-
1
-
-
0032438194
-
Fractional factors and activation energies for exchange of the low barrier hydrogen bonding proton in peptidyl trifluoromethyl ketone complexes of chymotrypsin
-
Lin J, Westler WM, Cleland WW, Markley JL, Frey PA. Fractional factors and activation energies for exchange of the low barrier hydrogen bonding proton in peptidyl trifluoromethyl ketone complexes of chymotrypsin. Proc Natl Acad Sci USA 1998;95:14664-14668.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 14664-14668
-
-
Lin, J.1
Westler, W.M.2
Cleland, W.W.3
Markley, J.L.4
Frey, P.A.5
-
2
-
-
0031688282
-
Enzymatic transition states and transition state analog design
-
Schramm VL. Enzymatic transition states and transition state analog design. Ann Rev Biochem 1998;67:693-720.
-
(1998)
Ann Rev Biochem
, vol.67
, pp. 693-720
-
-
Schramm, V.L.1
-
4
-
-
0017324044
-
Serine proteases: Structure and mechanism of catalysis
-
Kraut J. Serine proteases: structure and mechanism of catalysis. Ann Rev Biochem 1977;46:331-358.
-
(1977)
Ann Rev Biochem
, vol.46
, pp. 331-358
-
-
Kraut, J.1
-
5
-
-
0016089567
-
A family of protein-cutting proteins
-
Stroud RM. A family of protein-cutting proteins. Sci Am 1974;231: 74-88.
-
(1974)
Sci Am
, vol.231
, pp. 74-88
-
-
Stroud, R.M.1
-
7
-
-
0025873532
-
Evidence for a tetrahedral intermediate complex during serpin-proteinase interactions
-
Matheson NR, van Halbeek H, Travis J. Evidence for a tetrahedral intermediate complex during serpin-proteinase interactions. J Biol Chem 1991;266:13489-13491.
-
(1991)
J Biol Chem
, vol.266
, pp. 13489-13491
-
-
Matheson, N.R.1
Van Halbeek, H.2
Travis, J.3
-
8
-
-
0020020315
-
Crystallographic and NMR studies of the serine proteases
-
Steitz TA, Shulman RG. Crystallographic and NMR studies of the serine proteases. Annu Rev Biochem Biophys 1982;11:419-444.
-
(1982)
Annu Rev Biochem Biophys
, vol.11
, pp. 419-444
-
-
Steitz, T.A.1
Shulman, R.G.2
-
9
-
-
0014689979
-
Role of a buried acid group in the mechanism of action of chymotrypsin
-
Blow DM, Birktoft JJ, Hartley BS. Role of a buried acid group in the mechanism of action of chymotrypsin. Nature 1969;221:337-340.
-
(1969)
Nature
, vol.221
, pp. 337-340
-
-
Blow, D.M.1
Birktoft, J.J.2
Hartley, B.S.3
-
11
-
-
0032566351
-
Correlations of the basicity of His-57 with transition state analogue binding, substrate reactivity, and the strength of the low-barrier hydrogen bond in chymotrypsin
-
Lin J, Cassidy CS, Frey PA. Correlations of the basicity of His-57 with transition state analogue binding, substrate reactivity, and the strength of the low-barrier hydrogen bond in chymotrypsin. Biochemistry 1998;37:11940-11948.
-
(1998)
Biochemistry
, vol.37
, pp. 11940-11948
-
-
Lin, J.1
Cassidy, C.S.2
Frey, P.A.3
-
12
-
-
0030937806
-
A new concept for the mechanism of action of chymotrypsin: The role of the low-barrier hydrogen bond
-
Cassidy CS, Lin J, Frey PA. A new concept for the mechanism of action of chymotrypsin: the role of the low-barrier hydrogen bond. Biochemistry 1997;36:4576-4584.
-
(1997)
Biochemistry
, vol.36
, pp. 4576-4584
-
-
Cassidy, C.S.1
Lin, J.2
Frey, P.A.3
-
13
-
-
0028040716
-
A low-barrier hydrogen bond in the catalytic triad of serine proteases
-
Frey PA, Whitt SA, Tobin JB. A low-barrier hydrogen bond in the catalytic triad of serine proteases. Science 1994;264:1927-1930.
-
(1994)
Science
, vol.264
, pp. 1927-1930
-
-
Frey, P.A.1
Whitt, S.A.2
Tobin, J.B.3
-
14
-
-
0343006258
-
Site-directed mutagenesis and the role of the oxyanion hole in subtilisin
-
Bryan P, Pantoliano MW, Quill SG, Hsiao HY, Poulos T. Site-directed mutagenesis and the role of the oxyanion hole in subtilisin. Proc Natl Acad Sci USA 1986;83:3743-3745.
-
(1986)
Proc Natl Acad Sci USA
, vol.83
, pp. 3743-3745
-
-
Bryan, P.1
Pantoliano, M.W.2
Quill, S.G.3
Hsiao, H.Y.4
Poulos, T.5
-
15
-
-
0023659387
-
Semiquantitative calculation of catalytic free energies in genetically modified enzymes
-
Hwang JK, Warshel A. Semiquantitative calculation of catalytic free energies in genetically modified enzymes. Biochemistry 1987; 26:2669-2673.
-
(1987)
Biochemistry
, vol.26
, pp. 2669-2673
-
-
Hwang, J.K.1
Warshel, A.2
-
18
-
-
10544255345
-
A low-barrier hydrogen bond in subtilisin: 1H and 15N NMR studies with peptidyl trifluoromethyl ketones
-
Halkides CJ, Wu YQ, Murray CJ. A low-barrier hydrogen bond in subtilisin: 1H and 15N NMR studies with peptidyl trifluoromethyl ketones. Biochemistry 1996;35:15941-15948.
-
(1996)
Biochemistry
, vol.35
, pp. 15941-15948
-
-
Halkides, C.J.1
Wu, Y.Q.2
Murray, C.J.3
-
19
-
-
0032573171
-
On the electronic nature of low-barrier hydrogen bonds in enzymatic reactions
-
Schiott B, Iversen BB, Madsen GK, Larsen FK, Bruice TC. On the electronic nature of low-barrier hydrogen bonds in enzymatic reactions. Proc Natl Acad Sci USA 1998;95:12799-12802.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 12799-12802
-
-
Schiott, B.1
Iversen, B.B.2
Madsen, G.K.3
Larsen, F.K.4
Bruice, T.C.5
-
20
-
-
0029040169
-
On low-barrier hydrogen bonds and enzyme catalysis
-
Warshel A, Papazyan A, Kollman PA. On low-barrier hydrogen bonds and enzyme catalysis. Science 1995;269:102-106.
-
(1995)
Science
, vol.269
, pp. 102-106
-
-
Warshel, A.1
Papazyan, A.2
Kollman, P.A.3
-
21
-
-
0032538627
-
Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites
-
Warshel A. Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites. J Biol Chem 1998;273: 27035-27038.
-
(1998)
J Biol Chem
, vol.273
, pp. 27035-27038
-
-
Warshel, A.1
-
22
-
-
4243606192
-
Unified approach for molecular dynamics and density-functional theory
-
Car R, Parrinello M. Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett 1985;55:2471-2474.
-
(1985)
Phys Rev Lett
, vol.55
, pp. 2471-2474
-
-
Car, R.1
Parrinello, M.2
-
23
-
-
0000102553
-
Ab initio molecular dynamics studies of a synthetic biomimetic model of galactose oxidase
-
See, e.g. (a) Roethlisberger U., Carloni P. Ab initio molecular dynamics studies of a synthetic biomimetic model of galactose oxidase. Int J Quantum Chem 1999;73:209-219.
-
(1999)
Int J Quantum Chem
, vol.73
, pp. 209-219
-
-
Roethlisberger, U.1
Carloni, P.2
-
24
-
-
0032100630
-
Density functional studies on herpes simplex virus type 1 thymidine kinase-substrate interactions: The role of Tyr-172 and Met-128 in thymine fixation
-
(b) Alber F., Kuonen O., Scapozza L., Folkers G., Carloni P. Density functional studies on herpes simplex virus type 1 thymidine kinase-substrate interactions: the role of Tyr-172 and Met-128 in thymine fixation. Proteins 1998;31:453-459.
-
(1998)
Proteins
, vol.31
, pp. 453-459
-
-
Alber, F.1
Kuonen, O.2
Scapozza, L.3
Folkers, G.4
Carloni, P.5
-
25
-
-
0032507261
-
Glucose in aqueous solution by first principles molecular dynamics
-
(c) Molteni C., Parrinello, M. Glucose in aqueous solution by first principles molecular dynamics. J. Am. Chem. Soc. 1998;120:2168-2171.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 2168-2171
-
-
Molteni, C.1
Parrinello, M.2
-
26
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein FC, Koetzle TF, Williams GJB, et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
-
(1977)
J Mol Biol
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
-
27
-
-
0024519247
-
Crystal structure of the covalent complex formed by a peptidyl α, α-difluoro-β-keto amide with porcine pancreatic elastase at 1.78 Å resolution
-
Takahashi LH, Radhakrishnan R, Rosenfield RE, Meyer EF, Trainor DA. Crystal structure of the covalent complex formed by a peptidyl α, α-difluoro-β-keto amide with porcine pancreatic elastase at 1.78 Å resolution. J Am Chem Soc 1989;111:3368-3372.
-
(1989)
J Am Chem Soc
, vol.111
, pp. 3368-3372
-
-
Takahashi, L.H.1
Radhakrishnan, R.2
Rosenfield, R.E.3
Meyer, E.F.4
Trainor, D.A.5
-
29
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
-
30
-
-
0031189711
-
Molecular recognition of protein-ligand complexes: Application to drug design
-
Babine RE, Bender SL. Molecular recognition of protein-ligand complexes: application to drug design. Chem Rev 1997;97:1359-1472.
-
(1997)
Chem Rev
, vol.97
, pp. 1359-1472
-
-
Babine, R.E.1
Bender, S.L.2
-
31
-
-
10644250257
-
Inhomogeneous electron gas
-
Hohenberg P, Kohn W. Inhomogeneous electron gas. Phys Rev 1964;136:B864-B871.
-
(1964)
Phys Rev
, vol.136
-
-
Hohenberg, P.1
Kohn, W.2
-
32
-
-
0042113153
-
Self-consistent equations including exchange and correlation effects
-
Kohn W, Sham LJ. Self-consistent equations including exchange and correlation effects. Phys Rev 1965;140:A1133-A1138.
-
(1965)
Phys Rev
, vol.140
-
-
Kohn, W.1
Sham, L.J.2
-
33
-
-
33645426115
-
Efficient pseudopotentials for plane-wave calculations
-
Troullier N, Martins JL. Efficient pseudopotentials for plane-wave calculations. Phys Rev B 1991;43:1993-2006.
-
(1991)
Phys Rev B
, vol.43
, pp. 1993-2006
-
-
Troullier, N.1
Martins, J.L.2
-
34
-
-
4243553426
-
Density-functional exchange-energy approximation with correct asymptotic behaviour
-
Becke AD. Density-functional exchange-energy approximation with correct asymptotic behaviour. Phys Rev A 1988;38:3098-3100.
-
(1988)
Phys Rev A
, vol.38
, pp. 3098-3100
-
-
Becke, A.D.1
-
35
-
-
0345491105
-
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
-
Lee CL, Yang W, Parr RG. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 1988;37:785-789.
-
(1988)
Phys Rev B
, vol.37
, pp. 785-789
-
-
Lee, C.L.1
Yang, W.2
Parr, R.G.3
-
36
-
-
84986524957
-
Convergence acceleration of iterative sequences. The case of SCF iteration
-
Pulay P. Convergence acceleration of iterative sequences. The case of SCF iteration. Chem Phys Lett 1980;73:393-398.
-
(1980)
Chem Phys Lett
, vol.73
, pp. 393-398
-
-
Pulay, P.1
-
37
-
-
0028392759
-
Electronic structure optimization in plane-wave-based density functional calculations by direct inversion in the iterative subspace
-
Hutter J, Lüthi HP, Parrinello M. Electronic structure optimization in plane-wave-based density functional calculations by direct inversion in the iterative subspace. Comput Mater Sci 1994;2:244-248.
-
(1994)
Comput Mater Sci
, vol.2
, pp. 244-248
-
-
Hutter, J.1
Lüthi, H.P.2
Parrinello, M.3
-
38
-
-
34547809547
-
A unified formulation of the constant temperature molecular dynamics methods
-
Nosé S. A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys 1981;81:511-519.
-
(1981)
J Chem Phys
, vol.81
, pp. 511-519
-
-
Nosé, S.1
-
39
-
-
0000667030
-
Application of RESP charges to calculate conformational energies, hydrogen bond energies and free energies of solvation
-
Cornell WD, Cieplak P, Bayly CI, Kollman PA. Application of RESP charges to calculate conformational energies, hydrogen bond energies and free energies of solvation. J Am Chem Soc 1993;115:9620-9630.
-
(1993)
J Am Chem Soc
, vol.115
, pp. 9620-9630
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Kollman, P.A.4
-
41
-
-
84986513563
-
Representation of the molecular electrostatic potential by a net atomic charge model
-
Cox SR, Williams DE. Representation of the molecular electrostatic potential by a net atomic charge model. J Comput Chem 1982;2:304-323.
-
(1982)
J Comput Chem
, vol.2
, pp. 304-323
-
-
Cox, S.R.1
Williams, D.E.2
-
42
-
-
36549100412
-
A simple measure of electron localization in atomic and molecular systems
-
Becke AD, Edgecombe KE. A simple measure of electron localization in atomic and molecular systems. J Chem Phys 1990;92:5397-5403.
-
(1990)
J Chem Phys
, vol.92
, pp. 5397-5403
-
-
Becke, A.D.1
Edgecombe, K.E.2
-
43
-
-
0027946619
-
Classification of chemical bonds based on topological analysis of electron localization functions
-
Silvi B, Savin A. Classification of chemical bonds based on topological analysis of electron localization functions. Nature 1994;371:683-686.
-
(1994)
Nature
, vol.371
, pp. 683-686
-
-
Silvi, B.1
Savin, A.2
-
45
-
-
0023262075
-
Free energy perturbation calculations on binding and catalysis after mutating Asn-155 in subtilisin
-
Rao SN, Singh UC, Bash PA, Kollman PA. Free energy perturbation calculations on binding and catalysis after mutating Asn-155 in subtilisin. Nature 1987;328:551-554.
-
(1987)
Nature
, vol.328
, pp. 551-554
-
-
Rao, S.N.1
Singh, U.C.2
Bash, P.A.3
Kollman, P.A.4
-
47
-
-
0001650759
-
Theoretical correlation of structure and energetics in the catalytic reaction of trypsin
-
Warshel A, Russell S. Theoretical correlation of structure and energetics in the catalytic reaction of trypsin. J Am Chem Soc 1986;108:6569-6579.
-
(1986)
J Am Chem Soc
, vol.108
, pp. 6569-6579
-
-
Warshel, A.1
Russell, S.2
|