-
2
-
-
0023675175
-
Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulation
-
Anderson AG, Hermans J. 1988. Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulation. Proteins 3:262-265.
-
(1988)
Proteins
, vol.3
, pp. 262-265
-
-
Anderson, A.G.1
Hermans, J.2
-
4
-
-
3042524904
-
A well behaved electrostatic potential base method using charge restraints for deriving atomic charges: The RESP model
-
Bayly CI, Cieplak P, Cornell WD, Kollman PA. 1993. A well behaved electrostatic potential base method using charge restraints for deriving atomic charges: The RESP model. J Phys Chem 97:10269-10280.
-
(1993)
J Phys Chem
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
5
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. 1984. Molecular dynamics with coupling to an external bath. J Comp Phys 81:3684-3690.
-
(1984)
J Comp Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
6
-
-
0025279242
-
Zinc finger domains: Hypotheses and current knowledge
-
Berg JM. 1990. Zinc finger domains: Hypotheses and current knowledge. Annu Rev Biophys Biophys Chem 19:405-421.
-
(1990)
Annu Rev Biophys Biophys Chem
, vol.19
, pp. 405-421
-
-
Berg, J.M.1
-
7
-
-
0029151245
-
First-principles calculation of the folding free-energy of a 3-helix bundle protein
-
Boczko EM, Brooks CL III. 1995. First-principles calculation of the folding free-energy of a 3-helix bundle protein. Science 269:393-396.
-
(1995)
Science
, vol.269
, pp. 393-396
-
-
Boczko, E.M.1
Brooks C.L. III2
-
8
-
-
0030670359
-
Chaos in protein dynamics
-
Braxenthaler M, Unger R, Auesbach D, Geven JA, Moult J. 1997. Chaos in protein dynamics. Protein 29:417-425.
-
(1997)
Protein
, vol.29
, pp. 417-425
-
-
Braxenthaler, M.1
Unger, R.2
Auesbach, D.3
Geven, J.A.4
Moult, J.5
-
9
-
-
0028264860
-
Molecular-dynamics simulation of protein denaturation - Solvation of the hydrophobic cores and secondary structure of barnase
-
Caflisch A, Karplus M. 1994. Molecular-dynamics simulation of protein denaturation - Solvation of the hydrophobic cores and secondary structure of barnase. Proc Natl Acad Sci USA 91:1746-1750.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 1746-1750
-
-
Caflisch, A.1
Karplus, M.2
-
10
-
-
0015914783
-
Conformation of twisted β-pleated sheets in proteins
-
Chothia C. 1973. Conformation of twisted β-pleated sheets in proteins. J Mol Biol 75:295-302.
-
(1973)
J Mol Biol
, vol.75
, pp. 295-302
-
-
Chothia, C.1
-
11
-
-
0021095536
-
Role of inter-chain interactions in the stabilization of the right-handed twist of β-sheets
-
Chou K-C, Nemethy G, Scheraga HA. 1983. Role of inter-chain interactions in the stabilization of the right-handed twist of β-sheets. J Mol Biol 68:389-407.
-
(1983)
J Mol Biol
, vol.68
, pp. 389-407
-
-
Chou, K.-C.1
Nemethy, G.2
Scheraga, H.A.3
-
12
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Kenneth J, Merz M, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179-5197.
-
(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
Kenneth, J.5
Merz, M.6
Ferguson, D.M.7
Spellmeyer, D.C.8
Fox, T.9
Caldwell, J.W.10
Kollman, P.A.11
-
13
-
-
0027219504
-
Protein unfolding pathways explored through molecular dynamics simulations
-
Daggett V, Levitt M. 1993. Protein unfolding pathways explored through molecular dynamics simulations. J Mol Biol 232:600-619.
-
(1993)
J Mol Biol
, vol.232
, pp. 600-619
-
-
Daggett, V.1
Levitt, M.2
-
14
-
-
0030793767
-
De novo protein design: Fully automated sequence selection
-
Dahiyat BI, Mayo SL. 1997. De novo protein design: Fully automated sequence selection. Science 278:82-87.
-
(1997)
Science
, vol.278
, pp. 82-87
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
15
-
-
33846823909
-
Particle mesh ewald - An N·log(n) method for ewald sums in large systems
-
Darden T, York D, Pedersen L. 1993. Particle Mesh Ewald - An N·log(n) method for Ewald sums in large systems. J Chem Phys 98:10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
16
-
-
0025370815
-
Dominant forces in protein folding
-
Dill KA. 1990. Dominant forces in protein folding. Biochemistry 29:7133-7155.
-
(1990)
Biochemistry
, vol.29
, pp. 7133-7155
-
-
Dill, K.A.1
-
18
-
-
0027462173
-
Principles of protein stability derived from protein engineering experiments
-
Fersht AR, Serrano L. 1993. Principles of protein stability derived from protein engineering experiments. Current Opinion in Structural Biology 3:75-83.
-
(1993)
Current Opinion in Structural Biology
, vol.3
, pp. 75-83
-
-
Fersht, A.R.1
Serrano, L.2
-
19
-
-
0023375317
-
Metal-dependent folding of a single zinc finger from transcription factor IIIA
-
Frankel AD, Berg JM, Pabo CO. 1987. Metal-dependent folding of a single zinc finger from transcription factor IIIA. Proc Natl Acad Sci 84:4841.
-
(1987)
Proc Natl Acad Sci
, vol.84
, pp. 4841
-
-
Frankel, A.D.1
Berg, J.M.2
Pabo, C.O.3
-
20
-
-
0010922186
-
-
Pittsburg, Pennsylvania: Gaussian Inc.
-
Frisch MJ, Trucks GW, Schlegel HB, Gill PMW, Johnson BG, Robb MA, Cheeseman JR, Keith T, Petersson GA, Montegomery JA, Rahavachari K, Al-Laham MA, Zakrzewski VG, Ortiz JV, Foresman JB, Peng CY, Ayala PY, Chen W, Wong MW, Andres JL, Replogle ES, Gomperts R, Martin RL, Fox DJ, Binkley JS, Defrees DJ, Baker J, Stewart JP, Head-Gordon M, Gonzalez C, Pople JA. 1995. Gaussian 94, Revision B.3. Pittsburg, Pennsylvania: Gaussian Inc.
-
(1995)
Gaussian 94, Revision B.3
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Gill, P.M.W.4
Johnson, B.G.5
Robb, M.A.6
Cheeseman, J.R.7
Keith, T.8
Petersson, G.A.9
Montegomery, J.A.10
Rahavachari, K.11
Al-Laham, M.A.12
Zakrzewski, V.G.13
Ortiz, J.V.14
Foresman, J.B.15
Peng, C.Y.16
Ayala, P.Y.17
Chen, W.18
Wong, M.W.19
Andres, J.L.20
Replogle, E.S.21
Gomperts, R.22
Martin, R.L.23
Fox, D.J.24
Binkley, J.S.25
Defrees, D.J.26
Baker, J.27
Stewart, J.P.28
Head-Gordon, M.29
Gonzalez, C.30
Pople, J.A.31
more..
-
21
-
-
0027499733
-
Soluble proteins: Size, shape and function
-
Goodsell DS, Olson AJ. 1993. Soluble proteins: Size, shape and function. Trends Biochem Sci 18:65-68.
-
(1993)
Trends Biochem Sci
, vol.18
, pp. 65-68
-
-
Goodsell, D.S.1
Olson, A.J.2
-
22
-
-
0029011910
-
Molecular dynamics simulations of isolated helices of myoglobin
-
Hirst JD, Brooks CL III. 1995. Molecular dynamics simulations of isolated helices of myoglobin. Biochemistry 34:7614-7621.
-
(1995)
Biochemistry
, vol.34
, pp. 7614-7621
-
-
Hirst, J.D.1
Brooks C.L. III2
-
23
-
-
0023506457
-
Folding and association of proteins
-
Jaenicke R. 1987. Folding and association of proteins. Prog Biophys Mol Biol 49:117-237.
-
(1987)
Prog Biophys Mol Biol
, vol.49
, pp. 117-237
-
-
Jaenicke, R.1
-
24
-
-
0004016501
-
Comparisons of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. 1983. Comparisons of simple potential functions for simulating liquid water. J Chem Phys 79:926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
25
-
-
84893482610
-
A solution for the best rotation to relate two sets of vectors
-
Kabsch W. 1976. A solution for the best rotation to relate two sets of vectors. Acta Cryst A32:922-923.
-
(1976)
Acta Cryst
, vol.A32
, pp. 922-923
-
-
Kabsch, W.1
-
26
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
-
Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
27
-
-
0025345415
-
Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding
-
Kim PS, Baldwin RL. 1982. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Ann Rev Biochem 59:631-660.
-
(1982)
Ann Rev Biochem
, vol.59
, pp. 631-660
-
-
Kim, P.S.1
Baldwin, R.L.2
-
28
-
-
7044239742
-
Free energy calculations: Applications to chemical and biological phenomena
-
Kollman PA. 1993. Free energy calculations: Applications to chemical and biological phenomena. Chem Rev 93:2395-2417.
-
(1993)
Chem Rev
, vol.93
, pp. 2395-2417
-
-
Kollman, P.A.1
-
29
-
-
0002098417
-
The development/application of a "minimalist" organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data
-
van Gunsteren WF, ed. Dordrecht, The Netherlands: ESCOM
-
Kollman PA, Dixon RW, Cornell WD, Fox T, Chipot C, Pohorille A. 1997. The development/application of a "minimalist" organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data. In: van Gunsteren WF, ed. Computer simulations of biological systems. Dordrecht, The Netherlands: ESCOM.
-
(1997)
Computer Simulations of Biological Systems
-
-
Kollman, P.A.1
Dixon, R.W.2
Cornell, W.D.3
Fox, T.4
Chipot, C.5
Pohorille, A.6
-
30
-
-
84986519238
-
The weighted histogram analysis method for free energy calculations on biomolecules: I
-
Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM. 1992. The weighted histogram analysis method for free energy calculations on biomolecules: I. The method. J Comp Chem 13:1011-1021.
-
(1992)
The Method. J Comp Chem
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
31
-
-
0031465967
-
"New view" of protein folding reconciled with the old through multiple unfolding simulations
-
Lazaridis T, Karplus M. 1997. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 278:1928-1931.
-
(1997)
Science
, vol.278
, pp. 1928-1931
-
-
Lazaridis, T.1
Karplus, M.2
-
32
-
-
84912079256
-
Rapid approximation to molecular-surface area via the use of boolean logic and look-up tables
-
Le Grand SM, Merz KM. 1993. Rapid approximation to molecular-surface area via the use of boolean logic and look-up tables. J Comp Chem 14:349-352.
-
(1993)
J Comp Chem
, vol.14
, pp. 349-352
-
-
Le Grand, S.M.1
Merz, K.M.2
-
33
-
-
0029963345
-
Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
-
Li A, Daggett V. 1996. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J Mol Biol 257:412-429.
-
(1996)
J Mol Biol
, vol.257
, pp. 412-429
-
-
Li, A.1
Daggett, V.2
-
34
-
-
0027255479
-
Structural and genetic analysis of protein stability
-
Matthews BW. 1993. Structural and genetic analysis of protein stability. Ann Rev Biochem 62:139-60.
-
(1993)
Ann Rev Biochem
, vol.62
, pp. 139-160
-
-
Matthews, B.W.1
-
35
-
-
0031058410
-
NMR structure of the 35-residue villin headpiece subdomain
-
McKnight CJ, Matsudaira PT, Kim PS. 1997. NMR structure of the 35-residue villin headpiece subdomain. Nat Struct Biol 4:180-184.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 180-184
-
-
McKnight, C.J.1
Matsudaira, P.T.2
Kim, P.S.3
-
36
-
-
0015217634
-
The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions
-
Nozaki Y, Tanford CH. 1971. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. J Biol Chem 246:2211-2217.
-
(1971)
J Biol Chem
, vol.246
, pp. 2211-2217
-
-
Nozaki, Y.1
Tanford, C.H.2
-
37
-
-
0025134134
-
Spectroscopic studies of wild-type and mutant "zinc finger" peptides: Determinants of domain folding and structure
-
Parraga G, Horvath S, Hood L, Young ET, Klevit RE. 1990. Spectroscopic studies of wild-type and mutant "zinc finger" peptides: Determinants of domain folding and structure. Proc Natl Acad Sci USA 87:137-141.
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 137-141
-
-
Parraga, G.1
Horvath, S.2
Hood, L.3
Young, E.T.4
Klevit, R.E.5
-
38
-
-
0025773296
-
Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 Å
-
Pavletich NP, Pabo CO. 1991. Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 Å. Science 252:809-817.
-
(1991)
Science
, vol.252
, pp. 809-817
-
-
Pavletich, N.P.1
Pabo, C.O.2
-
39
-
-
0004023361
-
-
San Francisco: University of California
-
Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TEI, Ferguson DM, Seibel GL, Singh UC, Weiner PK, Kollman PA. 1995. AMBER. San Francisco: University of California.
-
(1995)
AMBER
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.I.5
Ferguson, D.M.6
Seibel, G.L.7
Singh, U.C.8
Weiner, P.K.9
Kollman, P.A.10
-
40
-
-
0024290488
-
Helix signals in proteins
-
Presta LG, Rose GD. 1988. Helix signals in proteins. Science 240:1632-1641.
-
(1988)
Science
, vol.240
, pp. 1632-1641
-
-
Presta, L.G.1
Rose, G.D.2
-
41
-
-
0019443447
-
The anatomy and taxonomy of protein structure
-
Richardson JS. 1981. The anatomy and taxonomy of protein structure. Adv Protein Chem 34:167-339.
-
(1981)
Adv Protein Chem
, vol.34
, pp. 167-339
-
-
Richardson, J.S.1
-
42
-
-
0024290472
-
Amino acid preferences for specific locations at the ends of alpha helices
-
Richardson JS, Richardson DC. 1988. Amino acid preferences for specific locations at the ends of alpha helices. Science 240:1648-1652.
-
(1988)
Science
, vol.240
, pp. 1648-1652
-
-
Richardson, J.S.1
Richardson, D.C.2
-
43
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert J-P, Ciccotti G, Berendsen HJC. 1977. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comp Phys 23:327-341.
-
(1977)
J Comp Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
44
-
-
0030220763
-
Engineering enzymes for stability
-
Shaw A, Bott R. 1996. Engineering enzymes for stability. Curr Opin Struct Biol 6:546-550.
-
(1996)
Curr Opin Struct Biol
, vol.6
, pp. 546-550
-
-
Shaw, A.1
Bott, R.2
-
45
-
-
0021844602
-
Beta-hairpin families in globular proteins
-
Sibanda BL, Thornton JM. 1985. Beta-hairpin families in globular proteins. Nature 316:170-174.
-
(1985)
Nature
, vol.316
, pp. 170-174
-
-
Sibanda, B.L.1
Thornton, J.M.2
-
46
-
-
48549111326
-
Why are enzymes so big?
-
Srere PA. 1984. Why are enzymes so big? Trends Biochem Sci 9:387-390.
-
(1984)
Trends Biochem Sci
, vol.9
, pp. 387-390
-
-
Srere, P.A.1
-
47
-
-
0030593029
-
Design of a monomeric 23-residue polypeptide with defined tertiary structure
-
Struthers MD, Cheng RP, Imperiali B. 1996a. Design of a monomeric 23-residue polypeptide with defined tertiary structure. Science 271:342-345.
-
(1996)
Science
, vol.271
, pp. 342-345
-
-
Struthers, M.D.1
Cheng, R.P.2
Imperiali, B.3
-
48
-
-
0030567375
-
Economy in protein design -evolution of a metal-independent β-β-α motif based on the zinc finger domains
-
Struthers MD, Cheng RP, Imperiali B. 1996b. Economy in protein design -Evolution of a metal-independent β-β-α motif based on the zinc finger domains. JACS 118:3073-3081.
-
(1996)
JACS
, vol.118
, pp. 3073-3081
-
-
Struthers, M.D.1
Cheng, R.P.2
Imperiali, B.3
-
49
-
-
0002543810
-
Design and NMR analyses of compact, independently folded BBA motifs
-
Struthers MD, Ottesen JJ, Imperiali B. 1998. Design and NMR analyses of compact, independently folded BBA motifs. Folding Design 3:95-103.
-
(1998)
Folding Design
, vol.3
, pp. 95-103
-
-
Struthers, M.D.1
Ottesen, J.J.2
Imperiali, B.3
-
50
-
-
0027316216
-
Molecular-dynamics simulations of the unfolding of apomyoglobin in water
-
Tirado-Rives J, Jorgensen WL. 1993. Molecular-dynamics simulations of the unfolding of apomyoglobin in water. Biochemistry 32:4175-4184.
-
(1993)
Biochemistry
, vol.32
, pp. 4175-4184
-
-
Tirado-Rives, J.1
Jorgensen, W.L.2
-
51
-
-
0025767212
-
Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides
-
Tobias DJ, Brooks CL III. 1991. Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. Biochemistry 30:6059-6070.
-
(1991)
Biochemistry
, vol.30
, pp. 6059-6070
-
-
Tobias, D.J.1
Brooks C.L. III2
-
52
-
-
0002531265
-
Methods for calculation of free energies and binding constants: Successes and problems
-
van Gunsteren WF, Weiner PK, eds. Leiden: ESCOM
-
van Gunsteren WF. 1989. Methods for calculation of free energies and binding constants: Successes and problems. In: van Gunsteren WF, Weiner PK, eds. Computer simulations of biomolecular systems. Leiden: ESCOM, pp 27-59.
-
(1989)
Computer Simulations of Biomolecular Systems
, pp. 27-59
-
-
Gunsteren, W.F.1
-
54
-
-
0030134514
-
Chaos in biomolecular dynamics
-
Zhou HB, Wang L. 1996. Chaos in biomolecular dynamics. J Phys Chem 100:8101-8105.
-
(1996)
J Phys Chem
, vol.100
, pp. 8101-8105
-
-
Zhou, H.B.1
Wang, L.2
|