., Scheraga H. A. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm with application to proline-containing peptides. J. Phys. Chem. 96:1992;6472-6484.
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 6472-6484
-
-
Némethy, G.1
Gibson, K.D.2
Palmer, K.A.3
Yoon, C.N.4
Paterlini, G.5
Zagari, A.6
Rumsey, S.7
Scheraga, H.A.8
-
22
-
-
84944201799
-
Implementation of ECEPP-based programs on the IBM SP2 and the SGI Power Challenge Computers
-
H. Liddell, A. Colbrook, B. Hertzberger, & P. Sloot. Berlin, Heidelberg, New York: Springer-Verlag
-
O'Donnell T. J., Hotovy S. G., Pottle M. S., Ripoll D. R., Scheraga H. A. Implementation of ECEPP-based programs on the IBM SP2 and the SGI Power Challenge Computers. Liddell H., Colbrook A., Hertzberger B., Sloot P. Lecture Notes in Computer Science; vol. 1067: High-Performance Computing and Networking. 1996;365-373 Springer-Verlag, Berlin, Heidelberg, New York.
-
(1996)
Lecture Notes in Computer Science; Vol. 1067: High-Performance Computing and Networking
, pp. 365-373
-
-
O'Donnell, T.J.1
Hotovy, S.G.2
Pottle, M.S.3
Ripoll, D.R.4
Scheraga, H.A.5
-
25
-
-
0019443447
-
The anatomy and taxonomy of protein structure
-
Richardson J. S. The anatomy and taxonomy of protein structure. Advan. Protein Chem. 34:1981;167-339.
-
(1981)
Advan. Protein Chem.
, vol.34
, pp. 167-339
-
-
Richardson, J.S.1
-
26
-
-
0024066560
-
On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method - tests on poly (L -alanine)
-
Ripoll D. R., Scheraga H. A. On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method - tests on poly (L -alanine). Biopolymers. 27:1988;1283-1303.
-
(1988)
Biopolymers
, vol.27
, pp. 1283-1303
-
-
Ripoll, D.R.1
Scheraga, H.A.2
-
27
-
-
0024604167
-
On the multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method: Tests on enkephalin
-
Ripoll D. R., Scheraga H. A. On the multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method: tests on enkephalin. J. Protein Chem. 8:1989;263-287.
-
(1989)
J. Protein Chem.
, vol.8
, pp. 263-287
-
-
Ripoll, D.R.1
Scheraga, H.A.2
-
28
-
-
0030582736
-
Coupling between folding and ionization equilibria: Effects of pH on the conformational preferences of polypeptides
-
Ripoll D. R., Vorobjev Y. N., Liwo A., Vila J. A., Scheraga H. A. Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides. J. Mol. Biol. 264:1996;770-783.
-
(1996)
J. Mol. Biol.
, vol.264
, pp. 770-783
-
-
Ripoll, D.R.1
Vorobjev, Y.N.2
Liwo, A.3
Vila, J.A.4
Scheraga, H.A.5
-
29
-
-
0032146488
-
New developments of the electrostatically driven Monte Carlo method: Test on the membrane-bound portion of melittin
-
Ripoll D. R., Liwo A., Scheraga H. A. New developments of the electrostatically driven Monte Carlo method: test on the membrane-bound portion of melittin. Biopolymers. 46:1998;117-126.
-
(1998)
Biopolymers
, vol.46
, pp. 117-126
-
-
Ripoll, D.R.1
Liwo, A.2
Scheraga, H.A.3
-
31
-
-
0000831520
-
Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment
-
Simonson T., Brünger A. T. Solvation free energies estimated from macroscopic continuum theory: an accuracy assessment. J. Phys. Chem. 98:1994;4683-4694.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 4683-4694
-
-
Simonson, T.1
Brünger, A.T.2
-
32
-
-
27244454740
-
Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O - H...O - C hydrogen bonds from packing configurations
-
Sippl M. J., Némethy G., Scheraga H. A. Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O - H...O - C hydrogen bonds from packing configurations. J. Phys. Chem. 88:1984;6231-6233.
-
(1984)
J. Phys. Chem.
, vol.88
, pp. 6231-6233
-
-
Sippl, M.J.1
Némethy, G.2
Scheraga, H.A.3
-
33
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff D., Sharp K. A., Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1994;1978-1988.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
34
-
-
0025784650
-
Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics
-
Skolnick J., Kolinski A. Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. J. Mol. Biol. 221:1991;449-531.
-
(1991)
J. Mol. Biol.
, vol.221
, pp. 449-531
-
-
Skolnick, J.1
Kolinski, A.2
-
35
-
-
0014347799
-
Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units
-
Venkatachalam C. M. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers. 6:1968;1425-1436.
-
(1968)
Biopolymers
, vol.6
, pp. 1425-1436
-
-
Venkatachalam, C.M.1
-
36
-
-
0026076082
-
Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor
-
Vila J., Williams R. L., Vásquez M., Scheraga H. A. Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor. Proteins: Struct. Funct. Genet. 10:1991;199-218.
-
(1991)
Proteins: Struct. Funct. Genet.
, vol.10
, pp. 199-218
-
-
Vila, J.1
Williams, R.L.2
Vásquez, M.3
Scheraga, H.A.4
-
38
-
-
0031768734
-
Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing α-Helices
-
Vila J. A., Ripoll D. R., Villegas M. E., Vorobjev Y. N., Scheraga H. A. Role of hydrophobicity and solvent-mediated charge-charge interactions in stabilizing α-Helices. Biophys. J. 75:1998b;2637-2646.
-
(1998)
Biophys. J.
, vol.75
, pp. 2637-2646
-
-
Vila, J.A.1
Ripoll, D.R.2
Villegas, M.E.3
Vorobjev, Y.N.4
Scheraga, H.A.5
-
39
-
-
0010924035
-
Interaction of a biomolecule with mobile ions in aqueous solution. Comparison of three fast approximate methods with the direct solution of the nonlinear Poisson-Boltzmann equation
-
Vorobjev Y. N., Scheraga H. A. Interaction of a biomolecule with mobile ions in aqueous solution. Comparison of three fast approximate methods with the direct solution of the nonlinear Poisson-Boltzmann equation. J. Phys. Chem. 97:1993;4855-4864.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 4855-4864
-
-
Vorobjev, Y.N.1
Scheraga, H.A.2
-
40
-
-
0001445346
-
A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent
-
Vorobjev Y. N., Scheraga H. A. A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent. J. Comput. Chem. 18:1997;569-583.
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 569-583
-
-
Vorobjev, Y.N.1
Scheraga, H.A.2
-
41
-
-
0001547345
-
A combined iterative and boundary element approach for solution of the nonlinear Poisson-Boltzmann equation
-
Vorobjev Y. N., Grant J. A., Scheraga H. A. A combined iterative and boundary element approach for solution of the nonlinear Poisson-Boltzmann equation. J. Am. Chem. Soc. 114:1992;3189-3196.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 3189-3196
-
-
Vorobjev, Y.N.1
Grant, J.A.2
Scheraga, H.A.3
-
42
-
-
0000084992
-
Theoretical modeling of electrostatic effects of titratable side-chain groups on protein conformation in a polar ionic solution. 1. Potential of mean force between charged lysine residues and titration of poly(L-lysine) in 95 % methanol solution
-
Vorobjev Y. N., Scheraga H. A., Hitz B., Honig B. Theoretical modeling of electrostatic effects of titratable side-chain groups on protein conformation in a polar ionic solution. 1. Potential of mean force between charged lysine residues and titration of poly(L-lysine) in 95 % methanol solution. J. Phys. Chem. 98:1994;10940-10948.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 10940-10948
-
-
Vorobjev, Y.N.1
Scheraga, H.A.2
Hitz, B.3
Honig, B.4
-
43
-
-
0023060081
-
Free energy of charges in solvated proteins: Microscopic calculations using a reversible charging process
-
Warshel A., Sussman F., King G. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. Biochemistry. 25:1986;8368-8372.
-
(1986)
Biochemistry
, vol.25
, pp. 8368-8372
-
-
Warshel, A.1
Sussman, F.2
King, G.3
-
44
-
-
0024279235
-
Analysis and prediction of the different types of β-turn in protein
-
Wilmot C. M., Thornton J. M. Analysis and prediction of the different types of β-turn in protein. J. Mol. Biol. 203:1988;221-232.
-
(1988)
J. Mol. Biol.
, vol.203
, pp. 221-232
-
-
Wilmot, C.M.1
Thornton, J.M.2
-
45
-
-
0025113022
-
Beta-turns and their distortions: A proposed new nomenclature
-
Wilmot C. M., Thornton J. M. Beta-turns and their distortions: a proposed new nomenclature. Protein Eng. 3:1990;479-493.
-
(1990)
Protein Eng.
, vol.3
, pp. 479-493
-
-
Wilmot, C.M.1
Thornton, J.M.2
-
46
-
-
0344374482
-
Folding of peptide fragments of protein in aqueous solution
-
D. Live, I. M. Armitage, & D. Patel. New York: A.R. Liss
-
Wright P. E., Dyson H. J., Feher V. A., Tennant L. L., Waltho J. P., Lerner R. A., Case D. A. Folding of peptide fragments of protein in aqueous solution. Live D., Armitage I. M., Patel D. Frontiers of NMR in Molecular Biology. 1990;1-13 A.R. Liss, New York.
-
(1990)
Frontiers of NMR in Molecular Biology
, pp. 1-13
-
-
Wright, P.E.1
Dyson, H.J.2
Feher, V.A.3
Tennant, L.L.4
Waltho, J.P.5
Lerner, R.A.6
Case, D.A.7
-
47
-
-
0027231258
-
On the pH dependence of protein stability
-
Yang A.-S., Honig B. On the pH dependence of protein stability. J. Mol. Biol. 231:1993;459-474.
-
(1993)
J. Mol. Biol.
, vol.231
, pp. 459-474
-
-
Yang, A.-S.1
Honig, B.2
-
49
-
-
0028068045
-
Stabilization of a type VI turn in a family of linear peptides in water solution
-
Yao J., Feher V. A., Espejo B. F., Reymond M. T., Wright P. E., Dyson H. J. Stabilization of a type VI turn in a family of linear peptides in water solution. J. Mol. Biol. 243:1994a;736-753.
-
(1994)
J. Mol. Biol.
, vol.243
, pp. 736-753
-
-
Yao, J.1
Feher, V.A.2
Espejo, B.F.3
Reymond, M.T.4
Wright, P.E.5
Dyson, H.J.6
-
50
-
-
0027937869
-
Three-dimensional structure of a type VI turn in a linear peptide in water solution. Evidence for stacking of aromatic rings as major stabilizing factor
-
Yao J., Dyson H. J., Wright P. E. Three-dimensional structure of a type VI turn in a linear peptide in water solution. Evidence for stacking of aromatic rings as major stabilizing factor. J. Mol. Biol. 243:1994b;754-766.
-
(1994)
J. Mol. Biol.
, vol.243
, pp. 754-766
-
-
Yao, J.1
Dyson, H.J.2
Wright, P.E.3
-
51
-
-
0028251938
-
Differential side chain hydration in a linear peptide containing a type VI turn
-
Yao J., Brüschweiler R., Dyson H. J., Wright P. E. Differential side chain hydration in a linear peptide containing a type VI turn. J. Am. Chem. Soc. 116:1994c;12051-12052.
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 12051-12052
-
-
Yao, J.1
Brüschweiler, R.2
Dyson, H.J.3
Wright, P.E.4
-
52
-
-
0028859420
-
Conformation and hydrogen ion titration of proteins: A continuum electrostatic model with conformational flexibility
-
You T. J., Bashford D. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. Biophys. J. 69:1995;1721-1733.
-
(1995)
Biophys. J.
, vol.69
, pp. 1721-1733
-
-
You, T.J.1
Bashford, D.2
-
54
-
-
0017355537
-
Influence of local interactions on protein structure. Conformational energy studies of N-acetyl-N′-methylamides of Pro-X and X-Pro dipeptides
-
Zimmerman S. S., Scheraga H. A. Influence of local interactions on protein structure. Conformational energy studies of N-acetyl-N′-methylamides of Pro-X and X-Pro dipeptides. Biopolymers. 16:1977b;811-843.
-
(1977)
Biopolymers
, vol.16
, pp. 811-843
-
-
Zimmerman, S.S.1
Scheraga, H.A.2
|