-
1
-
-
0014828908
-
An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity
-
Wu TT, Kabat EA. An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J Exp Med 1970;132:211-250
-
(1970)
J Exp Med
, vol.132
, pp. 211-250
-
-
Wu, T.T.1
Kabat, E.A.2
-
2
-
-
0024844388
-
Conformations of immunoglobulin hypervariable regions
-
Chothia C, Lesk AM, Tramontano A, Levitt M, Smith-Gil SJ, Air G, Sheriff S, Padlan EA, Davies D, Tulip WR. Conformations of immunoglobulin hypervariable regions. Nature 1989;342:877-883.
-
(1989)
Nature
, vol.342
, pp. 877-883
-
-
Chothia, C.1
Lesk, A.M.2
Tramontano, A.3
Levitt, M.4
Smith-Gil, S.J.5
Air, G.6
Sheriff, S.7
Padlan, E.A.8
Davies, D.9
Tulip, W.R.10
-
3
-
-
0027686741
-
Molecular basis of crossreactivity and limits of antibody-antigen complementarity
-
Arevalo JH, Taussig MJ, Wilson IA. Molecular basis of crossreactivity and limits of antibody-antigen complementarity. Nature 1993;365:859-863.
-
(1993)
Nature
, vol.365
, pp. 859-863
-
-
Arevalo, J.H.1
Taussig, M.J.2
Wilson, I.A.3
-
4
-
-
0027374551
-
26-10 Fab-digoxin complex: Affinity and specificity due to surface complementarity
-
Jeffrey PD, Strong RK, Sieker LC, Chang CYY, Campbell RL, Petsko GA, Haber E, Margolies MN, Sheriff S. 26-10 Fab-digoxin complex: affinity and specificity due to surface complementarity. Proc Natl Acad Sci USA 1993;90:10310-10314.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 10310-10314
-
-
Jeffrey, P.D.1
Strong, R.K.2
Sieker, L.C.3
Chang, C.Y.Y.4
Campbell, R.L.5
Petsko, G.A.6
Haber, E.7
Margolies, M.N.8
Sheriff, S.9
-
5
-
-
0031571157
-
Antibody fragment Fv4155 bound to two closely related steroid hormones: The structural basis of fine specificity
-
Trinh CH, Hemmington SD, Verhoeyen ME, Phillips SEV. Antibody fragment Fv4155 bound to two closely related steroid hormones: the structural basis of fine specificity. Science 1997;7:937-948.
-
(1997)
Science
, vol.7
, pp. 937-948
-
-
Trinh, C.H.1
Hemmington, S.D.2
Verhoeyen, M.E.3
Phillips, S.E.V.4
-
6
-
-
0035965352
-
Crystal structure of a recombinant anti-estradiol Fab fragment in complex
-
Lamminmak̈i U, Kankare JA. Crystal structure of a recombinant anti-estradiol Fab fragment in complex. J Biol Chem 2001;276:36687-36694.
-
(2001)
J Biol Chem
, vol.276
, pp. 36687-36694
-
-
Lamminmak̈i, U.1
Kankare, J.A.2
-
7
-
-
0037040289
-
Structural insights into steroid hormone binding. The crystal structure of a recombinant antitestosterone Fab fragment in free and testosterone-bound forms
-
Valjakka J, Takkinen K, Teerinen T, Söderlund H, Rouvinen J. Structural insights into steroid hormone binding. The crystal structure of a recombinant antitestosterone Fab fragment in free and testosterone-bound forms. J Biol Chem 2002;277:4183-4190.
-
(2002)
J Biol Chem
, vol.277
, pp. 4183-4190
-
-
Valjakka, J.1
Takkinen, K.2
Teerinen, T.3
Söderlund, H.4
Rouvinen, J.5
-
8
-
-
18444394317
-
Highly specific anti-estradiol antibodies: Structural characterisation and binding diversity
-
Monnet C, Bettsworth F, Stura EA, Le Du M-H, Ménez R, Derrien L, Zinn-Justin S, Gilquin G, Sibai G, Battail-Poirot N, Jolivet M, Ménez A, Arnaud M, Ducantel F, Charbonnier JB. Highly specific anti-estradiol antibodies: structural characterisation and binding diversity. J Mol Biol 2002;315:699-712.
-
(2002)
J Mol Biol
, vol.315
, pp. 699-712
-
-
Monnet, C.1
Bettsworth, F.2
Stura, E.A.3
Le Du, M.-H.4
Ménez, R.5
Derrien, L.6
Zinn-Justin, S.7
Gilquin, G.8
Sibai, G.9
Battail-Poirot, N.10
Jolivet, M.11
Ménez, A.12
Arnaud, M.13
Ducantel, F.14
Charbonnier, J.B.15
-
9
-
-
0031800681
-
Specificity improvement of a recombinant antitestosterone Fab fragment by CDRIII mutagenesis and phage display selection
-
Hemminki A, Niemi S, Hoffren A-M, Hakalahti L, Söderlund H, Takkinen K. Specificity improvement of a recombinant antitestosterone Fab fragment by CDRIII mutagenesis and phage display selection. Protein Eng 1998;11:311-319.
-
(1998)
Protein Eng
, vol.11
, pp. 311-319
-
-
Hemminki, A.1
Niemi, S.2
Hoffren, A.-M.3
Hakalahti, L.4
Söderlund, H.5
Takkinen, K.6
-
10
-
-
0034141394
-
X-ray studies of recombinant anti-testosterone fab-fragments: The use of PEG3350 in crystallization
-
Valjakka J, Hemminki A, Teerinen T, Takkinen K, Rouvinen J. X-ray studies of recombinant anti-testosterone fab-fragments: the use of PEG3350 in crystallization. Acta Crystallogr 2000;D56:218-221.
-
(2000)
Acta Crystallogr
, vol.D56
, pp. 218-221
-
-
Valjakka, J.1
Hemminki, A.2
Teerinen, T.3
Takkinen, K.4
Rouvinen, J.5
-
11
-
-
0031818010
-
Computational protein engineering
-
Hellinge HW Computational protein engineering. Nature Struct Biol 1998;5:525-527.
-
(1998)
Nature Struct Biol
, vol.5
, pp. 525-527
-
-
Hellinge, H.W.1
-
12
-
-
0033694923
-
De novo design of helical bundles as models for understanding protein folding and function
-
Hill RB, Raleigh DP, Lombardi WF. De novo design of helical bundles as models for understanding protein folding and function. Acc Chem Res 2000;33:745-754.
-
(2000)
Acc Chem Res
, vol.33
, pp. 745-754
-
-
Hill, R.B.1
Raleigh, D.P.2
Lombardi, W.F.3
-
13
-
-
0034625322
-
Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design
-
Mayo SL, Gordon DB. Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design. J Mol Biol 2000;299:789-803.
-
(2000)
J Mol Biol
, vol.299
, pp. 789-803
-
-
Mayo, S.L.1
Gordon, D.B.2
-
14
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE III. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000;33:889-897.
-
(2000)
Acc Chem Res
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham T.E. III15
-
15
-
-
0031872292
-
Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum models
-
Vorobjev YN, Almagro JC, Hermans J. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum models. Proteins 1998;32:399-413.
-
(1998)
Proteins
, vol.32
, pp. 399-413
-
-
Vorobjev, Y.N.1
Almagro, J.C.2
Hermans, J.3
-
16
-
-
0032556243
-
Free energy analysis of the conformational preferences of A and B forms of DNA in solution
-
Jayaram B, Sprous D, Young MA, Beveridge DL. Free energy analysis of the conformational preferences of A and B forms of DNA in solution. J Am Chem Soc 1998;120:10629-10633.
-
(1998)
J Am Chem Soc
, vol.120
, pp. 10629-10633
-
-
Jayaram, B.1
Sprous, D.2
Young, M.A.3
Beveridge, D.L.4
-
17
-
-
7044239742
-
Free energy calculations: Applications to chemical and biochemical phenomena
-
Kollman PA. Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev 1993;93:2395-2417.
-
(1993)
Chem Rev
, vol.93
, pp. 2395-2417
-
-
Kollman, P.A.1
-
18
-
-
0034212858
-
Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece
-
Lee MR, Duan Y, Kollman PA. Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece. Proteins 2000;39:309-316.
-
(2000)
Proteins
, vol.39
, pp. 309-316
-
-
Lee, M.R.1
Duan, Y.2
Kollman, P.A.3
-
19
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
-
Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case D. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Am Chem Soc 1998;120:9401-9409.
-
(1998)
J Am Chem Soc
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.5
-
20
-
-
0034614387
-
Investigating the binding specificity of U1A-RNA by computational mutagenesis
-
Reyes CM, Kollman PA. Investigating the binding specificity of U1A-RNA by computational mutagenesis. J Mol Biol 2000;295:1-6.
-
(2000)
J Mol Biol
, vol.295
, pp. 1-6
-
-
Reyes, C.M.1
Kollman, P.A.2
-
21
-
-
0034646574
-
Structure and thermodynamics of RNA-protein binding: Using MD and free energy analyses to calculate the free energies of binding and conformational change
-
Reyes CM, Kollman PA. Structure and thermodynamics of RNA-protein binding: using MD and free energy analyses to calculate the free energies of binding and conformational change. J Mol Biol 2000;297:1145-1158.
-
(2000)
J Mol Biol
, vol.297
, pp. 1145-1158
-
-
Reyes, C.M.1
Kollman, P.A.2
-
22
-
-
0034716751
-
A ligand that is predicted to bind better to avidin than biotin: Insights from computational fluorine scanning
-
Kuhn B, Kollman PA. A ligand that is predicted to bind better to avidin than biotin: insights from computational fluorine scanning. J Am Chem Soc 2000;122:3909-3916.
-
(2000)
J Am Chem Soc
, vol.122
, pp. 3909-3916
-
-
Kuhn, B.1
Kollman, P.A.2
-
23
-
-
0033405041
-
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7
-
Chong LT, Duan Y, Wang L, Massova I, Kollman PA. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc Natl Acad Sci USA 1999;96:14330-14335.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 14330-14335
-
-
Chong, L.T.1
Duan, Y.2
Wang, L.3
Massova, I.4
Kollman, P.A.5
-
24
-
-
0035668653
-
Energetic analysis of binding of progesterone and 5β-androstane-3,17-dione to anti-progesterone antibody DB3 using molecular dynamics and free energy calculations
-
Peräkylä M, Nordman N. Energetic analysis of binding of progesterone and 5β-androstane-3,17-dione to anti-progesterone antibody DB3 using molecular dynamics and free energy calculations. Protein Eng 2000;14:753-758.
-
(2000)
Protein Eng
, vol.14
, pp. 753-758
-
-
Peräkylä, M.1
Nordman, N.2
-
25
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. 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
Gould, I.R.4
Merz K.M., Jr.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
26
-
-
0000730887
-
Application of the RESP methodology in the parameterization of organic solvents
-
Fox T, Kollman PA. Application of the RESP methodology in the parameterization of organic solvents. J Phys Chem B 1998;102:8070-8079.
-
(1998)
J Phys Chem B
, vol.102
, pp. 8070-8079
-
-
Fox, T.1
Kollman, P.A.2
-
27
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
-
Bayly CI, Cieplak P, Cornell WD, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem 1993;97:10268-10280.
-
(1993)
J Phys Chem
, vol.97
, pp. 10268-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
28
-
-
0003712431
-
-
San Francisco, CA: University of California
-
Case DA, Pearlman DA, Caldwell JW, Cheatham TE III, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Ferguson DM, Radmer RJ, Seibel GL, Singh UC, Weiner PK, Kollman PA. AMBER 6.0. San Francisco, CA: University of California; 1997.
-
(1997)
AMBER 6.0
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham T.E. III4
Ross, W.S.5
Simmerling, C.L.6
Darden, T.A.7
Merz, K.M.8
Stanton, R.V.9
Cheng, A.L.10
Vincent, J.J.11
Crowley, M.12
Ferguson, D.M.13
Radmer, R.J.14
Seibel, G.L.15
Singh, U.C.16
Weiner, P.K.17
Kollman, P.A.18
-
29
-
-
0003045884
-
Force field parameters for sulfates and sulfamates based on ab initio calculations: Extensions of AMBER and CHARMm fields
-
Huige CJM, Altona C. Force field parameters for sulfates and sulfamates based on ab initio calculations: extensions of AMBER and CHARMm fields. J Comput Chem 1995;16:56-79.
-
(1995)
J Comput Chem
, vol.16
, pp. 56-79
-
-
Huige, C.J.M.1
Altona, C.2
-
30
-
-
0004133516
-
-
Pittsburgh, PA: Gaussian, Inc
-
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Peterson GA, Ayala PY, Cui G, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill PMW, Johnson BG, Chen W, Wong MW, Andres JL, Head-Gordon M, Replogle ES, Pople JA. Gaussian 98, Revision A.7. Pittsburgh, PA: Gaussian, Inc.; 1998.
-
(1998)
Gaussian 98, Revision A.7
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Zakrzewski, V.G.7
Montgomery, J.A.8
Stratmann, R.E.9
Burant, J.C.10
Dapprich, S.11
Millam, J.M.12
Daniels, A.D.13
Kudin, K.N.14
Strain, M.C.15
Farkas, O.16
Tomasi, J.17
Barone, V.18
Cossi, M.19
Cammi, R.20
Mennucci, B.21
Pomelli, C.22
Adamo, C.23
Clifford, S.24
Ochterski, J.25
Peterson, G.A.26
Ayala, P.Y.27
Cui, G.28
Morokuma, K.29
Malick, D.K.30
Rabuck, A.D.31
Raghavachari, K.32
Foresman, J.B.33
Cioslowski, J.34
Ortiz, J.V.35
Stefanov, B.B.36
Liu, G.37
Liashenko, A.38
Piskorz, P.39
Komaromi, I.40
Gomperts, R.41
Martin, R.L.42
Fox, D.J.43
Keith, T.44
Al-Laham, M.A.45
Peng, C.Y.46
Nanayakkara, A.47
Gonzalez, C.48
Challacombe, M.49
Gill, P.M.W.50
Johnson, B.G.51
Chen, W.52
Wong, M.W.53
Andres, J.L.54
Head-Gordon, M.55
Replogle, E.S.56
Pople, J.A.57
more..
-
31
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura J, Impley RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.3
Impley, R.W.4
Klein, M.L.5
-
33
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola AD, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.D.4
Haak, J.R.5
-
34
-
-
33646940952
-
Numerical-integration of Cartesian equations of motion of a system with constraints molecular-dynamics of N-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical-integration of Cartesian equations of motion of a system with constraints molecular-dynamics of N-alkanes. J Comp Phys 1977;23:327-341.
-
(1977)
J Comp Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
35
-
-
0003676577
-
-
New York: Department of Biochemistry and Molecular Biophysics, Columbia University
-
Nicholls A, Sharp KA, Honig B. Delphi. New York: Department of Biochemistry and Molecular Biophysics, Columbia University; 1990.
-
(1990)
Delphi
-
-
Nicholls, A.1
Sharp, K.A.2
Honig, B.3
-
36
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 1994;98:1978-1988.
-
(1994)
J Phys Chem
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
37
-
-
0030040323
-
Reduced surface - An efficient way to compute molecular surfaces
-
Sanner MF, Olson AJ, Spehner JC. Reduced surface - an efficient way to compute molecular surfaces. Biopolymers 1996;38:305-320.
-
(1996)
Biopolymers
, vol.38
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.C.3
-
38
-
-
0037079570
-
Computational alanine scanning of the 1:1 human growth hormone-receptor complex
-
Huo S, Massova I, Kollman PA. Computational alanine scanning of the 1:1 human growth hormone-receptor complex. J Comput Chem 2002;23:15-27.
-
(2002)
J Comput Chem
, vol.23
, pp. 15-27
-
-
Huo, S.1
Massova, I.2
Kollman, P.A.3
-
39
-
-
36449005776
-
The overlooked bond-stretching contribution in free energy perturbation calculations
-
Pearlman DA, Kollman PA. The overlooked bond-stretching contribution in free energy perturbation calculations. J Chem Phys 1991;94:4532-4545.
-
(1991)
J Chem Phys
, vol.94
, pp. 4532-4545
-
-
Pearlman, D.A.1
Kollman, P.A.2
-
40
-
-
84961980685
-
Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
-
Kuhn B, Kollman PA. Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J Med Chem 2000;43:3786-3791.
-
(2000)
J Med Chem
, vol.43
, pp. 3786-3791
-
-
Kuhn, B.1
Kollman, P.A.2
-
41
-
-
0029610794
-
Canonical structures repertoire of the antigen-binding site of immunoglobulins suggest strong geometrical restrictions associated to the mechanism of immune recognition
-
Vargas-Madrazo E, Lara-Ochoa F, Almagro JC. Canonical structures repertoire of the antigen-binding site of immunoglobulins suggest strong geometrical restrictions associated to the mechanism of immune recognition. J Mol Biol 1995;254:497-504.
-
(1995)
J Mol Biol
, vol.254
, pp. 497-504
-
-
Vargas-Madrazo, E.1
Lara-Ochoa, F.2
Almagro, J.C.3
-
42
-
-
0021978356
-
Antigen-binding specificities of antibodies are primary determined by seven residues of VH
-
Ohno S, Mori N, Matsunaga T. Antigen-binding specificities of antibodies are primary determined by seven residues of VH. Proc Natl Acad Sci USA 1985;82:2945-2949.
-
(1985)
Proc Natl Acad Sci USA
, vol.82
, pp. 2945-2949
-
-
Ohno, S.1
Mori, N.2
Matsunaga, T.3
|