-
1
-
-
0035107931
-
Solvation energetics and conformational change in EF-hand proteins
-
Ababou, A. and Desjarlais, J.R. 2001. Solvation energetics and conformational change in EF-hand proteins. Protein Sci. 10: 301-312.
-
(2001)
Protein Sci.
, vol.10
, pp. 301-312
-
-
Ababou, A.1
Desjarlais, J.R.2
-
2
-
-
0028305457
-
Prediction of pH-dependent properties of proteins
-
Antosiewicz, J., McCammon, J.A., and Gilson, M.K. 1994. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238: 415-436.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 415-436
-
-
Antosiewicz, J.1
McCammon, J.A.2
Gilson, M.K.3
-
3
-
-
0029665693
-
The determinants of pKas in proteins
-
-. 1996. The determinants of pKas in proteins. Biochemistry 35: 7819-7833.
-
(1996)
Biochemistry
, vol.35
, pp. 7819-7833
-
-
-
4
-
-
0025197061
-
pKas of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
-
Bashford, D. and Karplus, M. 1990. pKas of ionizable groups in proteins: Atomic detail from a continuum electrostatic model. Biochemistry 29: 10219-10225.
-
(1990)
Biochemistry
, vol.29
, pp. 10219-10225
-
-
Bashford, D.1
Karplus, M.2
-
5
-
-
0027485997
-
Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala → Ser and Val → Thr substitutions in T4 lysozyme
-
Blaber, M., Lindstrom, J.D., Gassner, N., Xu, J., Heinz, D.W., and Matthews, B.W. 1993. Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala → Ser and Val → Thr substitutions in T4 lysozyme. Biochemistry 32: 11363-11373.
-
(1993)
Biochemistry
, vol.32
, pp. 11363-11373
-
-
Blaber, M.1
Lindstrom, J.D.2
Gassner, N.3
Xu, J.4
Heinz, D.W.5
Matthews, B.W.6
-
6
-
-
0035964177
-
Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity
-
Bolon, D.N. and Mayo, S.L. 2001. Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity. Biochemistry 40: 10047-10053.
-
(2001)
Biochemistry
, vol.40
, pp. 10047-10053
-
-
Bolon, D.N.1
Mayo, S.L.2
-
7
-
-
0031891022
-
Computation of electrostatic complements to proteins: A case of charge stabilized binding
-
Chong, L.T., Dempster, S.E., Hendsch, Z.S., Lee, L.P., and Tidor, B. 1998. Computation of electrostatic complements to proteins: A case of charge stabilized binding. Protein Sci. 7: 206-210.
-
(1998)
Protein Sci.
, vol.7
, pp. 206-210
-
-
Chong, L.T.1
Dempster, S.E.2
Hendsch, Z.S.3
Lee, L.P.4
Tidor, B.5
-
8
-
-
0016606973
-
Structural invariants in protein folding
-
Chothia, C. 1975. Structural invariants in protein folding. Nature 254: 304-308.
-
(1975)
Nature
, vol.254
, pp. 304-308
-
-
Chothia, C.1
-
9
-
-
0030793767
-
De novo protein design: Fully automated sequence selection
-
Dahiyat, B.I. and Mayo, S.L. 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
-
10
-
-
0041387567
-
A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins
-
Dantas, G., Kuhlman, B., Callender, D., Wong, M., and Baker, D. 2003. A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins. J. Mol. Biol. 332: 449-460.
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 449-460
-
-
Dantas, G.1
Kuhlman, B.2
Callender, D.3
Wong, M.4
Baker, D.5
-
12
-
-
0042139644
-
Comparison of generalized Born and Poisson models: Energetics and dynamics of HIV protease
-
David, L., Luo, R., and Gilson, M.K. 2000. Comparison of generalized Born and Poisson models: Energetics and dynamics of HIV protease. J. Comp. Chem. 21: 295-309.
-
(2000)
J. Comp. Chem.
, vol.21
, pp. 295-309
-
-
David, L.1
Luo, R.2
Gilson, M.K.3
-
13
-
-
0028858499
-
De novo design of the hydrophobic cores of proteins
-
Desjarlais, J.R. and Handel, T.M. 1995. De novo design of the hydrophobic cores of proteins. Protein Sci. 4: 2006-2018.
-
(1995)
Protein Sci.
, vol.4
, pp. 2006-2018
-
-
Desjarlais, J.R.1
Handel, T.M.2
-
14
-
-
84961985307
-
Development of a generalized Born model parametrization for proteins and nucleic acids
-
Dominy, B. and Brooks, C. 1999. Development of a generalized Born model parametrization for proteins and nucleic acids, J. Phys. Chem. B 103: 3765-3773.
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 3765-3773
-
-
Dominy, B.1
Brooks, C.2
-
15
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack Jr., R.L. and Cohen, F.E. 1997. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6: 1661-1681.
-
(1997)
Protein Sci.
, vol.6
, pp. 1661-1681
-
-
Dunbrack Jr., R.L.1
Cohen, F.E.2
-
16
-
-
0031075977
-
Solvation free energies of peptides: Comparison of approximate continuum solvation models with accurate solution of the Poisson-Boltzmann equation
-
Edinger, S., Cortis, C., Shenkin, P., and Friesner, R. 1997. Solvation free energies of peptides: Comparison of approximate continuum solvation models with accurate solution of the Poisson-Boltzmann equation. J. Phys. Chem. B 101: 1190-1197.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 1190-1197
-
-
Edinger, S.1
Cortis, C.2
Shenkin, P.3
Friesner, R.4
-
17
-
-
0022596727
-
Solvation energy in protein folding and binding
-
Eisenberg, D. and McLachlan, A.D. 1986. Solvation energy in protein folding and binding. Nature 319: 199-203.
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
18
-
-
0035965145
-
Prediction of functionally important residues based solely on the computed energetics of protein structure
-
Elcock, A.H. 2001. Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol. 312: 885-896.
-
(2001)
J. Mol. Biol.
, vol.312
, pp. 885-896
-
-
Elcock, A.H.1
-
19
-
-
0036681394
-
Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized Born solvent model
-
Felts, A.K., Gallicchio, E., Wallqvist, A., and Levy, R.M. 2002. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized Born solvent model. Proteins 48: 404-422.
-
(2002)
Proteins
, vol.48
, pp. 404-422
-
-
Felts, A.K.1
Gallicchio, E.2
Wallqvist, A.3
Levy, R.M.4
-
20
-
-
0024412171
-
Can a simple function for the dielectric response model electrostatic effects in globular proteins?
-
Fersht, A.R. and Sternberg, M.J. 1989. Can a simple function for the dielectric response model electrostatic effects in globular proteins? Protein Eng. 2: 527-530.
-
(1989)
Protein Eng.
, vol.2
, pp. 527-530
-
-
Fersht, A.R.1
Sternberg, M.J.2
-
21
-
-
0036681440
-
Empirical relationships between protein structure and carboxyl pKa values in proteins
-
Forsyth, W.R., Antosiewicz, J.M., and Robertson, A.D. 2002. Empirical relationships between protein structure and carboxyl pKa values in proteins. Proteins 48: 388-403.
-
(2002)
Proteins
, vol.48
, pp. 388-403
-
-
Forsyth, W.R.1
Antosiewicz, J.M.2
Robertson, A.D.3
-
22
-
-
84988087911
-
Calculating the electrostatic potential of molecules in solution: Method and error assessment
-
Gilson, M.K., Sharp, K.A., and Honig, B. 1988. Calculating the electrostatic potential of molecules in solution: Method and error assessment. J. Comp. Chem. 9: 327-335.
-
(1988)
J. Comp. Chem.
, vol.9
, pp. 327-335
-
-
Gilson, M.K.1
Sharp, K.A.2
Honig, B.3
-
23
-
-
16944363590
-
Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism
-
Gonzalez, L., Brown, R.A., Richardson, D., and Alber, T. 1996a. Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism. Nat. Struct. Biol. 3: 1002-1009.
-
(1996)
Nat. Struct. Biol.
, vol.3
, pp. 1002-1009
-
-
Gonzalez, L.1
Brown, R.A.2
Richardson, D.3
Alber, T.4
-
24
-
-
16944366990
-
Buried polar residues and structural specificity in the GCN4 leucine zipper
-
Gonzalez, L., Woolfson, D.N., and Alber, T. 1996b. Buried polar residues and structural specificity in the GCN4 leucine zipper. Nat. Struct. Biol. 3: 1011-1018.
-
(1996)
Nat. Struct. Biol.
, vol.3
, pp. 1011-1018
-
-
Gonzalez, L.1
Woolfson, D.N.2
Alber, T.3
-
25
-
-
0141453063
-
Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii approximation
-
Grycuk, T. 2003. Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii approximation. J. Chem. Phys. 119: 4817-4826.
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 4817-4826
-
-
Grycuk, T.1
-
26
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois, R., Nielsen, J.E., and Serrano, L. 2002. Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. J. Mol. Biol. 320: 369-387.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
27
-
-
0033613164
-
Tanford-Kirkwood electrostatics for protein modeling
-
Havranek, J.J. and Harbury, P.B. 1999. Tanford-Kirkwood electrostatics for protein modeling. Proc. Natl. Acad. Sci. 96: 11145-11150.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 11145-11150
-
-
Havranek, J.J.1
Harbury, P.B.2
-
28
-
-
0037217406
-
Automated design of specificity in molecular recognition
-
-. 2003. Automated design of specificity in molecular recognition. Nat. Struct. Biol. 10: 45-52.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 45-52
-
-
-
29
-
-
0002636134
-
Pairwise solute descreening of solute charges from a dielectric medium
-
Hawkins, G., Cramer, C., and Truhlar, D. 1995. Pairwise solute descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 246: 122-129.
-
(1995)
Chem. Phys. Lett.
, vol.246
, pp. 122-129
-
-
Hawkins, G.1
Cramer, C.2
Truhlar, D.3
-
30
-
-
0028204490
-
Do salt bridges stabilize proteins? A continuum electrostatic analysis
-
Hendsch, Z.S. and Tidor, B. 1994. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 3: 211-226.
-
(1994)
Protein Sci.
, vol.3
, pp. 211-226
-
-
Hendsch, Z.S.1
Tidor, B.2
-
31
-
-
4243067681
-
Protein stabilization by removal of unsatisfied polar groups: Computational approaches and experimental tests
-
Hendsch, Z.S., Jonsson, T., Sauer, R.T., and Tidor, B. 1996. Protein stabilization by removal of unsatisfied polar groups: Computational approaches and experimental tests. Biochemistry 35: 7621-7625.
-
(1996)
Biochemistry
, vol.35
, pp. 7621-7625
-
-
Hendsch, Z.S.1
Jonsson, T.2
Sauer, R.T.3
Tidor, B.4
-
32
-
-
33751385054
-
Macroscopic models of aqueous solutions-Biological and chemical applications
-
Honig, B., Sharp, K., and Yang, A. 1993. Macroscopic models of aqueous solutions-Biological and chemical applications. J. Phys. Chem. 97: 1101-1109.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 1101-1109
-
-
Honig, B.1
Sharp, K.2
Yang, A.3
-
33
-
-
0037108748
-
Folding free energy function selects native-like protein sequences in the core but not on the surface
-
Jaramillo, A., Wernisch, L., Hery, S., and Wodak, S.J. 2002. Folding free energy function selects native-like protein sequences in the core but not on the surface. Proc. Natl. Acad. Sci. 99: 13554-13559.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 13554-13559
-
-
Jaramillo, A.1
Wernisch, L.2
Hery, S.3
Wodak, S.J.4
-
34
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen, W.L., Maxwell, D.S., and Tirado-Rives, J. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118: 11225-11236.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
35
-
-
0028343413
-
Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
-
Koehl, P. and Delarue, M. 1994. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 239: 249-275.
-
(1994)
J. Mol. Biol.
, vol.239
, pp. 249-275
-
-
Koehl, P.1
Delarue, M.2
-
36
-
-
0033550206
-
De novo protein design. I. In search of stability and specificity
-
Koehl, P. and Levitt, M. 1999. De novo protein design. I. In search of stability and specificity. J. Mol. Biol. 293: 1161-1181.
-
(1999)
J. Mol. Biol.
, vol.293
, pp. 1161-1181
-
-
Koehl, P.1
Levitt, M.2
-
37
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
Kuhlman, B. and Baker, D. 2000. Native protein sequences are close to optimal for their structures. Proc. Natl. Acad. Sci. 97: 10383-10388.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
-
38
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis, T. and Karplus, M. 1999. Effective energy function for proteins in solution. Proteins 35: 133-152.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
39
-
-
84912079256
-
Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables
-
LeGrand, S.M. and Merz, K. 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
-
-
LeGrand, S.M.1
Merz, K.2
-
40
-
-
0026766573
-
Structural and energetic consequences of disruptive mutations in a protein core
-
Lim, W.A., Farruggio, D.C., and Sauer, R.T. 1992. Structural and energetic consequences of disruptive mutations in a protein core. Biochemistry 31: 4324-4333.
-
(1992)
Biochemistry
, vol.31
, pp. 4324-4333
-
-
Lim, W.A.1
Farruggio, D.C.2
Sauer, R.T.3
-
41
-
-
0033554840
-
Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface
-
Loladze, V.V., Ibarra-Molero, B., Sanchez-Ruiz, J.M., and Makhatadze, G.I. 1999. Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface. Biochemistry 38: 16419-16423.
-
(1999)
Biochemistry
, vol.38
, pp. 16419-16423
-
-
Loladze, V.V.1
Ibarra-Molero, B.2
Sanchez-Ruiz, J.M.3
Makhatadze, G.I.4
-
42
-
-
0038752617
-
Computational design of receptor and sensor proteins with novel functions
-
Looger, L.L., Dwyer, M.A., Smith, J.J., and Hellinga, H.W. 2003. Computational design of receptor and sensor proteins with novel functions. Nature 423: 185-190.
-
(2003)
Nature
, vol.423
, pp. 185-190
-
-
Looger, L.L.1
Dwyer, M.A.2
Smith, J.J.3
Hellinga, H.W.4
-
43
-
-
0029008590
-
A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil
-
Lumb, K.J. and Kim, P.S. 1995. A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil. Biochemistry 34: 8642-8648.
-
(1995)
Biochemistry
, vol.34
, pp. 8642-8648
-
-
Lumb, K.J.1
Kim, P.S.2
-
44
-
-
0031779918
-
Design, structure and stability of a hyperthermophilic protein variant
-
Malakauskas, S.M. and Mayo, S.L. 1998. Design, structure and stability of a hyperthermophilic protein variant. Nat. Struct. Biol. 5: 470-475.
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 470-475
-
-
Malakauskas, S.M.1
Mayo, S.L.2
-
45
-
-
0036679837
-
Distance and exposure dependent effective dielectric function
-
Mallik, B., Masunov, A., and Lazaridis, T. 2002. Distance and exposure dependent effective dielectric function. J. Comput. Chem. 23: 1090-1099.
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1090-1099
-
-
Mallik, B.1
Masunov, A.2
Lazaridis, T.3
-
46
-
-
0035910266
-
Achieving stability and conformational specificity in designed proteins via binary patterning
-
Marshall, S.A. and Mayo, S.L. 2001. Achieving stability and conformational specificity in designed proteins via binary patterning. J. Mol. Biol. 305: 619-631.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 619-631
-
-
Marshall, S.A.1
Mayo, S.L.2
-
47
-
-
0036307678
-
Electrostatics significantly affect the stability of designed homeodomain variants
-
Marshall, S.A., Morgan, C.S., and Mayo, S.L. 2002. Electrostatics significantly affect the stability of designed homeodomain variants. J. Mol. Biol. 316: 189-199.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 189-199
-
-
Marshall, S.A.1
Morgan, C.S.2
Mayo, S.L.3
-
48
-
-
0000703443
-
Self-consistent, free energy based approximation to calculate pH dependent electrostatic effects in proteins
-
Mehler, E. 1996. Self-consistent, free energy based approximation to calculate pH dependent electrostatic effects in proteins. J. Phys. Chem. 100: 16006-16018.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 16006-16018
-
-
Mehler, E.1
-
49
-
-
0036667732
-
Energy estimation in protein design
-
Mendes, J., Guerois, R., and Serrano, L. 2002. Energy estimation in protein design. Curr. Opin. Struct. Biol. 12: 441-446.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 441-446
-
-
Mendes, J.1
Guerois, R.2
Serrano, L.3
-
50
-
-
0037422359
-
Evaluation of models of electrostatic interactions in proteins
-
Morozov, A.V., Kortemme, T., and Baker, D. 2003. Evaluation of models of electrostatic interactions in proteins. J. Phys. Chem. B 107: 2075-2090.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 2075-2090
-
-
Morozov, A.V.1
Kortemme, T.2
Baker, D.3
-
51
-
-
0034964196
-
Computer-based redesign of a protein folding pathway
-
Nauli, S., Kuhlman, B., and Baker, D. 2001. Computer-based redesign of a protein folding pathway. Nat. Struct. Biol. 8: 602-605.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 602-605
-
-
Nauli, S.1
Kuhlman, B.2
Baker, D.3
-
52
-
-
0029155380
-
A designed heterotrimeric coiled coil
-
Nautiyal, S., Woolfson, D.N., King, D.S., and Alber, T. 1995. A designed heterotrimeric coiled coil. Biochemistry 34: 11645-11651.
-
(1995)
Biochemistry
, vol.34
, pp. 11645-11651
-
-
Nautiyal, S.1
Woolfson, D.N.2
King, D.S.3
Alber, T.4
-
53
-
-
84986486656
-
A rapid finite difference algorithm, utilizing successive over-relaxation to solve Poisson-Boltzmann equations
-
Nicholls, A. and Honig, B. 1991. A rapid finite difference algorithm, utilizing successive over-relaxation to solve Poisson-Boltzmann equations. J. Comp. Chem. 12: 435.
-
(1991)
J. Comp. Chem.
, vol.12
, pp. 435
-
-
Nicholls, A.1
Honig, B.2
-
54
-
-
0035853162
-
Altering dimerization specificity by changes in surface electrostatics
-
Nohaile, M.J., Hendsch, Z.S., Tidor, B., and Sauer, R.T. 2001. Altering dimerization specificity by changes in surface electrostatics. Proc. Natl. Acad. Sci. 98: 3109-3114.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 3109-3114
-
-
Nohaile, M.J.1
Hendsch, Z.S.2
Tidor, B.3
Sauer, R.T.4
-
55
-
-
0032497322
-
A buried polar interaction can direct the relative orientation of helices in a coiled coil
-
Oakley, M.G. and Kim, P.S. 1998. A buried polar interaction can direct the relative orientation of helices in a coiled coil. Biochemistry 37: 12603-12610.
-
(1998)
Biochemistry
, vol.37
, pp. 12603-12610
-
-
Oakley, M.G.1
Kim, P.S.2
-
56
-
-
0035940421
-
THEMATICS: A simple computational predictor of enzyme function from structure
-
Ondrechen, M.J., Clifton, J.G., and Ringe, D. 2001. THEMATICS: A simple computational predictor of enzyme function from structure. Proc. Natl. Acad. Sci. 98: 12473-12478.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 12473-12478
-
-
Ondrechen, M.J.1
Clifton, J.G.2
Ringe, D.3
-
57
-
-
20644449471
-
Modification of the generalized Born model suitable for macromolecules
-
Onufriev, A., Bashford, D., and Case, D. 2000. Modification of the generalized Born model suitable for macromolecules. J. Phys. Chem. B 104: 3712-3720.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 3712-3720
-
-
Onufriev, A.1
Bashford, D.2
Case, D.3
-
58
-
-
0037110472
-
Effective Born radii in the generalized Born approximation: The importance of being perfect
-
Onufriev, A., Case, D.A., and Bashford, D. 2002. Effective Born radii in the generalized Born approximation: The importance of being perfect. J. Comput. Chem. 23: 1297-1304.
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1297-1304
-
-
Onufriev, A.1
Case, D.A.2
Bashford, D.3
-
59
-
-
0026571898
-
Mechanism of specificity in the Fos-Jun oncoprotein heterodimer
-
O'Shea, E.K., Rutkowski, R., and Kim, P.S. 1992. Mechanism of specificity in the Fos-Jun oncoprotein heterodimer. Cell 68: 699-708.
-
(1992)
Cell
, vol.68
, pp. 699-708
-
-
O'Shea, E.K.1
Rutkowski, R.2
Kim, P.S.3
-
60
-
-
0000236570
-
Peptide velcro: Design of a heterodimeric coiled-coil
-
O'Shea, E.K., Lumb, K.J., and Kim, P.S. 1993. Peptide velcro: Design of a heterodimeric coiled-coil. Curr. Biol. 3: 658-667.
-
(1993)
Curr. Biol.
, vol.3
, pp. 658-667
-
-
O'Shea, E.K.1
Lumb, K.J.2
Kim, P.S.3
-
61
-
-
0035782661
-
Review: Protein design - Where we were, where we are, where we're going
-
Pokala, N. and Handel, T.M. 2001. Review: Protein design - Where we were, where we are, where we're going. J. Struct. Biol. 134: 269-281.
-
(2001)
J. Struct. Biol.
, vol.134
, pp. 269-281
-
-
Pokala, N.1
Handel, T.M.2
-
62
-
-
0023155210
-
Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
Ponder, J.W. and Richards, F.M. 1987. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193: 775-791.
-
(1987)
J. Mol. Biol.
, vol.193
, pp. 775-791
-
-
Ponder, J.W.1
Richards, F.M.2
-
63
-
-
0004161838
-
-
Cambridge University Press, Cambridge, UK
-
Press, W.H., Teukolsky, S.A., Vetterling, W.T., and Flannery, B.P. 1999. Numerical recipes in C: The art of scientific computing. Cambridge University Press, Cambridge, UK.
-
(1999)
Numerical Recipes in C: The Art of Scientific Computing
-
-
Press, W.H.1
Teukolsky, S.A.2
Vetterling, W.T.3
Flannery, B.P.4
-
64
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
-
Qiu, D., Shenkin, P.S., Hollinger, F.P., and Still, W.C. 1997. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. A 101: 3005-3014.
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
65
-
-
0033919287
-
Prediction of amino acid sequence from structure
-
Raha, K., Wollacott, A.M., Italia, M.J., and Desjarlais, J.R. 2000. Prediction of amino acid sequence from structure. Protein Sci. 9: 1106-1119.
-
(2000)
Protein Sci.
, vol.9
, pp. 1106-1119
-
-
Raha, K.1
Wollacott, A.M.2
Italia, M.J.3
Desjarlais, J.R.4
-
66
-
-
0012227656
-
A comprehensive analytical treatment of continuum electrostatics
-
Schaefer, M. and Karplus, M. 1996. A comprehensive analytical treatment of continuum electrostatics. J. Phys. Chem. 100: 1578-1599.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 1578-1599
-
-
Schaefer, M.1
Karplus, M.2
-
67
-
-
0035451052
-
What are the dielectric "constants" of proteins and how to validate electrostatics models?
-
Schutz, C.N. and Warshel, A. 2001. What are the dielectric "constants" of proteins and how to validate electrostatics models? Proteins 44: 400-417.
-
(2001)
Proteins
, vol.44
, pp. 400-417
-
-
Schutz, C.N.1
Warshel, A.2
-
68
-
-
0028896311
-
A relationship between protein stability and protein function
-
Shoichet, B.K., Baase, W.A., Kuroki, R., and Matthews, B.W. 1995. A relationship between protein stability and protein function. Proc. Natl. Acad. Sci. 92: 452-456.
-
(1995)
Proc. Natl. Acad. Sci.
, vol.92
, pp. 452-456
-
-
Shoichet, B.K.1
Baase, W.A.2
Kuroki, R.3
Matthews, B.W.4
-
69
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff, D., Sharp, K.A., and Honig, B. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98: 1978-1988.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
70
-
-
0034620528
-
Rational modification of protein stability by the mutation of charged surface residues
-
Spector, S., Wang, M., Carp, S.A., Robblee, J., Hendsch, Z.S., Fairman, R., Tidor, B., and Raleigh, D.P. 2000. Rational modification of protein stability by the mutation of charged surface residues. Biochemistry 39: 872-879.
-
(2000)
Biochemistry
, vol.39
, pp. 872-879
-
-
Spector, S.1
Wang, M.2
Carp, S.A.3
Robblee, J.4
Hendsch, Z.S.5
Fairman, R.6
Tidor, B.7
Raleigh, D.P.8
-
71
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, W., Tempczyk, A., Hawley, R., and Hendrickson, T. 1990. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112: 6127-6129.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.1
Tempczyk, A.2
Hawley, R.3
Hendrickson, T.4
-
72
-
-
0025879501
-
In a staphylococcal nuclease mutant the side-chain of a lysine replacing valine 66 is fully buried in the hydrophobic core
-
Stites, W.E., Gittis, A.G., Lattman, E.E., and Shortle, D. 1991. In a staphylococcal nuclease mutant the side-chain of a lysine replacing valine 66 is fully buried in the hydrophobic core. J. Mol. Biol. 221: 7-14.
-
(1991)
J. Mol. Biol.
, vol.221
, pp. 7-14
-
-
Stites, W.E.1
Gittis, A.G.2
Lattman, E.E.3
Shortle, D.4
-
73
-
-
0031844416
-
Pairwise calculation of protein solvent-accessible surface areas
-
Street, A.G. and Mayo, S.L. 1998. Pairwise calculation of protein solvent-accessible surface areas. Fold. Des. 3: 253-258.
-
(1998)
Fold. Des.
, vol.3
, pp. 253-258
-
-
Street, A.G.1
Mayo, S.L.2
-
74
-
-
33947468892
-
Theory of protein titration I: General equations for impenetrable spheres
-
Tanford, C. and Kirkwood, J. 1957. Theory of protein titration I: General equations for impenetrable spheres. J. Am. Chem. Soc. 79: 5333-5339.
-
(1957)
J. Am. Chem. Soc.
, vol.79
, pp. 5333-5339
-
-
Tanford, C.1
Kirkwood, J.2
-
75
-
-
0015520587
-
Interpretation of protein titration curves: Application to lysozyme
-
Tanford, C. and Roxby, R. 1972. Interpretation of protein titration curves: Application to lysozyme. Biochemistry 11: 2192-2198.
-
(1972)
Biochemistry
, vol.11
, pp. 2192-2198
-
-
Tanford, C.1
Roxby, R.2
-
76
-
-
0034625322
-
Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design
-
Voigt, C.A., Gordon, D.B., and Mayo, S.L. 2000. Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design. J. Mol. Biol. 299: 789-803.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 789-803
-
-
Voigt, C.A.1
Gordon, D.B.2
Mayo, S.L.3
-
77
-
-
0029564595
-
Are buried salt bridges important for protein stability and conformational specificity?
-
Waldburger, C.D., Schildbach, J.F., and Sauer, R.T. 1995. Are buried salt bridges important for protein stability and conformational specificity? Nat. Struct. Biol. 2: 122-128.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 122-128
-
-
Waldburger, C.D.1
Schildbach, J.F.2
Sauer, R.T.3
-
78
-
-
0037963208
-
An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants
-
Wisz, M.S. and Hellinga, H.W. 2003. An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants. Proteins 51: 360-377.
-
(2003)
Proteins
, vol.51
, pp. 360-377
-
-
Wisz, M.S.1
Hellinga, H.W.2
-
79
-
-
0001018540
-
Analytical approximation to the accessible surface-area of proteins
-
Wodak, S. and Janin, J. 1980. Analytical approximation to the accessible surface-area of proteins. Proc. Natl. Acad. Sci. 77: 1736-1740.
-
(1980)
Proc. Natl. Acad. Sci.
, vol.77
, pp. 1736-1740
-
-
Wodak, S.1
Janin, J.2
|