-
1
-
-
0003880161
-
Molecular biology of the cell
-
4th ed. New York, NY: Garland Science; .
-
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Molecular biology of the cell, 4th ed. New York, NY: Garland Science; 2002.
-
(2002)
-
-
Alberts, B.1
Johnson, A.2
Lewis, J.3
Raff, M.4
Roberts, K.5
Walter, P.6
-
2
-
-
0035727902
-
Engineered antibodies take center stage
-
Huston JS, George AJ. Engineered antibodies take center stage. Hum Antibodies 2001; 10: 127-142.
-
(2001)
Hum Antibodies
, vol.10
, pp. 127-142
-
-
Huston, J.S.1
George, A.J.2
-
3
-
-
27144432842
-
Engineered antibody fragments and the rise of single domains
-
Holliger P, Hudson PJ. Engineered antibody fragments and the rise of single domains. Nat Biotechnol 2005; 23: 1126-1136.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 1126-1136
-
-
Holliger, P.1
Hudson, P.J.2
-
4
-
-
0037470415
-
Isomeric antibodies
-
Foote J. Isomeric antibodies. Science 2003; 299: 1327-1328.
-
(2003)
Science
, vol.299
, pp. 1327-1328
-
-
Foote, J.1
-
5
-
-
0027943261
-
Conformational isomerism and the diversity of antibodies
-
Foote J, Milstein C. Conformational isomerism and the diversity of antibodies. Proc Natl Acad Sci USA 1994; 91: 10370-10374.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 10370-10374
-
-
Foote, J.1
Milstein, C.2
-
6
-
-
1642315560
-
Polyreactivity of antibody molecules
-
Notkins AL. Polyreactivity of antibody molecules. Trends Immunol 2004; 25: 174-179.
-
(2004)
Trends Immunol
, vol.25
, pp. 174-179
-
-
Notkins, A.L.1
-
7
-
-
0344628804
-
Germline antibody recognition of distinct carbohydrate epitopes
-
Nguyen HP, Seto NOL, MacKenzie CR, Brade L, Kosma P, Brade H, Evans SV. Germline antibody recognition of distinct carbohydrate epitopes. Nature Structural Biology DEC 2003; 10(12): 1019-1025.
-
(2003)
Nature Structural Biology DEC
, vol.10
, Issue.12
, pp. 1019-1025
-
-
Nguyen, H.P.1
Seto, N.O.L.2
MacKenzie, C.R.3
Brade, L.4
Kosma, P.5
Brade, H.6
Evans, S.V.7
-
8
-
-
24644521419
-
Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition
-
James LC, Tawfik DS. Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition. Proc Natl Acad Sci USA 2005; 102: 12730-12735.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 12730-12735
-
-
James, L.C.1
Tawfik, D.S.2
-
9
-
-
0032966864
-
Antigen recognition by conformational selection
-
Berger C, Weber-Bornhauser S, Eggenberger J, Hanes J, Pluckthun A, Bosshard HR. Antigen recognition by conformational selection. Febs Letters 1999; 450: 149-153.
-
(1999)
Febs Letters
, vol.450
, pp. 149-153
-
-
Berger, C.1
Weber-Bornhauser, S.2
Eggenberger, J.3
Hanes, J.4
Pluckthun, A.5
Bosshard, H.R.6
-
10
-
-
0033634681
-
Maturation of an antibody response is governed by modulations in flexibility of the antigen-combining site
-
Manivel V, Sahoo NC, Salunke DM, Rao KVS. Maturation of an antibody response is governed by modulations in flexibility of the antigen-combining site. Immunity 2000; 13: 611-620.
-
(2000)
Immunity
, vol.13
, pp. 611-620
-
-
Manivel, V.1
Sahoo, N.C.2
Salunke, D.M.3
Rao, K.V.S.4
-
11
-
-
0037634024
-
Changes in structure and dynamics of the Fv fragment of a catalytic antibody upon binding of inhibitor
-
Kroon GJ, Mo H, Martinez-Yamout MA, Dyson HJ, Wright PE. Changes in structure and dynamics of the Fv fragment of a catalytic antibody upon binding of inhibitor. Prot Sci 2003; 12: 1386-1394.
-
(2003)
Prot Sci
, vol.12
, pp. 1386-1394
-
-
Kroon, G.J.1
Mo, H.2
Martinez-Yamout, M.A.3
Dyson, H.J.4
Wright, P.E.5
-
12
-
-
0036606759
-
Solution structure and backbone dynamics of an antigen-free heavy chain variable domain (VHH) from Llama
-
Renisio JG, Perez J, Czisch M, et al. Solution structure and backbone dynamics of an antigen-free heavy chain variable domain (VHH) from Llama. Proteins 2002; 47: 546-555.
-
(2002)
Proteins
, vol.47
, pp. 546-555
-
-
Renisio, J.G.1
Perez, J.2
Czisch, M.3
-
13
-
-
33748797691
-
Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics
-
Zimmermann J, Oakman EL, Thorpe IF, et al. Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proc Natl Acad Sci USA 2006; 103: 13722-13727.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 13722-13727
-
-
Zimmermann, J.1
Oakman, E.L.2
Thorpe, I.F.3
-
14
-
-
34547460183
-
Molecular evolution of affinity and flexibility in the immune system
-
Thorpe IF, Brooks CL, III. Molecular evolution of affinity and flexibility in the immune system. Proc Natl Acad Sci U SA 2007; 104: 8821-8826.
-
(2007)
Proc Natl Acad Sci U SA
, vol.104
, pp. 8821-8826
-
-
Thorpe, I.F.1
Brooks III, C.L.2
-
15
-
-
34548304888
-
Understanding antibody-antigen associations by molecular dynamics simulations: detection of important intra- and inter-molecular salt bridges
-
Sinha N, Li Y, Lipschultz CA, Smith-Gill SJ. Understanding antibody-antigen associations by molecular dynamics simulations: detection of important intra- and inter-molecular salt bridges. Cell Biochem Biophys 2007; 47: 361-375.
-
(2007)
Cell Biochem Biophys
, vol.47
, pp. 361-375
-
-
Sinha, N.1
Li, Y.2
Lipschultz, C.A.3
Smith-Gill, S.J.4
-
16
-
-
66149181778
-
Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility
-
Babor M, Kortemme T. Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility. Proteins 2009; 75: 846-858.
-
(2009)
Proteins
, vol.75
, pp. 846-858
-
-
Babor, M.1
Kortemme, T.2
-
17
-
-
79551471402
-
-
AMBER [computer program]. Version 82004.
-
AMBER [computer program]. Version 82004.
-
-
-
-
18
-
-
84952104504
-
An analysis of the accuracy of langevin and molecular-dynamics algorithms
-
Pastor RW, Brooks BR, Szabo A. An analysis of the accuracy of langevin and molecular-dynamics algorithms. Mol Phys 1988; 65: 1409-1419.
-
(1988)
Mol Phys
, vol.65
, pp. 1409-1419
-
-
Pastor, R.W.1
Brooks, B.R.2
Szabo, A.3
-
19
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized born model
-
Onufriev A, Bashford D, Case DA. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 2004; 55: 383-394.
-
(2004)
Proteins
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
20
-
-
0026869597
-
Langevin dynamics of peptides-The frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide
-
Loncharich RJ, Brooks BR, Pastor RW. Langevin dynamics of peptides-The frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide. Biopolymers 1992; 32: 523-535.
-
(1992)
Biopolymers
, vol.32
, pp. 523-535
-
-
Loncharich, R.J.1
Brooks, B.R.2
Pastor, R.W.3
-
21
-
-
0037174385
-
All-atom structure prediction and folding simulations of a stable protein
-
Simmerling C, Strockbine B, Roitberg AE. All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 2002; 124: 11258-11259.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 11258-11259
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.E.3
-
23
-
-
79551503220
-
AMBER
-
10. San Francisco, CA: University of California, San Francisco; .
-
AMBER 10. San Francisco, CA: University of California, San Francisco; 2010.
-
(2010)
-
-
-
24
-
-
17044444457
-
Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement
-
Mundorff EC, Hanson MA, Varvak A, Ulrich H, Schultz PG, Stevens RC. Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement. Biochemistry 2000; 39: 627-632.
-
(2000)
Biochemistry
, vol.39
, pp. 627-632
-
-
Mundorff, E.C.1
Hanson, M.A.2
Varvak, A.3
Ulrich, H.4
Schultz, P.G.5
Stevens, R.C.6
-
25
-
-
0032514647
-
Structural and kinetic evidence for strain in biological catalysis
-
Romesberg FE, Santarsiero BD, Spiller B, et al. Structural and kinetic evidence for strain in biological catalysis. Biochemistry 1998; 37: 14404-14409.
-
(1998)
Biochemistry
, vol.37
, pp. 14404-14409
-
-
Romesberg, F.E.1
Santarsiero, B.D.2
Spiller, B.3
-
26
-
-
0037417866
-
Structural evidence for substrate strain in antibody catalysis
-
Yin J, Andryski SE, Beuscher AE, Stevens RC, Schultz PG. Structural evidence for substrate strain in antibody catalysis. Proc Natl Acad Sci USA 2003; 100: 856-861.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 856-861
-
-
Yin, J.1
Andryski, S.E.2
Beuscher, A.E.3
Stevens, R.C.4
Schultz, P.G.5
-
27
-
-
0042744723
-
Structural plasticity and the evolution of antibody affinity and specificity
-
Yin J, Beuscher AE, Andryski SE, Stevens RC, Schultz PG. Structural plasticity and the evolution of antibody affinity and specificity. J Mol Biol 2003; 330: 651-656.
-
(2003)
J Mol Biol
, vol.330
, pp. 651-656
-
-
Yin, J.1
Beuscher, A.E.2
Andryski, S.E.3
Stevens, R.C.4
Schultz, P.G.5
-
28
-
-
0035845637
-
A comparative analysis of the immunological evolution of antibody 28B4
-
Yin J, Mundorff EC, Yang PL, et al. A comparative analysis of the immunological evolution of antibody 28B4. Biochemistry 2001; 40: 10764-10773.
-
(2001)
Biochemistry
, vol.40
, pp. 10764-10773
-
-
Yin, J.1
Mundorff, E.C.2
Yang, P.L.3
-
29
-
-
0030012589
-
Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9-angstrom resolution
-
HsiehWilson LC, Schultz PG, Stevens RC. Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9-angstrom resolution. Proc Natl Acad Sci USA 1996; 93: 5363-5367.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 5363-5367
-
-
HsiehWilson, L.C.1
Schultz, P.G.2
Stevens, R.C.3
-
30
-
-
0030821164
-
Structural insights into the evolution of an antibody combining site
-
Erratum in Science 1997; 277:1423.
-
Wedemayer GJ, Stevens RC. Structural insights into the evolution of an antibody combining site. Science 1997; 276: 1665-1669. Erratum in Science 1997; 277:1423.
-
(1997)
Science
, vol.276
, pp. 1665-1669
-
-
Wedemayer, G.J.1
Stevens, R.C.2
-
31
-
-
0033579560
-
Mutational analysis of the affinity maturation of antibody 48G7
-
Priscilla Y, Schultz PG. Mutational analysis of the affinity maturation of antibody 48G7. J Mol Biol 1999; 294: 1191-1201.
-
(1999)
J Mol Biol
, vol.294
, pp. 1191-1201
-
-
Priscilla, Y.1
Schultz, P.G.2
-
32
-
-
0029991227
-
The immunological evolution of catalysis
-
Patten PA, Gray NS, Yang PL, et al. The immunological evolution of catalysis. Science 1996; 271: 1086-1091.
-
(1996)
Science
, vol.271
, pp. 1086-1091
-
-
Patten, P.A.1
Gray, N.S.2
Yang, P.L.3
-
33
-
-
0141704162
-
Free energy landscape of protein folding in water: explicit vs. implicit solvent
-
Zhou RH. Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins 2003; 53: 148-161.
-
(2003)
Proteins
, vol.53
, pp. 148-161
-
-
Zhou, R.H.1
-
34
-
-
17344362313
-
Ligand recognition by alpha beta T cell receptors
-
Davis MM, Boniface JJ, Reich Z, et al. Ligand recognition by alpha beta T cell receptors. Annu Rev Immunol 1998; 16: 523-544.
-
(1998)
Annu Rev Immunol
, vol.16
, pp. 523-544
-
-
Davis, M.M.1
Boniface, J.J.2
Reich, Z.3
-
35
-
-
0032536197
-
Conformations of the third hypervariable region in the VH domain of immunoglobulins
-
Morea V, Tramontano A, Rustici M, Chothia C, Lesk AM. Conformations of the third hypervariable region in the VH domain of immunoglobulins. J Mol Biol 1998; 275: 269-294.
-
(1998)
J Mol Biol
, vol.275
, pp. 269-294
-
-
Morea, V.1
Tramontano, A.2
Rustici, M.3
Chothia, C.4
Lesk, A.M.5
-
36
-
-
0024844388
-
Conformations of immunoglobulin hypervariable regions
-
Chothia C, Lesk AM, Tramontano A, et al. 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
-
37
-
-
0032006927
-
Conserved motifs in T-cell receptor CDR1 and CDR2: implications for ligand and CD8 co-receptor binding
-
Arden B. Conserved motifs in T-cell receptor CDR1 and CDR2: implications for ligand and CD8 co-receptor binding. Curr Opin Immunol 1998; 10: 74-81.
-
(1998)
Curr Opin Immunol
, vol.10
, pp. 74-81
-
-
Arden, B.1
-
38
-
-
0033711628
-
Diversity in the CDR3 region of VH is sufficient for most antibody specificities
-
Xu J, Davis M. Diversity in the CDR3 region of VH is sufficient for most antibody specificities. Immunity 2000; 13: 37-45.
-
(2000)
Immunity
, vol.13
, pp. 37-45
-
-
Xu, J.1
Davis, M.2
-
39
-
-
0028927329
-
Effect of point mutations on the kinetics and the inhibition of human immunodeficiency virus type 1 protease: relationship to drug resistance
-
Lin Y, Lin X, Hong L, et al. Effect of point mutations on the kinetics and the inhibition of human immunodeficiency virus type 1 protease: relationship to drug resistance. Biochemistry 1995; 34: 1143-1152.
-
(1995)
Biochemistry
, vol.34
, pp. 1143-1152
-
-
Lin, Y.1
Lin, X.2
Hong, L.3
-
40
-
-
34848820304
-
Molecular dynamics studies on HIV-1 protease: a comparison of the flap motions between wild type protease and the M46I/G51D double mutant
-
Lauria A, Ippolito M, Almerico AM. Molecular dynamics studies on HIV-1 protease: a comparison of the flap motions between wild type protease and the M46I/G51D double mutant. J Mol Model 2007; 13: 1151-1156.
-
(2007)
J Mol Model
, vol.13
, pp. 1151-1156
-
-
Lauria, A.1
Ippolito, M.2
Almerico, A.M.3
-
41
-
-
33846690468
-
Insights into amprenavir resistance in E35D HIV-1 protease mutations from molecular dynamics and binding free-energy calculations
-
Meiselbach H, Horn A, Harrer T, Sticht H. Insights into amprenavir resistance in E35D HIV-1 protease mutations from molecular dynamics and binding free-energy calculations. J Mol Model 2007; 13: 297-304.
-
(2007)
J Mol Model
, vol.13
, pp. 297-304
-
-
Meiselbach, H.1
Horn, A.2
Harrer, T.3
Sticht, H.4
-
42
-
-
0035432947
-
Molecular recognition by induced fit: how fit is the concept?
-
Bosshard HR. Molecular recognition by induced fit: how fit is the concept? News Physiol Sci 2001; 16: 171-173.
-
(2001)
News Physiol Sci
, vol.16
, pp. 171-173
-
-
Bosshard, H.R.1
-
43
-
-
0038148710
-
Conformational diversity and protein evolution-a 60-year-old hypothesis revisited
-
James LC, Tawfik DS. Conformational diversity and protein evolution-a 60-year-old hypothesis revisited. Trends Biochem Sci 2003; 28: 361-368.
-
(2003)
Trends Biochem Sci
, vol.28
, pp. 361-368
-
-
James, L.C.1
Tawfik, D.S.2
-
44
-
-
17044444457
-
Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangment
-
Mundorff EC, Hanson MA, Varvak A, Ulrich E, Schultz PG, Steens RC. Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangment. Biochemistry 2000; 39: 627-632.
-
(2000)
Biochemistry
, vol.39
, pp. 627-632
-
-
Mundorff, E.C.1
Hanson, M.A.2
Varvak, A.3
Ulrich, E.4
Schultz, P.G.5
Steens, R.C.6
-
45
-
-
0030930805
-
The interplay between binding energy and catalysis in the evolution of a catalytic antibody
-
Ulrich HD, Mundroff E, Santarsiero BD, Driggers EM, Stevens RC, Schultz PG. The interplay between binding energy and catalysis in the evolution of a catalytic antibody. Nature 1997; 389: 271-275.
-
(1997)
Nature
, vol.389
, pp. 271-275
-
-
Ulrich, H.D.1
Mundroff, E.2
Santarsiero, B.D.3
Driggers, E.M.4
Stevens, R.C.5
Schultz, P.G.6
-
46
-
-
0033405041
-
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7
-
Chong L, Duan Y, Wang L, Massova I, Kollman P. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc Natl Acad Sci U S A 1999; 96: 14330-14335.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 14330-14335
-
-
Chong, L.1
Duan, Y.2
Wang, L.3
Massova, I.4
Kollman, P.5
-
47
-
-
33645990894
-
Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response
-
Sethi DK, Agarwal A, Manivel V, Rao KVS, Salunke DM. Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response. Immunity 2006; 24: 429-438.
-
(2006)
Immunity
, vol.24
, pp. 429-438
-
-
Sethi, D.K.1
Agarwal, A.2
Manivel, V.3
Rao, K.V.S.4
Salunke, D.M.5
-
48
-
-
4444221565
-
UCSF chimera-a visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, et al. UCSF chimera-a visualization system for exploratory research and analysis. J Comput Chem 2004; 25: 1605-1612.
-
(2004)
J Comput Chem
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
|