-
1
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
2
-
-
0033954256
-
The protein data bank
-
Herman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Herman, 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
-
3
-
-
0024290472
-
Amino acid preferences for specific locations at the ends of alpha helices
-
Richardson JS, Richardson DC. Amino acid preferences for specific locations at the ends of alpha helices. Science 1988;240:1648-1652.
-
(1988)
Science
, vol.240
, pp. 1648-1652
-
-
Richardson, J.S.1
Richardson, D.C.2
-
4
-
-
0034994293
-
The interrelationships of side-chain and main-chain conformations in proteins
-
Chakrabarti P, Pal D. The interrelationships of side-chain and main-chain conformations in proteins. Prog Biophys Mol Biol 2001;76:1-102.
-
(2001)
Prog Biophys Mol Biol
, vol.76
, pp. 1-102
-
-
Chakrabarti, P.1
Pal, D.2
-
5
-
-
1842523274
-
Amino acid propensities are position-dependent throughout the length of alpha helices
-
Engel DE, DeGrado WF. Amino acid propensities are position-dependent throughout the length of alpha helices. J Mol Biol 2004;337:1195-1205.
-
(2004)
J Mol Biol
, vol.337
, pp. 1195-1205
-
-
Engel, D.E.1
DeGrado, W.F.2
-
6
-
-
0019776488
-
Dipoles of the alpha helix and beta sheet: Their role in protein folding
-
Hol WG, Halie LM, Sander C. Dipoles of the alpha helix and beta sheet: their role in protein folding. Nature 1981;294:532-536.
-
(1981)
Nature
, vol.294
, pp. 532-536
-
-
Hol, W.G.1
Halie, L.M.2
Sander, C.3
-
8
-
-
0034826730
-
Alpha- and 3(10) helix interconversion: A quantum-chemical study on polyalanine systems in the gas phase and in aqueous solvent
-
Topol IA, Burt SK, Deretey E, Tang TH, Perczel A, Rashin A, Csizmadia IG. alpha- and 3(10) helix interconversion: a quantum-chemical study on polyalanine systems in the gas phase and in aqueous solvent. J Am Chem Soc 2001;123:6054-6060.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 6054-6060
-
-
Topol, I.A.1
Burt, S.K.2
Deretey, E.3
Tang, T.H.4
Perczel, A.5
Rashin, A.6
Csizmadia, I.G.7
-
9
-
-
0034806675
-
A theoretical study on the origin of cooperativity in the formation of 3(10)- and alpha helices
-
Wu YD, Zhao YL. A theoretical study on the origin of cooperativity in the formation of 3(10)- and alpha helices. J Am Chem Soc 2001;123:5313-5319.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 5313-5319
-
-
Wu, Y.D.1
Zhao, Y.L.2
-
10
-
-
2342487975
-
Structure, spectra and the effects of twisting of beta sheet peptides. A density functional theory study
-
Bour P, Keiderling T. Structure, spectra and the effects of twisting of beta sheet peptides. A density functional theory study. J Mol Struct-Theochem 2004;675:95-105.
-
(2004)
J Mol Struct-Theochem
, vol.675
, pp. 95-105
-
-
Bour, P.1
Keiderling, T.2
-
11
-
-
0001731266
-
Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects
-
Bergner A, Günther J, Hendlich M, Klebe G, Verdenk M. Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects. Biopolymers 2001;61:99-110.
-
(2001)
Biopolymers
, vol.61
, pp. 99-110
-
-
Bergner, A.1
Günther, J.2
Hendlich, M.3
Klebe, G.4
Verdenk, M.5
-
12
-
-
0037436339
-
Relibase: Design and development of a database for comprehensive analysis of protein-ligand interactions
-
Hendlich M, Bergner A, Günther J, Klebe G. Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J Mol Biol 2003;326:607-620.
-
(2003)
J Mol Biol
, vol.326
, pp. 607-620
-
-
Hendlich, M.1
Bergner, A.2
Günther, J.3
Klebe, G.4
-
15
-
-
0028205447
-
Enlarged representative set of protein structures
-
Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3:522-524.
-
(1994)
Protein Sci
, vol.3
, pp. 522-524
-
-
Hobohm, U.1
Sander, C.2
-
16
-
-
0035314041
-
Pex, analytical tools for PDB files. II. H-Pex: Noncanonical H-bonds in alpha helices
-
Thomas A, Benhabiles N, Meurisse R, Ngwabije R, Brasseur R. Pex, analytical tools for PDB files. II. H-Pex: Noncanonical H-bonds in alpha helices. Proteins 2001;43:37-44.
-
(2001)
Proteins
, vol.43
, pp. 37-44
-
-
Thomas, A.1
Benhabiles, N.2
Meurisse, R.3
Ngwabije, R.4
Brasseur, R.5
-
17
-
-
0142104233
-
Atomic resolution density maps reveal secondary structure dependent differences in electronic distribution
-
Lario PI, Vrielink A. Atomic resolution density maps reveal secondary structure dependent differences in electronic distribution. J Am Chem Soc 2003;125:12787-12794.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 12787-12794
-
-
Lario, P.I.1
Vrielink, A.2
-
18
-
-
0037434686
-
Density functional theory study of the cooperativity of hydrogen bonds in finite and infinite alphahelices
-
Ireta J, Neugebauer J, Scheffler M, Rojo A, Galvan M. Density functional theory study of the cooperativity of hydrogen bonds in finite and infinite alphahelices. J Phys Chem B 2003;107:1432-1437.
-
(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
-
19
-
-
0034829669
-
Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-alpha-aminoisobutyric acid in vacuo
-
Improta R, Barone V, Kudin K, Scuseria G. Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-alpha-aminoisobutyric acid in vacuo. J Am Chem Soc 2001;123:3311-3322.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 3311-3322
-
-
Improta, R.1
Barone, V.2
Kudin, K.3
Scuseria, G.4
-
20
-
-
0347578256
-
Cooperativity in amide hydrogen bonding chains. Relation between energy, position, and H-bond chain length in peptide and protein folding models
-
Kobko N, Dannenberg 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 2003;107:10389-10395.
-
(2003)
J Phys Chem A
, vol.107
, pp. 10389-10395
-
-
Kobko, N.1
Dannenberg, J.2
-
21
-
-
0035063642
-
Observation of the closing of individual hydrogen bonds during TFE-induced helix formation in a peptide
-
Jaravine V, Alexandrescu A, Grzesiek S. Observation of the closing of individual hydrogen bonds during TFE-induced helix formation in a peptide. Protein Sci 2001;10:943-950.
-
(2001)
Protein Sci
, vol.10
, pp. 943-950
-
-
Jaravine, V.1
Alexandrescu, A.2
Grzesiek, S.3
-
22
-
-
0035138648
-
A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method
-
Cui Q, Elstner M, Kaxiras E, Frauenheim T, Karplus M. A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. J Phys Chem B 2001;105:569-585.
-
(2001)
J Phys Chem B
, vol.105
, pp. 569-585
-
-
Cui, Q.1
Elstner, M.2
Kaxiras, E.3
Frauenheim, T.4
Karplus, M.5
-
23
-
-
0034656826
-
DFT studies on helix formation in N-acetyl-(L-alanyl)(n)-N′- methylamide for n = 1-20
-
Elstner M, Jalkanen K, Knapp-Mohammady M, Frauenheim T, Suhai S. DFT studies on helix formation in N-acetyl-(L-alanyl)(n)-N′-methylamide for n = 1-20. Chem Phys 2000;256:15-27.
-
(2000)
Chem Phys
, vol.256
, pp. 15-27
-
-
Elstner, M.1
Jalkanen, K.2
Knapp-Mohammady, M.3
Frauenheim, T.4
Suhai, S.5
-
24
-
-
77949975511
-
Potentials and algorithms for incorporating polarizability in computer simulations
-
Rick S, Stuart S. Potentials and algorithms for incorporating polarizability in computer simulations. Rev Comp Ch 2002:89-146.
-
(2002)
Rev Comp Ch
, pp. 89-146
-
-
Rick, S.1
Stuart, S.2
-
25
-
-
0036296028
-
Twist and shear in beta sheets and beta-ribbons
-
Ho B, Curmi P. Twist and shear in beta sheets and beta-ribbons. J Mol Biol 2002;317:291-308.
-
(2002)
J Mol Biol
, vol.317
, pp. 291-308
-
-
Ho, B.1
Curmi, P.2
-
26
-
-
0021978310
-
The role of the alpha helix dipole in protein function and structure
-
Hol WG. The role of the alpha helix dipole in protein function and structure. Prog Biophys Mol Biol 1985;45:149-195.
-
(1985)
Prog Biophys Mol Biol
, vol.45
, pp. 149-195
-
-
Hol, W.G.1
-
27
-
-
4444306767
-
Crystal structure of phenylalanine ammonia lyase: Multiple helix dipoles implicated in catalysis
-
Calabrese JC, Jordan DB, Boodhoo A, Sariaslani S, Vannelli T. Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis. Biochemistry 2004;43:11403-11416.
-
(2004)
Biochemistry
, vol.43
, pp. 11403-11416
-
-
Calabrese, J.C.1
Jordan, D.B.2
Boodhoo, A.3
Sariaslani, S.4
Vannelli, T.5
-
28
-
-
0032478818
-
The structure of the potassium channel: Molecular basis of K+ conduction and selectivity
-
Doyle DA, Morais Cabral J, Pfuetzner RA, Kuo A, Gulbis JM, Cohen SL, Chait BT, MacKinnon R. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 1998;280:69-77
-
(1998)
Science
, vol.280
, pp. 69-77
-
-
Doyle, D.A.1
Morais Cabral, J.2
Pfuetzner, R.A.3
Kuo, A.4
Gulbis, J.M.5
Cohen, S.L.6
Chait, B.T.7
MacKinnon, R.8
-
29
-
-
0037122805
-
X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity
-
Dutzler R, Campbell EB, Cadene M, Chait BT, MacKinnon R. X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity. Nature 2002;415:287-294.
-
(2002)
Nature
, vol.415
, pp. 287-294
-
-
Dutzler, R.1
Campbell, E.B.2
Cadene, M.3
Chait, B.T.4
MacKinnon, R.5
-
31
-
-
26444593637
-
-
St. Louis, MI: Tripos Inc
-
Tripos. SYBYL 7.0. St. Louis, MI: Tripos Inc.
-
SYBYL 7.0
-
-
|