-
1
-
-
0042710087
-
Computational alanine scanning to probe protein-protein Interactions: a novel approach to evaluate binding free energies
-
Massova I, Kollman PA. Computational alanine scanning to probe protein-protein Interactions: a novel approach to evaluate binding free energies. J Am Chem Soc 1999; 121: 8133-8143.
-
(1999)
J Am Chem Soc
, vol.121
, pp. 8133-8143
-
-
Massova, I.1
Kollman, P.A.2
-
2
-
-
33646166928
-
Probing the effect of point mutations at protein-protein interfaces with free energy calculations
-
Almlof M, Aqvist J, Smalas AO, Brandsdal BO. Probing the effect of point mutations at protein-protein interfaces with free energy calculations. Biophys J 2006; 90: 433-442.
-
(2006)
Biophys J
, vol.90
, pp. 433-442
-
-
Almlof, M.1
Aqvist, J.2
Smalas, A.O.3
Brandsdal, B.O.4
-
3
-
-
0037195144
-
A simple physical model for binding energy hot spots in protein-protein complexes
-
Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci USA 2002; 99: 14116-14121.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 14116-14121
-
-
Kortemme, T.1
Baker, D.2
-
4
-
-
58149247893
-
Predicting free energy changes using structural ensemble
-
Benedix A, Becker CM, de Groot BL, Caflisch A, Böckmann RA. Predicting free energy changes using structural ensemble. Nat Methods 2009; 6: 3-4.
-
(2009)
Nat Methods
, vol.6
, pp. 3-4
-
-
Benedix, A.1
Becker, C.M.2
de Groot, B.L.3
Caflisch, A.4
Böckmann, R.A.5
-
5
-
-
0027177102
-
Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering
-
Schreiber G, Fersht A. Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering. Biochemistry 1993; 32: 5145-5150.
-
(1993)
Biochemistry
, vol.32
, pp. 5145-5150
-
-
Schreiber, G.1
Fersht, A.2
-
6
-
-
0028810673
-
Ionizable P1 residues in serine proteinase inhibitors undergo large pK shifts on complex formation
-
Qasim MA, Ranjbar MR, Wynn R, Anderson S, Laskowski M, Jr. Ionizable P1 residues in serine proteinase inhibitors undergo large pK shifts on complex formation. J Biol Chem 1995; 270: 27419-27422.
-
(1995)
J Biol Chem
, vol.270
, pp. 27419-27422
-
-
Qasim, M.A.1
Ranjbar, M.R.2
Wynn, R.3
Anderson, S.4
Laskowski Jr., M.5
-
7
-
-
34548229364
-
FcRn: the neonatal Fc receptor comes of age
-
Roopenian DC, Akilesh S. FcRn: the neonatal Fc receptor comes of age. Nat Rev Immunol 2007; 7: 715-725.
-
(2007)
Nat Rev Immunol
, vol.7
, pp. 715-725
-
-
Roopenian, D.C.1
Akilesh, S.2
-
8
-
-
33747631571
-
Properties of human IgG1s engineered for enhanced binding to the neonatal Fc receptor (FcRn)
-
Dall'Acqua WF, Kiener PA, Wu H. Properties of human IgG1s engineered for enhanced binding to the neonatal Fc receptor (FcRn). J Biol Chem 2006; 281: 23514-23524.
-
(2006)
J Biol Chem
, vol.281
, pp. 23514-23524
-
-
Dall'Acqua, W.F.1
Kiener, P.A.2
Wu, H.3
-
9
-
-
78149320579
-
Antibody recycling by engineered pH-dependent antigen binding improves the duration of antigen neutralization
-
Igawa T, Ishii S, Tachibana T, Maeda A, Higuchi Y, Shimaoka S, Moriyama C, Watanabe T, Takubo R, Doi Y, Wakabayashi T, Hayasaka A, Kadono S, Miyazaki T, Haraya K, Sekimori Y, Kojima T, Nabuchi Y, Aso Y, Kawabe Y, Hattori K. Antibody recycling by engineered pH-dependent antigen binding improves the duration of antigen neutralization. Nat Biotechnol 2010; 28: 1203-1208.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 1203-1208
-
-
Igawa, T.1
Ishii, S.2
Tachibana, T.3
Maeda, A.4
Higuchi, Y.5
Shimaoka, S.6
Moriyama, C.7
Watanabe, T.8
Takubo, R.9
Doi, Y.10
Wakabayashi, T.11
Hayasaka, A.12
Kadono, S.13
Miyazaki, T.14
Haraya, K.15
Sekimori, Y.16
Kojima, T.17
Nabuchi, Y.18
Aso, Y.19
Kawabe, Y.20
Hattori, K.21
more..
-
10
-
-
84859510090
-
Increasing serum half-life and extending cholesterol lowering in vivo by engineering antibody with pH-sensitive binding to PCSK9
-
Chaparro-Riggers J, Liang H, DeVay RM, Bai L, Sutton JE, Chen W, Geng T, Lindquist K, Casas MG, Boustany LM, Brown CL, Chabot J, Gomes B, Garzonel P, Rossi A, Strop P, Shelton D, Pons J, Rajpal A. Increasing serum half-life and extending cholesterol lowering in vivo by engineering antibody with pH-sensitive binding to PCSK9. J Biol Chem 2012; 287: 11090-11097
-
(2012)
J Biol Chem
, vol.287
, pp. 11090-11097
-
-
Chaparro-Riggers, J.1
Liang, H.2
DeVay, R.M.3
Bai, L.4
Sutton, J.E.5
Chen, W.6
Geng, T.7
Lindquist, K.8
Casas, M.G.9
Boustany, L.M.10
Brown, C.L.11
Chabot, J.12
Gomes, B.13
Garzonel, P.14
Rossi, A.15
Strop, P.16
Shelton, D.17
Pons, J.18
Rajpal, A.19
-
11
-
-
0016699207
-
Macromolecular binding
-
Schellman JA. Macromolecular binding. Biopolymers 1975; 14: 999-1018.
-
(1975)
Biopolymers
, vol.14
, pp. 999-1018
-
-
Schellman, J.A.1
-
12
-
-
0031076776
-
pH-dependence of protein stability: absolute electrostatic free energy differences between conformations
-
Schaefer M, Sommer M, Karplus MJ. pH-dependence of protein stability: absolute electrostatic free energy differences between conformations. J Phys Chem B 1997;101: 1663-1683.
-
(1997)
J Phys Chem B
, vol.101
, pp. 1663-1683
-
-
Schaefer, M.1
Sommer, M.2
Karplus, M.J.3
-
13
-
-
0031754295
-
Electrostatic contributions to the binding free energy of the [lambda] cI repressor to DNA
-
Vinod K, Misra VK, Hecht JL, Yang AS, Honig B. Electrostatic contributions to the binding free energy of the [lambda] cI repressor to DNA. Biophys J 1998; 75: 2262-2273.
-
(1998)
Biophys J
, vol.75
, pp. 2262-2273
-
-
Vinod, K.1
Misra, V.K.2
Hecht, J.L.3
Yang, A.S.4
Honig, B.5
-
14
-
-
3142708566
-
Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes
-
Alexov E. Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes. Proteins 2004; 56: 572-584.
-
(2004)
Proteins
, vol.56
, pp. 572-584
-
-
Alexov, E.1
-
15
-
-
0031659673
-
Electrostatic coupling to pH-titrating sites as a source of cooperativity in protein-ligand binding
-
Spassov V, Bashford D. Electrostatic coupling to pH-titrating sites as a source of cooperativity in protein-ligand binding. Protein Sci 1998; 7: 2012-2025.
-
(1998)
Protein Sci
, vol.7
, pp. 2012-2025
-
-
Spassov, V.1
Bashford, D.2
-
16
-
-
84874803064
-
-
Discovery Studio Modeling Environment, Release 3.5. Accelrys Software Inc.: San Diego
-
Discovery Studio Modeling Environment, Release 3.5. Accelrys Software Inc.: San Diego; 2012.
-
(2012)
-
-
-
17
-
-
55549111898
-
A fast and accurate computational approach to protein ionization
-
Spassov VZ, Yan L. A fast and accurate computational approach to protein ionization. Protein Sci 2008; 17: 1955-1970.
-
(2008)
Protein Sci
, vol.17
, pp. 1955-1970
-
-
Spassov, V.Z.1
Yan, L.2
-
18
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
-
Qiu D, Shenkin PS, Hollinger FP, Still WC. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J Phys Chem 1997; 101: 3005-3014.
-
(1997)
J Phys Chem
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
19
-
-
84961985307
-
-
Development of a generalized born model parameterization for proteins and nucleic acids. J Phys Chem B
-
Dominy BN, Brooks CL, III. Development of a generalized born model parameterization for proteins and nucleic acids. J Phys Chem B 1999; 103: 3765-3773.
-
(1999)
, vol.103
, pp. 3765-3773
-
-
Dominy, B.N.1
Brooks III, C.L.2
-
20
-
-
0037194983
-
Introducing an implicit membrane in generalized born/solvent accessibility continuum solvent models
-
Spassov VZ, Yan L, Szalma SZ. Introducing an implicit membrane in generalized born/solvent accessibility continuum solvent models. J Phys Chem B 2002; 106: 8726-8738.
-
(2002)
J Phys Chem B
, vol.106
, pp. 8726-8738
-
-
Spassov, V.Z.1
Yan, L.2
Szalma, S.Z.3
-
21
-
-
0025197061
-
pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model
-
Bashford D, Karplus M. pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 1990; 29: 10219-10225.
-
(1990)
Biochemistry
, vol.29
, pp. 10219-10225
-
-
Bashford, D.1
Karplus, M.2
-
22
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano LJ. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002; 320: 369-387.
-
(2002)
J Mol Biol
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.J.3
-
23
-
-
67650500988
-
the biomolecular simulation program
-
Brooks BR, Brooks CLIII, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor R, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. CHARMM: the biomolecular simulation program. J Comput Chem 2009;30: 1545-1615.
-
(2009)
J Comput Chem
, vol.30
, pp. 1545-1615
-
-
Brooks, B.R.1
Brooks III, C.L.2
Mackerell, A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.C.35
more..
-
24
-
-
84986505827
-
Validation of the general purpose QUANTA 3.2/CHARMm force field
-
Momany F, Rone R. Validation of the general purpose QUANTA 3.2/CHARMm force field. J Comput Chem 1992; 13: 888-900.
-
(1992)
J Comput Chem
, vol.13
, pp. 888-900
-
-
Momany, F.1
Rone, R.2
-
25
-
-
0028871798
-
Side-chain conformational entropy in protein folding
-
Doig AJ, Sternberg MJE. Side-chain conformational entropy in protein folding. Protein Sci 1995; 4: 2247-2251.
-
(1995)
Protein Sci
, vol.4
, pp. 2247-2251
-
-
Doig, A.J.1
Sternberg, M.J.E.2
-
26
-
-
0027955787
-
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
-
Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994; 235: 983-1002.
-
(1994)
J Mol Biol
, vol.235
, pp. 983-1002
-
-
Abagyan, R.1
Totrov, M.2
-
27
-
-
0014718113
-
Protein denaturation. C. Theoretical models for the mechanism of denaturation
-
Tanford C. Protein denaturation. C. Theoretical models for the mechanism of denaturation. Adv Protein Chem 1970; 24: 1-95.
-
(1970)
Adv Protein Chem
, vol.24
, pp. 1-95
-
-
Tanford, C.1
-
28
-
-
0033544710
-
Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability
-
Elcock AH. Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability. J Mol Biol 1999; 294: 1051-1062.
-
(1999)
J Mol Biol
, vol.294
, pp. 1051-1062
-
-
Elcock, A.H.1
-
29
-
-
0031754295
-
Electrostatic contributions to the binding free energy of the cI repressor to DNA
-
Misra VK, Hecht JL, Yang A, Honig B. Electrostatic contributions to the binding free energy of the cI repressor to DNA. Biophys J 1998; 75: 2262-2273.
-
(1998)
Biophys J
, vol.75
, pp. 2262-2273
-
-
Misra, V.K.1
Hecht, J.L.2
Yang, A.3
Honig, B.4
-
30
-
-
0000174762
-
Multiple-site ligand binding to flexible macromolecules: separation of global and local conformational change and an iterative mobile clustering approach
-
Spassov VZ, Bashford D. Multiple-site ligand binding to flexible macromolecules: separation of global and local conformational change and an iterative mobile clustering approach. J Comput Chem 1999; 20: 1091-1111.
-
(1999)
J Comput Chem
, vol.20
, pp. 1091-1111
-
-
Spassov, V.Z.1
Bashford, D.2
-
31
-
-
20644449471
-
Modification of the generalized born model suitable for macromolecules
-
Onufriev A, Bashford D, Case DA. Modification of the generalized born model suitable for macromolecules. J Phys Chem B 2000; 104: 3712-3720.
-
(2000)
J Phys Chem B
, vol.104
, pp. 3712-3720
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
32
-
-
33847261239
-
The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: a side-chain prediction algorithm based on side-chain backbone interactions
-
Spassov VZ, Yan L, Flook PK. The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: a side-chain prediction algorithm based on side-chain backbone interactions. Protein Sci 2007; 16: 494-506.
-
(2007)
Protein Sci
, vol.16
, pp. 494-506
-
-
Spassov, V.Z.1
Yan, L.2
Flook, P.K.3
-
33
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993; 234: 779-815.
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
34
-
-
0028808880
-
Analysis of the pH dependence of the neonatal Fc receptor/immunoglobulin G interaction using antibody and receptor variants
-
Raghavan M, Bonagura VR, Morrison SL, Bjorkman PJ. Analysis of the pH dependence of the neonatal Fc receptor/immunoglobulin G interaction using antibody and receptor variants. Biochemistry 1995; 34: 14649-14657.
-
(1995)
Biochemistry
, vol.34
, pp. 14649-14657
-
-
Raghavan, M.1
Bonagura, V.R.2
Morrison, S.L.3
Bjorkman, P.J.4
-
35
-
-
0022845301
-
A physicochemical study of protein G, a molecule with unique immunoglobulin G-binding properties
-
Åkerström B, Björck LJ. A physicochemical study of protein G, a molecule with unique immunoglobulin G-binding properties. J Biol Chem 1986; 261: 10240-10247.
-
(1986)
J Biol Chem
, vol.261
, pp. 10240-10247
-
-
Åkerström, B.1
Björck, L.J.2
-
36
-
-
0035012654
-
Crystal structure at 2.8 Å of an FcRn/heterodimeric Fc complex: mechanism of pH-dependent binding
-
Martin WL, West AP, Gan L, Bjorkman PJ. Crystal structure at 2.8 Å of an FcRn/heterodimeric Fc complex: mechanism of pH-dependent binding. Molecular Cell 2001; 7: 867-877.
-
(2001)
Molecular Cell
, vol.7
, pp. 867-877
-
-
Martin, W.L.1
West, A.P.2
Gan, L.3
Bjorkman, P.J.4
-
37
-
-
0031566036
-
Identification of critical IgG binding epitopes on the neonatal Fc receptor
-
Vaughn DE, Milburn CM, Penny DM, Martin WL, Johnson JL, Bjorkman PJ. Identification of critical IgG binding epitopes on the neonatal Fc receptor. J Mol Biol 1997; 274: 597-607.
-
(1997)
J Mol Biol
, vol.274
, pp. 597-607
-
-
Vaughn, D.E.1
Milburn, C.M.2
Penny, D.M.3
Martin, W.L.4
Johnson, J.L.5
Bjorkman, P.J.6
-
38
-
-
0030796064
-
Increasing the serum persistence of an IgG fragment by random mutagenesis
-
Ghetie V, Popov S, Borval J, Radu C, Matesoi D, Medesan C, Ober RJ, Ward ES. Increasing the serum persistence of an IgG fragment by random mutagenesis. Nat Biotechnol 1997; 15: 637-640.
-
(1997)
Nat Biotechnol
, vol.15
, pp. 637-640
-
-
Ghetie, V.1
Popov, S.2
Borval, J.3
Radu, C.4
Matesoi, D.5
Medesan, C.6
Ober, R.J.7
Ward, E.S.8
-
39
-
-
80052598705
-
Neonatal Fc receptor and IgG-based therapeutics
-
Kuo TT, Aveson VG. Neonatal Fc receptor and IgG-based therapeutics. MAbs 2011; 3: 5: 422-430.
-
(2011)
MAbs
, vol.5
, Issue.3
, pp. 422-430
-
-
Kuo, T.T.1
Aveson, V.G.2
|