-
1
-
-
0000762204
-
Cumulant expansion of the free energy: Application to free energy derivatives and component analysis
-
Archontis G, Karplus M. 1996. Cumulant expansion of the free energy: Application to free energy derivatives and component analysis. J Chem Phys 105:11246-11260.
-
(1996)
J Chem Phys
, vol.105
, pp. 11246-11260
-
-
Archontis, G.1
Karplus, M.2
-
2
-
-
0032488817
-
Specific amino acid recognition by aspartyl-tRNA synthrtase studied by free energy simulations
-
Archontis G, Simonson T, Moras D, Karplus M. 1998. Specific amino acid recognition by aspartyl-tRNA synthrtase studied by free energy simulations. J Mol Biol 275:823-846.
-
(1998)
J Mol Biol
, vol.275
, pp. 823-846
-
-
Archontis, G.1
Simonson, T.2
Moras, D.3
Karplus, M.4
-
3
-
-
3943103200
-
Standard thermodynamics of transfer. Uses and misuses
-
Ben Naim A. 1973. Standard thermodynamics of transfer. Uses and misuses. J Phys Chem 82:792-803.
-
(1973)
J Phys Chem
, vol.82
, pp. 792-803
-
-
Ben Naim, A.1
-
4
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen H, Postma J, van Gunsteren W, DiNola A, Haak J. 1984. Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.1
Postma, J.2
Van Gunsteren, W.3
DiNola, A.4
Haak, J.5
-
5
-
-
0029879058
-
Quantitative structure-activity analysis correlating Ras/Raf interaction in vitro to Raf activation in vivo
-
Block C, Janknecht R, Herrmann C, Nassar N, Wittinghofer A. 1996. Quantitative structure-activity analysis correlating Ras/Raf interaction in vitro to Raf activation in vivo. Nat Struct Biol 3:244-251.
-
(1996)
Nat Struct Biol
, vol.3
, pp. 244-251
-
-
Block, C.1
Janknecht, R.2
Herrmann, C.3
Nassar, N.4
Wittinghofer, A.5
-
6
-
-
0027968902
-
Free energy simulations: The meaning of the individual contributions from a component analysis
-
Boresch S, Archontis G, Karplus M. 1994. Free energy simulations: The meaning of the individual contributions from a component analysis. Proteins 20:25-33.
-
(1994)
Proteins
, vol.20
, pp. 25-33
-
-
Boresch, S.1
Archontis, G.2
Karplus, M.3
-
7
-
-
0029584358
-
The meaning of component analysis: Decomposition of the free energy in terms of specific interactions
-
Boresch S, Karplus M. 1995. The meaning of component analysis: Decomposition of the free energy in terms of specific interactions. J Mol Biol 254:801-807.
-
(1995)
J Mol Biol
, vol.254
, pp. 801-807
-
-
Boresch, S.1
Karplus, M.2
-
8
-
-
0030601861
-
On the decomposition of free energies
-
Brady G, Szabo A, Sharp K. 1996. On the decomposition of free energies. J Mol Biol 263:123-125.
-
(1996)
J Mol Biol
, vol.263
, pp. 123-125
-
-
Brady, G.1
Szabo, A.2
Sharp, K.3
-
9
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and molecular dynamics calculations
-
Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, Karplus M. 1983. CHARMM: A program for macromolecular energy, minimization, and molecular dynamics calculations. J Comp Chem 4:187-217.
-
(1983)
J Comp Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Bruccoleri, R.2
Olafson, B.3
States, D.4
Swaminathan, S.5
Karplus, M.6
-
10
-
-
0022068152
-
Active site dynamics in proteins: A stochastic boundary molecular dynamics approach
-
Brooks C, Brünger AT, Karplus M. 1985. Active site dynamics in proteins: A stochastic boundary molecular dynamics approach. Biopolymers 24:843-865.
-
(1985)
Biopolymers
, vol.24
, pp. 843-865
-
-
Brooks, C.1
Brünger, A.T.2
Karplus, M.3
-
11
-
-
36749119973
-
Deformable stochastic boundaries in molecular dynamics
-
Brooks C, Karplus M. 1984. Deformable stochastic boundaries in molecular dynamics. J Chem Phys 79:6312-6325.
-
(1984)
J Chem Phys
, vol.79
, pp. 6312-6325
-
-
Brooks, C.1
Karplus, M.2
-
13
-
-
0345721058
-
Three-dimensional structure of an oncogene protein: The catalytic domain of c-H-Ras
-
deVos A, Tong L, Milburn M, Matias P, Jancarik J, Noguchi S, Nishimura S, Miura K, Ohtsuka E, Kim S. 1988. Three-dimensional structure of an oncogene protein: The catalytic domain of c-H-Ras. Science 247:939-945.
-
(1988)
Science
, vol.247
, pp. 939-945
-
-
DeVos, A.1
Tong, L.2
Milburn, M.3
Matias, P.4
Jancarik, J.5
Noguchi, S.6
Nishimura, S.7
Miura, K.8
Ohtsuka, E.9
Kim, S.10
-
14
-
-
0000307306
-
On the use of normal modes in thermal parameter refinement: Theory and application to the bovine pancreatic trypsin inhibitor
-
Diamond R. 1990. On the use of normal modes in thermal parameter refinement: Theory and application to the bovine pancreatic trypsin inhibitor. Acta Cryst A46:425-435.
-
(1990)
Acta Cryst
, vol.A46
, pp. 425-435
-
-
Diamond, R.1
-
15
-
-
0029041347
-
Solution structure of the Ras-binding domain of c-Raf-1 and identification of its Ras interaction sites
-
Emerson SD, Madison VS, Palermo RE, Waugh DS, Scheffler JE, Tsao KL, Kiefer ST, Liu SP, Fry DC. 1995. Solution structure of the Ras-binding domain of c-Raf-1 and identification of its Ras interaction sites. Biochemistry 30:6911-6918.
-
(1995)
Biochemistry
, vol.30
, pp. 6911-6918
-
-
Emerson, S.D.1
Madison, V.S.2
Palermo, R.E.3
Waugh, D.S.4
Scheffler, J.E.5
Tsao, K.L.6
Kiefer, S.T.7
Liu, S.P.8
Fry, D.C.9
-
16
-
-
0028341334
-
A single amino acid change in Raf-1 inhibits Ras binding and alters Raf-1 function
-
Fabian J, Vojtek A, Cooper J, Morrison D. 1994. A single amino acid change in Raf-1 inhibits Ras binding and alters Raf-1 function. Proc Natl Acad Sci USA 91:5982-5986.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 5982-5986
-
-
Fabian, J.1
Vojtek, A.2
Cooper, J.3
Morrison, D.4
-
17
-
-
0028019830
-
The minimal fragments of c-Raf-1 and NFI that can suppress v-Ha-Ras-induced malignant phenotype
-
Fridman M, Tikoo A, Varga M, Murphy A, Nur-El-Kamal M, Manila H. 1994. The minimal fragments of c-Raf-1 and NFI that can suppress v-Ha-Ras-induced malignant phenotype. J Biol Chem 269:30105-30108.
-
(1994)
J Biol Chem
, vol.269
, pp. 30105-30108
-
-
Fridman, M.1
Tikoo, A.2
Varga, M.3
Murphy, A.4
Nur-El-Kamal, M.5
Manila, H.6
-
18
-
-
0024365336
-
Hidden thermodynamics of mutant proteins: A molecular dynamics analysis
-
Gao J, Kuczera K, Tidor B, Karplus M. 1989. Hidden thermodynamics of mutant proteins: A molecular dynamics analysis. Science 244:1069-1072.
-
(1989)
Science
, vol.244
, pp. 1069-1072
-
-
Gao, J.1
Kuczera, K.2
Tidor, B.3
Karplus, M.4
-
19
-
-
0031228462
-
Structure of the Ras-binding domain of RalGEF and implications for Ras binding and signaling
-
Geyer M, Herrmann C, Wohlgemuth S, Wittinghofer A, Kalbitzer HR. 1997. Structure of the Ras-binding domain of RalGEF and implications for Ras binding and signaling. Nat Struct Biol 4:694-699.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 694-699
-
-
Geyer, M.1
Herrmann, C.2
Wohlgemuth, S.3
Wittinghofer, A.4
Kalbitzer, H.R.5
-
20
-
-
0000811664
-
Intrinsic GTPase activity distinguishes normal and oncogenic ras p21 molecules
-
Gibbs J, Sigal I, Poe M, Scolnic E. 1984. Intrinsic GTPase activity distinguishes normal and oncogenic ras p21 molecules. Proc Natl Acad Sci USA 81:5704-5708.
-
(1984)
Proc Natl Acad Sci USA
, vol.81
, pp. 5704-5708
-
-
Gibbs, J.1
Sigal, I.2
Poe, M.3
Scolnic, E.4
-
21
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: A critical review
-
Gilson M, Given J, Bush B, McCammon JA. 1997. The statistical-thermodynamic basis for computation of binding affinities: A critical review. Biophys J 72:1047-1069.
-
(1997)
Biophys J
, vol.72
, pp. 1047-1069
-
-
Gilson, M.1
Given, J.2
Bush, B.3
McCammon, J.A.4
-
23
-
-
84986468475
-
Precision of free energies calculated by molecular dynamics simulations of peptides in solution
-
Hermans J, Yun RH, Anderson AG. 1992. Precision of free energies calculated by molecular dynamics simulations of peptides in solution. J Comp Chem 13:429-442.
-
(1992)
J Comp Chem
, vol.13
, pp. 429-442
-
-
Hermans, J.1
Yun, R.H.2
Anderson, A.G.3
-
24
-
-
0023684064
-
A general method of in vitro preparation and specific mutagenesis of DNA fragments: Study of protein and DNA interactions
-
Higuchi R, Krummel B, Saiki R. 1988. A general method of in vitro preparation and specific mutagenesis of DNA fragments: Study of protein and DNA interactions. Nucl Acids Res 16:7351-7367.
-
(1988)
Nucl Acids Res
, vol.16
, pp. 7351-7367
-
-
Higuchi, R.1
Krummel, B.2
Saiki, R.3
-
25
-
-
0024520745
-
Site-directed mutagenesis by overlap extension using the polymerase chain reaction
-
Ho S, Hunt H, Horton R, Pullen J, Pease L. 1989. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51-59.
-
(1989)
Gene
, vol.77
, pp. 51-59
-
-
Ho, S.1
Hunt, H.2
Horton, R.3
Pullen, J.4
Pease, L.5
-
26
-
-
0028948495
-
Proline cis-trans isomerization in staphylococcal nuclease: Multi-substate free energy perturbation calculations
-
Hodel A, Rice L, Simonson T, Fox RO, Brünger AT. 1995. Proline cis-trans isomerization in staphylococcal nuclease: Multi-substate free energy perturbation calculations. Protein Sci 4:634-654.
-
(1995)
Protein Sci
, vol.4
, pp. 634-654
-
-
Hodel, A.1
Rice, L.2
Simonson, T.3
Fox, R.O.4
Brünger, A.T.5
-
27
-
-
0000441039
-
Conformational substates and uncertainty in macromolecular free energy calculations
-
Hodel A, Simonson T, Fox RO, Brünger AT. 1993. Conformational substates and uncertainty in macromolecular free energy calculations. J Phys Chem 97:3409-3417.
-
(1993)
J Phys Chem
, vol.97
, pp. 3409-3417
-
-
Hodel, A.1
Simonson, T.2
Fox, R.O.3
Brünger, A.T.4
-
28
-
-
84944815380
-
Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model
-
Howlin B, Moss D, Harris G. 1990. Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model. Acta Cryst A45:851-861.
-
(1990)
Acta Cryst
, vol.A45
, pp. 851-861
-
-
Howlin, B.1
Moss, D.2
Harris, G.3
-
29
-
-
0030863611
-
Three-dimensional structure of the Ras-interacting domain of RalGDS
-
Huang L, Weng X, Hofer F, Martin GS, Kim S. 1997. Three-dimensional structure of the Ras-interacting domain of RalGDS. Nat Struct Biol 4:609-615.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 609-615
-
-
Huang, L.1
Weng, X.2
Hofer, F.3
Martin, G.S.4
Kim, S.5
-
30
-
-
0029421048
-
Protein-protein recognition
-
Janin J. 1995. Protein-protein recognition. Prog Boiphy Mol Biol 64:145-166.
-
(1995)
Prog Boiphy Mol Biol
, vol.64
, pp. 145-166
-
-
Janin, J.1
-
31
-
-
0024246956
-
Surface, subunit interfaces and interior of oligomeric proteins
-
Janin J, Miller S, Chothia C 1988. Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol 204:155-164.
-
(1988)
J Mol Biol
, vol.204
, pp. 155-164
-
-
Janin, J.1
Miller, S.2
Chothia, C.3
-
32
-
-
0029109468
-
Protein-protein interactions: A review of protein dimer structures
-
Jones S, Thornton J. 1995. Protein-protein interactions: A review of protein dimer structures. Prog Biophys Mol Biol 63:31-65.
-
(1995)
Prog Biophys Mol Biol
, vol.63
, pp. 31-65
-
-
Jones, S.1
Thornton, J.2
-
33
-
-
33645941402
-
The OPLS potential function for proteins, energy minimization for crystals of cyclic peptides and crambin
-
Jorgensen W, Tirado-Rives J. 1988. The OPLS potential function for proteins, energy minimization for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657-1666.
-
(1988)
J Am Chem Soc
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.1
Tirado-Rives, J.2
-
34
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekar J, Madura J, Impey R, Klein M. 1983. Comparison 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
Chandrasekar, J.2
Madura, J.3
Impey, R.4
Klein, M.5
-
35
-
-
0028204451
-
Solution structure and dynamics of ras p21:GDP determined by heteronuclear three-and four-dimensional NMR spectroscopy
-
Kraulis P, Domaille P, Campbell-Burk S, van Aken T, Lane E. 1994. Solution structure and dynamics of ras p21:GDP determined by heteronuclear three-and four-dimensional NMR spectroscopy. Biochemistry 33:3515-3531.
-
(1994)
Biochemistry
, vol.33
, pp. 3515-3531
-
-
Kraulis, P.1
Domaille, P.2
Campbell-Burk, S.3
Van Aken, T.4
Lane, E.5
-
36
-
-
0028354926
-
Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant
-
Lau F, Karplus M. 1994. Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant. J Mol Biol 87:1049-1066.
-
(1994)
J Mol Biol
, vol.87
, pp. 1049-1066
-
-
Lau, F.1
Karplus, M.2
-
37
-
-
0041784950
-
An all-atom empirical potential for molecular modelling and dynamics study of proteins
-
Mackerell A, Bashford D, Bellott M, Dunbrack R, Evanseck J, Field M, Fischer S, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau F, Mattos C, Michnick S, Ngo T, Nguyen D, Prodhom B, Reiher W, Roux B, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. 1998. An all-atom empirical potential for molecular modelling and dynamics study of proteins. J Phys Chem B 102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.4
Evanseck, J.5
Field, M.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.18
Prodhom, B.19
Reiher, W.20
Roux, B.21
Smith, J.22
Stote, R.23
Straub, J.24
Watanabe, M.25
Wiorkiewicz-Kuczera, J.26
Yin, D.27
Karplus, M.28
more..
-
38
-
-
6344260593
-
An all-atom empirical energy force-field for the study of nucleic acids
-
Mackerell A, Wiorkiewicz-Kuczera J, Karplus M. 1995. An all-atom empirical energy force-field for the study of nucleic acids. J Am Chem Soc 117:11946-11975.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 11946-11975
-
-
Mackerell, A.1
Wiorkiewicz-Kuczera, J.2
Karplus, M.3
-
39
-
-
0028334097
-
Decomposition of the free energy of a system in terms of specific interactions
-
Mark AE, Gunsteren WFV. 1994. Decomposition of the free energy of a system in terms of specific interactions. J Mol Biol 240:167-176.
-
(1994)
J Mol Biol
, vol.240
, pp. 167-176
-
-
Mark, A.E.1
Gunsteren, W.F.V.2
-
40
-
-
0026017886
-
The residues of Ras and Rap proteins that determine their GAP specificities
-
Maruta H, Holden J, Sizeland A, D'Abaco G. 1991. The residues of Ras and Rap proteins that determine their GAP specificities. J Biol Chem 266:11661-11668.
-
(1991)
J Biol Chem
, vol.266
, pp. 11661-11668
-
-
Maruta, H.1
Holden, J.2
Sizeland, A.3
D'Abaco, G.4
-
41
-
-
0030221148
-
Interactions between Ras proteins and their effectors
-
McCormick F, Willinghofer A. 1996. Interactions between Ras proteins and their effectors. Curr Opin Biotech 7:449-456.
-
(1996)
Curr Opin Biotech
, vol.7
, pp. 449-456
-
-
McCormick, F.1
Willinghofer, A.2
-
43
-
-
0027321958
-
Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches
-
Miyamoto S, Kollman PA. 1993. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins 16:226-245.
-
(1993)
Proteins
, vol.16
, pp. 226-245
-
-
Miyamoto, S.1
Kollman, P.A.2
-
44
-
-
0027337519
-
Complexes of Ras-GTP with Raf-1 and mitogen-activated protein kinase kinase
-
Moodie SA, Willumsen BM, Weber MJ, Wolfman A. 1993. Complexes of Ras-GTP with Raf-1 and mitogen-activated protein kinase kinase. Science 260:1658-1661.
-
(1993)
Science
, vol.260
, pp. 1658-1661
-
-
Moodie, S.A.1
Willumsen, B.M.2
Weber, M.J.3
Wolfman, A.4
-
45
-
-
0029745645
-
Ras/Rap effector specificity determined by charge reversal
-
Nassar N, Horn G, Herrmann C, Block C, Janknecht R, Wittinghofer A. 1996. Ras/Rap effector specificity determined by charge reversal. Nat Struct Biol 3:723-729.
-
(1996)
Nat Struct Biol
, vol.3
, pp. 723-729
-
-
Nassar, N.1
Horn, G.2
Herrmann, C.3
Block, C.4
Janknecht, R.5
Wittinghofer, A.6
-
46
-
-
0029107760
-
The 2.2 Å crystal structure of the Ras-binding domain of the serine/ threonine kinase c-Raf-1 in complex with Rap1A and a GTP analogue
-
Nassar N, Horn G, Herrmann C, Scherer A, McCormick F, Wittinghofer, A. 1995. The 2.2 Å crystal structure of the Ras-binding domain of the serine/ threonine kinase c-Raf-1 in complex with Rap1A and a GTP analogue. Nature 375:554-560.
-
(1995)
Nature
, vol.375
, pp. 554-560
-
-
Nassar, N.1
Horn, G.2
Herrmann, C.3
Scherer, A.4
McCormick, F.5
Wittinghofer, A.6
-
47
-
-
0000036869
-
Simulation of activation free energies in molecular systems
-
Neria E, Fischer S, Karplus M. 1996. Simulation of activation free energies in molecular systems. J Chem Phys 105:1902-1921.
-
(1996)
J Chem Phys
, vol.105
, pp. 1902-1921
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
48
-
-
0031167555
-
Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations
-
Nina M, Beglov D, Roux B. 1997. Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations. J Phys Chem 101:5239-5248.
-
(1997)
J Phys Chem
, vol.101
, pp. 5239-5248
-
-
Nina, M.1
Beglov, D.2
Roux, B.3
-
49
-
-
0024463212
-
Structure of the guanine-nucleotide-binding domain of the Ha-Ras oncogene product p21 in the triphosphate conformation
-
Pai E, Kabsch W, Krengel U, Holmes K, John J, Wittinghofer A. 1989. Structure of the guanine-nucleotide-binding domain of the Ha-Ras oncogene product p21 in the triphosphate conformation. Nature 341:209-214.
-
(1989)
Nature
, vol.341
, pp. 209-214
-
-
Pai, E.1
Kabsch, W.2
Krengel, U.3
Holmes, K.4
John, J.5
Wittinghofer, A.6
-
50
-
-
0028867856
-
Free energy simulations of the HyHEL-10/HEL antibody-antigen complex
-
Pomes R, Wilson R, McCammon JA. 1995. Free energy simulations of the HyHEL-10/HEL antibody-antigen complex. Protein Eng 8:663-675.
-
(1995)
Protein Eng
, vol.8
, pp. 663-675
-
-
Pomes, R.1
Wilson, R.2
McCammon, J.A.3
-
51
-
-
0000656021
-
Studies on free energy calculations. II. A theoretical approach to molecular solvation
-
Resat H, Mezei M. 1994. Studies on free energy calculations. II. A theoretical approach to molecular solvation. J Chem Phys 222:6126-6140.
-
(1994)
J Chem Phys
, vol.222
, pp. 6126-6140
-
-
Resat, H.1
Mezei, M.2
-
52
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion for a system with constraints
-
Ryckaert J, Ciccotti G, Berendsen H. 1977. Numerical integration of the Cartesian equations of motion for a system with constraints. J Comput Phys 23:327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.1
Ciccotti, G.2
Berendsen, H.3
-
53
-
-
0028206113
-
Mutations that abolish the ability of Ha-Ras to associate with Raf-1
-
Shirouzu M, Koide H, Fuita-Yoshigaki J, Oshio H, Toyama Y, Yamasaki K, Fuhrman SA, Villafranca E, Kaziro Y, Yokovama S. 1994. Mutations that abolish the ability of Ha-Ras to associate with Raf-1. Oncogene 9:2153-2157.
-
(1994)
Oncogene
, vol.9
, pp. 2153-2157
-
-
Shirouzu, M.1
Koide, H.2
Fuita-Yoshigaki, J.3
Oshio, H.4
Toyama, Y.5
Yamasaki, K.6
Fuhrman, S.A.7
Villafranca, E.8
Kaziro, Y.9
Yokovama, S.10
-
54
-
-
84872607890
-
Free energy of particle insertion. An exact analysis of the origin singularity for simple liquids
-
Simonson T. 1993. Free energy of particle insertion. An exact analysis of the origin singularity for simple liquids. Mol Phys 80:441-447.
-
(1993)
Mol Phys
, vol.80
, pp. 441-447
-
-
Simonson, T.1
-
55
-
-
0026641163
-
Thermodynamics of protein-peptide binding in the ribonuclease S system studied by molecular dynamics and free energy calculations
-
Simonson T, Brünger AT. 1992. Thermodynamics of protein-peptide binding in the ribonuclease S system studied by molecular dynamics and free energy calculations. Biochemistry 31:8661-8674.
-
(1992)
Biochemistry
, vol.31
, pp. 8661-8674
-
-
Simonson, T.1
Brünger, A.T.2
-
56
-
-
0018800867
-
Dynamic information from protein crystallography
-
Sternberg M, Grace D, Phillips D. 1979. Dynamic information from protein crystallography. J Mol Biol 130:231-253.
-
(1979)
J Mol Biol
, vol.130
, pp. 231-253
-
-
Sternberg, M.1
Grace, D.2
Phillips, D.3
-
57
-
-
0029929557
-
Free energy calculations of the mutation of Ile96 → Ala in barnase: Contributions to the difference in stability
-
Sun Y, Veenstra D, Kollman P. 1996. Free energy calculations of the mutation of Ile96 → Ala in barnase: Contributions to the difference in stability. Prot Eng 9:273-281.
-
(1996)
Prot Eng
, vol.9
, pp. 273-281
-
-
Sun, Y.1
Veenstra, D.2
Kollman, P.3
-
60
-
-
0027250250
-
Mammalian Ras interacts directly with the serine/threonine kinase Raf
-
Vojtek AB, Hollenberg SM, Cooper JA. 1993. Mammalian Ras interacts directly with the serine/threonine kinase Raf. Cell 74:205-214.
-
(1993)
Cell
, vol.74
, pp. 205-214
-
-
Vojtek, A.B.1
Hollenberg, S.M.2
Cooper, J.A.3
-
61
-
-
0026696688
-
Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side chain conformations
-
Wade R, McCammon JA. 1992. Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side chain conformations. J Mol Biol 225:679-712.
-
(1992)
J Mol Biol
, vol.225
, pp. 679-712
-
-
Wade, R.1
McCammon, J.A.2
-
62
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner S, Kollman P, Case D, Singh U, Ghio C, Alagona G, Profeta S, Weiner P. 1984. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 106:765-784.
-
(1984)
J Am Chem Soc
, vol.106
, pp. 765-784
-
-
Weiner, S.1
Kollman, P.2
Case, D.3
Singh, U.4
Ghio, C.5
Alagona, G.6
Profeta, S.7
Weiner, P.8
-
63
-
-
0032080535
-
The conformation of the Ras-binding domain of Raf studied by molecular dynamics and free energy simulations
-
Zeng J, Treutlein HR, Simonson T. 1998. The conformation of the Ras-binding domain of Raf studied by molecular dynamics and free energy simulations. Proteins 31:186-200.
-
(1998)
Proteins
, vol.31
, pp. 186-200
-
-
Zeng, J.1
Treutlein, H.R.2
Simonson, T.3
-
64
-
-
0033120983
-
Molecular dynamics simulations of the Ras:Raf and Ras:Rap complexes
-
In press
-
Zeng J, Treutlein HR, Simonson T. 1999. Molecular dynamics simulations of the Ras:Raf and Ras:Rap complexes. Proteins. In press.
-
(1999)
Proteins
-
-
Zeng, J.1
Treutlein, H.R.2
Simonson, T.3
-
65
-
-
0027337248
-
Ras proteins bind to the amino-terminal regulatory domain of c-Raf-1
-
Ras proteins bind to the amino-terminal regulatory domain of c-Raf-1. Nature 364:308-313.
-
(1993)
Nature
, vol.364
, pp. 308-313
-
-
Zhang, X.F.1
Settleman, J.2
Kyriakis, J.M.3
Takeuchi-Suzuki, E.4
Elledge, S.J.5
Marshall, M.S.6
Bruder, J.T.7
Rapp, U.R.8
Avruch, J.9
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