-
1
-
-
0029421048
-
Protein-protein recognition
-
[CrossRef]
-
Janin, J. Protein-protein recognition. Prog. Biophys. Mol. Biol. 1995, 64, 145–166. [CrossRef]
-
(1995)
Prog. Biophys. Mol. Biol
, vol.64
, pp. 145-166
-
-
Janin, J.1
-
2
-
-
0035096292
-
Recognition between flexible protein molecules: Induced and assisted folding
-
[CrossRef]
-
Demchenko, A.P. Recognition between flexible protein molecules: Induced and assisted folding. J. Mol. Recognit. 2001, 14, 42–61. [CrossRef]
-
(2001)
J. Mol. Recognit
, vol.14
, pp. 42-61
-
-
Demchenko, A.P.1
-
3
-
-
77950650980
-
Towards accurate free energy calculations in ligand protein-binding studies
-
[CrossRef] [PubMed]
-
Steinbrecher, T.; Labahn, A. Towards accurate free energy calculations in ligand protein-binding studies. Curr. Med. Chem. 2010, 17, 767–785. [CrossRef] [PubMed]
-
(2010)
Curr. Med. Chem
, vol.17
, pp. 767-785
-
-
Steinbrecher, T.1
Labahn, A.2
-
4
-
-
0035826155
-
Exploring complex networks
-
[CrossRef] [PubMed]
-
Strogatz, S.H. Exploring complex networks. Nature 2001, 410, 268–276. [CrossRef] [PubMed]
-
(2001)
Nature
, vol.410
, pp. 268-276
-
-
Strogatz, S.H.1
-
5
-
-
77956398004
-
Conformational ensembles, signal transduction and residue hot spots: Application to drug discovery
-
Acuner Ozbabacan, S.E.; Gursoy, A.; Keskin, O.; Nussinov, R. Conformational ensembles, signal transduction and residue hot spots: Application to drug discovery. Curr. Opin. Drug Discov. Dev. 2010, 13, 527–537.
-
(2010)
Curr. Opin. Drug Discov. Dev
, vol.13
, pp. 527-537
-
-
Acuner Ozbabacan, S.E.1
Gursoy, A.2
Keskin, O.3
Nussinov, R.4
-
6
-
-
3543005385
-
Thermodynamics of protein-ligand interactions: History, presence, and future aspects
-
[CrossRef] [PubMed]
-
Perozzo, R.; Folkers, G.; Scapozza, L. Thermodynamics of protein-ligand interactions: History, presence, and future aspects. J. Recept. Signal. Transduct. Res. 2004, 24, 1–52. [CrossRef] [PubMed]
-
(2004)
J. Recept. Signal. Transduct. Res
, vol.24
, pp. 1-52
-
-
Perozzo, R.1
Folkers, G.2
Scapozza, L.3
-
7
-
-
48249102785
-
Calorimetry and thermodynamics in drug design
-
[CrossRef] [PubMed]
-
Chaires, J.B. Calorimetry and thermodynamics in drug design. Annu. Rev. Biophys. 2008, 37, 135–151. [CrossRef] [PubMed]
-
(2008)
Annu. Rev. Biophys
, vol.37
, pp. 135-151
-
-
Chaires, J.B.1
-
8
-
-
0030266484
-
Sensing the heat: The application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions
-
[CrossRef]
-
Ladbury, J.E.; Chowdhry, B.Z. Sensing the heat: The application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions. Chem. Biol. 1996, 3, 791–801. [CrossRef]
-
(1996)
Chem. Biol
, vol.3
, pp. 791-801
-
-
Ladbury, J.E.1
Chowdhry, B.Z.2
-
9
-
-
0026045194
-
Real-time biospecific interaction analysis using surface plasmon resonance and a sensor chip technology
-
[PubMed]
-
Jönsson, U.; Fägerstam, L.; Ivarsson, B.; Johnsson, B.; Karlsson, R.; Lundh, K.; Löfås, S.; Persson, B.; Roos, H.; Rönnberg, I.; et al. Real-time biospecific interaction analysis using surface plasmon resonance and a sensor chip technology. Biotechniques 1991, 11, 620–627. [PubMed]
-
(1991)
Biotechniques
, vol.11
, pp. 620-627
-
-
Jönsson, U.1
Fägerstam, L.2
Ivarsson, B.3
Johnsson, B.4
Karlsson, R.5
Lundh, K.6
Löfås, S.7
Persson, B.8
Roos, H.9
Rönnberg, I.10
-
10
-
-
33646850951
-
Biomolecular interactions by Surface Plasmon Resonance technology
-
[PubMed]
-
Torreri, P.; Ceccarini, M.; Macioce, P.; Petrucci, T.C. Biomolecular interactions by Surface Plasmon Resonance technology. Ann. Ist. Super Sanita. 2005, 41, 437–441. [PubMed]
-
(2005)
Ann. Ist. Super Sanita
, vol.41
, pp. 437-441
-
-
Torreri, P.1
Ceccarini, M.2
Macioce, P.3
Petrucci, T.C.4
-
11
-
-
76949127690
-
Polarization of the fluorescence of macromolecules. I. Theory and experimental method
-
[CrossRef] [PubMed]
-
Weber, G. Polarization of the fluorescence of macromolecules. I. Theory and experimental method. Biochem. J. 1952, 51, 145–155. [CrossRef] [PubMed]
-
(1952)
Biochem. J
, vol.51
, pp. 145-155
-
-
Weber, G.1
-
12
-
-
79952385103
-
Analysis of protein-ligand interactions by fluorescence polarization
-
[CrossRef] [PubMed]
-
Rossi, A.; Taylor, C. Analysis of protein-ligand interactions by fluorescence polarization. Nat. Protoc. 2011, 6, 365–387. [CrossRef] [PubMed]
-
(2011)
Nat. Protoc
, vol.6
, pp. 365-387
-
-
Rossi, A.1
Taylor, C.2
-
13
-
-
84904819424
-
Challenges, applications, and recent advances of protein–ligand docking in structure-based drug design
-
[CrossRef] [PubMed]
-
Grinter, S.Z.; Zou, X. Challenges, applications, and recent advances of protein–ligand docking in structure-based drug design. Molecules 2014, 19, 10150–10176. [CrossRef] [PubMed]
-
(2014)
Molecules
, vol.19
, pp. 10150-10176
-
-
Grinter, S.Z.1
Zou, X.2
-
14
-
-
84877933286
-
Protein-ligand docking in the new millennium-a retrospective of 10 years in the field
-
[CrossRef] [PubMed]
-
Sousa, S.F.; Ribeiro, A.J.; Coimbra, J.T.; Neves, R.P.; Martins, S.A.; Moorthy, N.S.; Fernandes, P.A.; Ramos, M.J. Protein-ligand docking in the new millennium-a retrospective of 10 years in the field. Curr. Med. Chem. 2013, 20, 2296–2314. [CrossRef] [PubMed]
-
(2013)
Curr. Med. Chem
, vol.20
, pp. 2296-2314
-
-
Sousa, S.F.1
Ribeiro, A.J.2
Coimbra, J.T.3
Neves, R.P.4
Martins, S.A.5
Moorthy, N.S.6
Fernandes, P.A.7
Ramos, M.J.8
-
15
-
-
34347224684
-
Calculation of protein-ligand binding affinities. Annu
-
[CrossRef] [PubMed]
-
Gilson, M.K.; Zhou, H.X. Calculation of protein-ligand binding affinities. Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 21–42. [CrossRef] [PubMed]
-
(2007)
Rev. Biophys. Biomol. Struct
, vol.36
, pp. 21-42
-
-
Gilson, M.K.1
Zhou, H.X.2
-
16
-
-
0000914494
-
A method of geometrical representation of the thermodynamic properties of substances by means of surfaces
-
Gibbs, J.W. A method of geometrical representation of the thermodynamic properties of substances by means of surfaces. Trans. Conn. Acad. Arts Sci. 1873, 2, 382–404.
-
(1873)
Trans. Conn. Acad. Arts Sci
, vol.2
, pp. 382-404
-
-
Gibbs, J.W.1
-
17
-
-
84895930751
-
. Physicochemical bases for protein folding, dynamics, and protein-ligand binding
-
[CrossRef] [PubMed]
-
Li, H.; Xie, Y.; Liu, C.; Liu, S. Physicochemical bases for protein folding, dynamics, and protein-ligand binding. Sci. China Life Sci. 2014, 57, 287–302. [CrossRef] [PubMed]
-
(2014)
Sci. China Life Sci
, vol.57
, pp. 287-302
-
-
Li, H.1
Xie, Y.2
Liu, C.3
Liu, S.4
-
18
-
-
0028098629
-
Introduction to microcalorimetry and biomolecular energetics
-
[PubMed]
-
Cooper, A.; Johnson, C.M. Introduction to microcalorimetry and biomolecular energetics. Methods Mol. Biol. 1994, 22, 109–124. [PubMed]
-
(1994)
Methods Mol. Biol
, vol.22
, pp. 109-124
-
-
Cooper, A.1
Johnson, C.M.2
-
19
-
-
84882294645
-
Protein folding, binding and energy landscape: A synthesis
-
Kaumaya, P.T.P., Ed.; InTech: Rijeka, Croatia
-
Liu, S.Q.; Xie, Y.H.; Ji, X.L.; Tao, Y.; Tan, D.Y.; Zhang, K.Q.; Fu, Y.X. Protein folding, binding and energy landscape: A synthesis. In Protein Engineering; Kaumaya, P.T.P., Ed.; InTech: Rijeka, Croatia, 2012; pp. 207–252.
-
(2012)
Protein Engineering
, pp. 207-252
-
-
Liu, S.Q.1
Xie, Y.H.2
Ji, X.L.3
Tao, Y.4
Tan, D.Y.5
Zhang, K.Q.6
Fu, Y.X.7
-
20
-
-
34047136004
-
Global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein
-
[CrossRef] [PubMed]
-
MacRaild, C.A.; Daranas, A.H.; Bronowska, A.; Homans, S.W. Global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein. J. Mol. Biol. 2007, 368, 822–832. [CrossRef] [PubMed]
-
(2007)
J. Mol. Biol
, vol.368
, pp. 822-832
-
-
Macraild, C.A.1
Daranas, A.H.2
Bronowska, A.3
Homans, S.W.4
-
21
-
-
84884277426
-
Thermodynamics of ligand-protein interactions: Implications for molecular design
-
Moreno-Piraján, J.C., Ed.; InTech: Rijeka, Croatia
-
Bronowska, A.K. Thermodynamics of ligand-protein interactions: Implications for molecular design. In Thermodynamics—Interaction Studies—Solids, Liquids and Gases; Moreno-Piraján, J.C., Ed.; InTech: Rijeka, Croatia, 2011; pp. 1–48.
-
(2011)
Thermodynamics—Interaction Studies—Solids, Liquids and Gases
, pp. 1-48
-
-
Bronowska, A.K.1
-
22
-
-
0030917908
-
Loss of translational entropy in binding, folding, and catalysis
-
[CrossRef]
-
Amzel, L.M. Loss of translational entropy in binding, folding, and catalysis. Proteins 1997, 28, 144–149. [CrossRef]
-
(1997)
Proteins
, vol.28
, pp. 144-149
-
-
Amzel, L.M.1
-
23
-
-
0033655709
-
Calculation of entropy changes in biological processes: Folding, binding, and oligomerization
-
[PubMed]
-
Amzel, L.M. Calculation of entropy changes in biological processes: Folding, binding, and oligomerization. Methods Enzymol. 2000, 323, 167–177. [PubMed]
-
(2000)
Methods Enzymol
, vol.323
, pp. 167-177
-
-
Amzel, L.M.1
-
24
-
-
0032824805
-
Folding funnels and binding mechanisms
-
[CrossRef] [PubMed]
-
Ma, B.; Kumar, S.; Tsai, C.J.; Nussinov, R. Folding funnels and binding mechanisms. Protein Eng. 1999, 12, 713–720. [CrossRef] [PubMed]
-
(1999)
Protein Eng
, vol.12
, pp. 713-720
-
-
Ma, B.1
Kumar, S.2
Tsai, C.J.3
Nussinov, R.4
-
25
-
-
0031868211
-
Protein folding via binding and vice versa
-
[CrossRef]
-
Tsai, C.J.; Xu, D.; Nussinov, R. Protein folding via binding and vice versa. Fold. Des. 1998, 3, R71–R80. [CrossRef]
-
(1998)
Fold. Des
, vol.3
, pp. R71-R80
-
-
Tsai, C.J.1
Xu, D.2
Nussinov, R.3
-
26
-
-
0033056708
-
Folding funnels, binding funnels, and protein function
-
[CrossRef] [PubMed]
-
Tsai, C.J.; Kumar, S.; Ma, B.; Nussinov, R. Folding funnels, binding funnels, and protein function. Protein Sci. 1999, 8, 1181–1190. [CrossRef] [PubMed]
-
(1999)
Protein Sci
, vol.8
, pp. 1181-1190
-
-
Tsai, C.J.1
Kumar, S.2
Ma, B.3
Nussinov, R.4
-
27
-
-
0033621104
-
Folding and binding cascades: Shifts in energy landscapes
-
[CrossRef] [PubMed]
-
Tsai, C.J.; Ma, B.; Nussinov, R. Folding and binding cascades: Shifts in energy landscapes. Proc. Natl. Acad. Sci. USA 1999, 96, 9970–9972. [CrossRef] [PubMed]
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 9970-9972
-
-
Tsai, C.J.1
Ma, B.2
Nussinov, R.3
-
28
-
-
0026723063
-
Protein folding funnels: A kinetic approach to the sequence-structure relationship
-
[CrossRef] [PubMed]
-
Leopold, P.E.; Montal, M.; Onuchic, J.N. Protein folding funnels: A kinetic approach to the sequence-structure relationship. Proc. Natl. Acad. Sci. USA 1992, 89, 8721–8725. [CrossRef] [PubMed]
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 8721-8725
-
-
Leopold, P.E.1
Montal, M.2
Onuchic, J.N.3
-
29
-
-
84895918749
-
154 Protein folding and binding funnels: A common driving force and a common mechanism
-
[CrossRef]
-
Xie, Y.H.; Sang, P.; Tao, Y.; Liu, S.Q. 154 Protein folding and binding funnels: A common driving force and a common mechanism. J. Biomol. Struct. Dyn. 2013, 31, 100–101. [CrossRef]
-
(2013)
J. Biomol. Struct. Dyn
, vol.31
, pp. 100-101
-
-
Xie, Y.H.1
Sang, P.2
Tao, Y.3
Liu, S.Q.4
-
30
-
-
0029395478
-
Win some, lose some: Enthalpy-entropy compensation in weak intermolecular interactions
-
[CrossRef]
-
Dunitz, J.D. Win some, lose some: Enthalpy-entropy compensation in weak intermolecular interactions. Chem. Biol. 1995, 2, 709–712. [CrossRef]
-
(1995)
Chem. Biol
, vol.2
, pp. 709-712
-
-
Dunitz, J.D.1
-
31
-
-
0001176490
-
Statistical interpretation of enthalpy-entropy compensation
-
[CrossRef]
-
Krug, R.R.; Hunter, W.G.; Grieger, R.A. Statistical interpretation of enthalpy-entropy compensation. Nature 1976, 261, 566–567. [CrossRef]
-
(1976)
Nature
, vol.261
, pp. 566-567
-
-
Krug, R.R.1
Hunter, W.G.2
Grieger, R.A.3
-
32
-
-
0036120608
-
Enthalpy-entropy compensation: A phantom phenomenon
-
[CrossRef] [PubMed]
-
Cornish-Bowden, A. Enthalpy-entropy compensation: A phantom phenomenon. J. Biosci. 2002, 27, 121–126. [CrossRef] [PubMed]
-
(2002)
J. Biosci
, vol.27
, pp. 121-126
-
-
Cornish-Bowden, A.1
-
33
-
-
0035965868
-
Heat does not come in different colours: Entropy-enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions
-
[CrossRef]
-
Cooper, A.; Johnson, C.M.; Lakey, J.H.; Nöllmann, M. Heat does not come in different colours: Entropy-enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions. Biophys. Chem. 2001, 93, 215–230. [CrossRef]
-
(2001)
Biophys. Chem
, vol.93
, pp. 215-230
-
-
Cooper, A.1
Johnson, C.M.2
Lakey, J.H.3
Nöllmann, M.4
-
34
-
-
82955164342
-
The mathematical origins of the kinetic compensation effect: 1. The effect of random experimental errors
-
[CrossRef] [PubMed]
-
Barrie, P.J. The mathematical origins of the kinetic compensation effect: 1. The effect of random experimental errors. Phys. Chem. Chem. Phys. 2012, 14, 318–326. [CrossRef] [PubMed]
-
(2012)
Phys. Chem. Chem. Phys
, vol.14
, pp. 318-326
-
-
Barrie, P.J.1
-
35
-
-
82955241242
-
The mathematical origins of the kinetic compensation effect: 2. The effect of systematic errors
-
[CrossRef] [PubMed]
-
Barrie, P.J. The mathematical origins of the kinetic compensation effect: 2. The effect of systematic errors. Phys. Chem. Chem. Phys. 2012, 14, 327–336. [CrossRef] [PubMed]
-
(2012)
Phys. Chem. Chem. Phys
, vol.14
, pp. 327-336
-
-
Barrie, P.J.1
-
36
-
-
84860390480
-
Extent of enthalpy-entropy compensation in protein-ligand interactions
-
[CrossRef] [PubMed]
-
Olsson, T.S.; Ladbury, J.E.; Pitt, W.R.; Williams, M.A. Extent of enthalpy-entropy compensation in protein-ligand interactions. Protein Sci. 2011, 20, 1607–1618. [CrossRef] [PubMed]
-
(2011)
Protein Sci
, vol.20
, pp. 1607-1618
-
-
Olsson, T.S.1
Ladbury, J.E.2
Pitt, W.R.3
Williams, M.A.4
-
37
-
-
0034618512
-
Entropy-enthalpy compensation and anticompensation: Solvation and ligand binding
-
[CrossRef]
-
Exner, O. Entropy-enthalpy compensation and anticompensation: Solvation and ligand binding. Chem. Commun. 2000, 2000, 1655–1656. [CrossRef]
-
(2000)
Chem. Commun. 2000
, pp. 1655-1656
-
-
Exner, O.1
-
38
-
-
0001594721
-
Entropy-enthalpy compensation in solvation and ligand binding revisited
-
[CrossRef]
-
Gallicchio, E.; Kubo, M.M.; Levy, R.M. Entropy-enthalpy compensation in solvation and ligand binding revisited. J. Am. Chem. Soc. 1998, 120, 4526–4527. [CrossRef]
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 4526-4527
-
-
Gallicchio, E.1
Kubo, M.M.2
Levy, R.M.3
-
39
-
-
0021093448
-
Enthalpy-entropy compensation and heat capacity changes for protein-ligand interactions: General thermodynamic models and data for the binding of nucleotides to ribonuclease A
-
[CrossRef] [PubMed]
-
Eftink, M.R.; Anusiem, A.C.; Biltonen, R.L. Enthalpy-entropy compensation and heat capacity changes for protein-ligand interactions: General thermodynamic models and data for the binding of nucleotides to ribonuclease A. Biochemistry 1983, 22, 3884–3896. [CrossRef] [PubMed]
-
(1983)
Biochemistry
, vol.22
, pp. 3884-3896
-
-
Eftink, M.R.1
Anusiem, A.C.2
Biltonen, R.L.3
-
40
-
-
0014722597
-
Enthalpy-entropy compensation phenomena in water solutions of proteins and small molecules: A ubiquitous property of water
-
[CrossRef] [PubMed]
-
Lumry, R.; Rajender, S. Enthalpy-entropy compensation phenomena in water solutions of proteins and small molecules: A ubiquitous property of water. Biopolymers 1970, 9, 1125–1227. [CrossRef] [PubMed]
-
(1970)
Biopolymers
, vol.9
, pp. 1125-1227
-
-
Lumry, R.1
Rajender, S.2
-
41
-
-
33748563642
-
Designing ligands to bind proteins
-
[CrossRef] [PubMed]
-
Whitesides, G.M.; Krishnamurthy, V.M. Designing ligands to bind proteins. Q. Rev. Biophys. 2005, 38, 385–395. [CrossRef] [PubMed]
-
(2005)
Q. Rev. Biophys
, vol.38
, pp. 385-395
-
-
Whitesides, G.M.1
Krishnamurthy, V.M.2
-
42
-
-
84870579518
-
Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding
-
[CrossRef] [PubMed]
-
Fenley, A.T.; Muddana, H.S.; Gilson, M.K. Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding. Proc. Natl. Acad. Sci. USA 2012, 109, 20006–20011. [CrossRef] [PubMed]
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 20006-20011
-
-
Fenley, A.T.1
Muddana, H.S.2
Gilson, M.K.3
-
43
-
-
79959243001
-
Thermodynamics of ligand binding and efficiency
-
[CrossRef] [PubMed]
-
Reynolds, C.H.; Holloway, M.K. Thermodynamics of ligand binding and efficiency. ACS Med. Chem. Lett. 2011, 2, 433–437. [CrossRef] [PubMed]
-
(2011)
ACS Med. Chem. Lett
, vol.2
, pp. 433-437
-
-
Reynolds, C.H.1
Holloway, M.K.2
-
44
-
-
0001199087
-
Entropy-enthalpy compensation: Conformational fluctuation and induced-fit
-
[CrossRef]
-
Qian, H. Entropy-enthalpy compensation: Conformational fluctuation and induced-fit. J. Chem. Phys. 1998, 109, 10015–10017. [CrossRef]
-
(1998)
J. Chem. Phys
, vol.109
, pp. 10015-10017
-
-
Qian, H.1
-
45
-
-
5644287368
-
Free energy, entropy, and induced fit in host-guest recognition: Calculations with the second-generation mining minima algorithm
-
[CrossRef] [PubMed]
-
Chang, C.E.; Gilson, M.K. Free energy, entropy, and induced fit in host-guest recognition: Calculations with the second-generation mining minima algorithm. J. Am. Chem. Soc. 2004, 126, 13156–13164. [CrossRef] [PubMed]
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 13156-13164
-
-
Chang, C.E.1
Gilson, M.K.2
-
46
-
-
33751157207
-
Enthalpy-entropy compensation in drug receptor binding
-
[CrossRef]
-
Gilli, P.; Ferretti, V.; Gilli, G.; Borea, P.A. Enthalpy-entropy compensation in drug receptor binding. J. Phys. Chem. B 1994, 98, 1515–1518. [CrossRef]
-
(1994)
J. Phys. Chem. B
, vol.98
, pp. 1515-1518
-
-
Gilli, P.1
Ferretti, V.2
Gilli, G.3
Borea, P.A.4
-
47
-
-
84877768087
-
Entropy-enthalpy compensation: Role and ramifications in biomolecular ligand recognition and design
-
[CrossRef] [PubMed]
-
Chodera, J.D.; Mobley, D.L. Entropy-enthalpy compensation: Role and ramifications in biomolecular ligand recognition and design. Annu. Rev. Biophys. 2013, 42, 121–142. [CrossRef] [PubMed]
-
(2013)
Annu. Rev. Biophys
, vol.42
, pp. 121-142
-
-
Chodera, J.D.1
Mobley, D.L.2
-
48
-
-
84906539098
-
A fundamental view of enthalpy-entropy compensation
-
[CrossRef]
-
Ryde, U. A fundamental view of enthalpy-entropy compensation. Med. Chem. Commun. 2014, 5, 1324–1336. [CrossRef]
-
(2014)
Med. Chem. Commun
, vol.5
, pp. 1324-1336
-
-
Ryde, U.1
-
49
-
-
84886933840
-
Water networks contribute to enthalpy/entropy compensation in protein-ligand binding
-
[CrossRef] [PubMed]
-
Breiten, B.; Lockett, M.R.; Sherman, W.; Fujita, S.; Al-Sayah, M.; Lange, H.; Bowers, C.M.; Heroux, A.; Krilov, G.; Whitesides, G.M. Water networks contribute to enthalpy/entropy compensation in protein-ligand binding. J. Am. Chem. Soc. 2013, 135, 15579–15584. [CrossRef] [PubMed]
-
(2013)
J. Am. Chem. Soc
, vol.135
, pp. 15579-15584
-
-
Breiten, B.1
Lockett, M.R.2
Sherman, W.3
Fujita, S.4
Al-Sayah, M.5
Lange, H.6
Bowers, C.M.7
Heroux, A.8
Krilov, G.9
Whitesides, G.M.10
-
50
-
-
0001289724
-
Einfluss der configuration auf die wirkung der enzyme
-
Fischer, E. Einfluss der configuration auf die wirkung der enzyme. Ber. Dtsch. Chem. Ges. 1894, 27, 2984–2993.
-
(1894)
Ber. Dtsch. Chem. Ges
, vol.27
, pp. 2984-2993
-
-
Fischer, E.1
-
51
-
-
0001858251
-
Application of a theory of enzyme specificity to protein synthesis
-
[CrossRef] [PubMed]
-
Koshland, D.E.J. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA 1958, 44, 98–104. [CrossRef] [PubMed]
-
(1958)
Proc. Natl. Acad. Sci. USA
, vol.44
, pp. 98-104
-
-
Koshland, D.1
-
52
-
-
30044434744
-
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
-
[CrossRef] [PubMed]
-
Tobi, D.; Bahar, I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc. Natl. Acad. Sci. USA 2005, 102, 18908–18913. [CrossRef] [PubMed]
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 18908-18913
-
-
Tobi, D.1
Bahar, I.2
-
53
-
-
77957231785
-
Induced fit, conformational selection and independent dynamic segments: An extended view of binding events. Trends Biochem
-
[CrossRef] [PubMed]
-
Csermely, P.; Palotai, R.; Nussinov, R. Induced fit, conformational selection and independent dynamic segments: An extended view of binding events. Trends Biochem. Sci. 2010, 35, 539–546. [CrossRef] [PubMed]
-
(2010)
Sci
, vol.35
, pp. 539-546
-
-
Csermely, P.1
Palotai, R.2
Nussinov, R.3
-
54
-
-
0026320866
-
The energy landscapes and motions of proteins
-
[CrossRef] [PubMed]
-
Frauenfelder, H.; Sligar, S.G.; Wolynes, P.G. The energy landscapes and motions of proteins. Science 1991, 254, 1598–1603. [CrossRef] [PubMed]
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.G.2
Wolynes, P.G.3
-
55
-
-
37249032102
-
Dynamic personalities of proteins
-
[CrossRef] [PubMed]
-
Henzler-Wildman, K.A.; Kern, D. Dynamic personalities of proteins. Nature 2007, 450, 964–972. [CrossRef] [PubMed]
-
(2007)
Nature
, vol.450
, pp. 964-972
-
-
Henzler-Wildman, K.A.1
Kern, D.2
-
56
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein Folding
-
[CrossRef] [PubMed]
-
Bryngelson, J.D.; Onuchic, J.N.; Socci, N.D.; Wolynes, P.G. Funnels, pathways, and the energy landscape of protein Folding: A synthesis. Proteins 1995, 21, 167–195. [CrossRef] [PubMed]
-
(1995)
A Synthesis. Proteins
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
57
-
-
0030867610
-
Ligand binding to proteins: The binding landscape model
-
[CrossRef] [PubMed]
-
Miller, D.W.; Dill, K.A. Ligand binding to proteins: The binding landscape model. Protein Sci. 1997, 6, 2166–2179. [CrossRef] [PubMed]
-
(1997)
Protein Sci
, vol.6
, pp. 2166-2179
-
-
Miller, D.W.1
Dill, K.A.2
-
58
-
-
80053539881
-
Conformational selection or induced fit? 50 years of debate resolved
-
[CrossRef] [PubMed]
-
Changeux, J.P.; Edelstein, S. Conformational selection or induced fit? 50 years of debate resolved. F1000 Biol. Rep. 2011, 3, 19. [CrossRef] [PubMed]
-
(2011)
F1000 Biol. Rep
, vol.3
, pp. 19
-
-
Changeux, J.P.1
Edelstein, S.2
-
59
-
-
70350340728
-
The role of dynamic conformational ensembles in biomolecular recognition
-
[CrossRef] [PubMed]
-
Boehr, D.D.; Nussinov, R.; Wright, P.E. The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol. 2009, 5, 789–796. [CrossRef] [PubMed]
-
(2009)
Nat. Chem. Biol
, vol.5
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
60
-
-
84894246676
-
Multiple conformational selection and induced fit events take place in allosteric propagation
-
[CrossRef] [PubMed]
-
Nussinov, R.; Ma, B.; Tsai, C.J. Multiple conformational selection and induced fit events take place in allosteric propagation. Biophys. Chem. 2014, 186, 22–30. [CrossRef] [PubMed]
-
(2014)
Biophys. Chem
, vol.186
, pp. 22-30
-
-
Nussinov, R.1
Ma, B.2
Tsai, C.J.3
-
61
-
-
0001160952
-
Ligand-receptor interactions
-
[CrossRef]
-
Bongrand, P. Ligand-receptor interactions. Rep. Prog. Phys. 1999, 62, 921–968. [CrossRef]
-
(1999)
Rep. Prog. Phys
, vol.62
, pp. 921-968
-
-
Bongrand, P.1
-
62
-
-
84895922490
-
153 Wonderful roles of the entropy in protein dynamics, binding and folding
-
[CrossRef]
-
Xie, Y.H.; Tao, Y.; Liu, S.Q. 153 Wonderful roles of the entropy in protein dynamics, binding and folding. J. Biomol. Struct. Dyn. 2013, 31, 98–100. [CrossRef]
-
(2013)
J. Biomol. Struct. Dyn
, vol.31
, pp. 98-100
-
-
Xie, Y.H.1
Tao, Y.2
Liu, S.Q.3
-
63
-
-
79551678422
-
Mechanisms of protein-ligand association and its modulation by protein mutations
-
[CrossRef] [PubMed]
-
Held, M.; Metzner, P.; Prinz, J.H.; Noé, F. Mechanisms of protein-ligand association and its modulation by protein mutations. Biophys. J. 2011, 100, 701–710. [CrossRef] [PubMed]
-
(2011)
Biophys. J
, vol.100
, pp. 701-710
-
-
Held, M.1
Metzner, P.2
Prinz, J.H.3
Noé, F.4
-
64
-
-
54849429367
-
Dynamics of protein-protein encounter: A Langevin equation approach with reaction patches
-
[CrossRef] [PubMed]
-
Schluttig, J.; Alamanova, D.; Helms, V.; Schwarz, U.S. Dynamics of protein-protein encounter: A Langevin equation approach with reaction patches. J. Chem. Phys. 2008, 129, 155106. [CrossRef] [PubMed]
-
(2008)
J. Chem. Phys
, vol.129
-
-
Schluttig, J.1
Alamanova, D.2
Helms, V.3
Schwarz, U.S.4
-
65
-
-
36549102274
-
Brownian dynamics simulation of diffusion-influenced bimolecular reactions
-
[CrossRef]
-
Northrup, S.H.; Allison, S.A.; McCammon, J.A. Brownian dynamics simulation of diffusion-influenced bimolecular reactions. J. Chem. Phys. 1984, 80, 1517–1524. [CrossRef]
-
(1984)
J. Chem. Phys
, vol.80
, pp. 1517-1524
-
-
Northrup, S.H.1
Allison, S.A.2
McCammon, J.A.3
-
66
-
-
33646005543
-
Diffusional encounter of barnase and barstar
-
[CrossRef] [PubMed]
-
Spaar, A.; Dammer, C.; Gabdoulline, R.R.; Wade, R.C.; Helms, V. Diffusional encounter of barnase and barstar. Biophys. J. 2006, 90, 1913–1924. [CrossRef] [PubMed]
-
(2006)
Biophys. J
, vol.90
, pp. 1913-1924
-
-
Spaar, A.1
Dammer, C.2
Gabdoulline, R.R.3
Wade, R.C.4
Helms, V.5
-
67
-
-
77950219326
-
Lock and key colloids
-
[CrossRef] [PubMed]
-
Sacanna, S.; Irvine, W.T.; Chaikin, P.M.; Pine, D.J. Lock and key colloids. Nature 2010, 464, 575–578. [CrossRef] [PubMed]
-
(2010)
Nature
, vol.464
, pp. 575-578
-
-
Sacanna, S.1
Irvine, W.T.2
Chaikin, P.M.3
Pine, D.J.4
-
68
-
-
84877730460
-
Shaping colloids for self-assembly
-
[CrossRef] [PubMed]
-
Sacanna, S.; Korpics, M.; Rodriguez, K.; Colon-Melendez, L.; Kim, S.-H.; Pine, D.J.; Yi, G.R. Shaping colloids for self-assembly. Nat. Commun. 2013, 4, 1688. [CrossRef] [PubMed]
-
(2013)
Nat. Commun
, vol.4
, pp. 1688
-
-
Sacanna, S.1
Korpics, M.2
Rodriguez, K.3
Colon-Melendez, L.4
Kim, S.-H.5
Pine, D.J.6
Yi, G.R.7
-
69
-
-
79951548761
-
Hybrid MC-DFT method for studying multidimensional entropic forces
-
[CrossRef] [PubMed]
-
Jin, Z.; Wu, J. Hybrid MC-DFT method for studying multidimensional entropic forces. J. Phys. Chem. B 2011, 115, 1450–1460. [CrossRef] [PubMed]
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 1450-1460
-
-
Jin, Z.1
Wu, J.2
-
70
-
-
0037016484
-
Depletion effects on the lock and key steric interactions between macromolecules
-
[CrossRef]
-
Kinoshita, M.; Oguni, T. Depletion effects on the lock and key steric interactions between macromolecules. Chem. Phys. Lett. 2002, 351, 79–84. [CrossRef]
-
(2002)
Chem. Phys. Lett
, vol.351
, pp. 79-84
-
-
Kinoshita, M.1
Oguni, T.2
-
71
-
-
31644437525
-
Roles of entropic excluded-volume effects in colloidal and biological systems: Analyses using the three-dimensional integral equation theory
-
[CrossRef]
-
Kinoshita, M. Roles of entropic excluded-volume effects in colloidal and biological systems: Analyses using the three-dimensional integral equation theory. Chem. Eng. Sci. 2006, 61, 2150–2160. [CrossRef]
-
(2006)
Chem. Eng. Sci
, vol.61
, pp. 2150-2160
-
-
Kinoshita, M.1
-
72
-
-
84949664751
-
Assembly of lock-and-key colloids mediated by polymeric depletant
-
[CrossRef] [PubMed]
-
Chang, H.Y.; Huang, C.W.; Chen, Y.F.; Chen, S.Y.; Sheng, Y.J.; Tsao, H.K. Assembly of lock-and-key colloids mediated by polymeric depletant. Langmuir 2015, 31, 13085–13093. [CrossRef] [PubMed]
-
(2015)
Langmuir
, vol.31
, pp. 13085-13093
-
-
Chang, H.Y.1
Huang, C.W.2
Chen, Y.F.3
Chen, S.Y.4
Sheng, Y.J.5
Tsao, H.K.6
-
74
-
-
84874616598
-
Statistical mechanics approach to lock-key supramolecular chemistry interactions
-
[CrossRef] [PubMed]
-
Odriozola, G.; Lozada-Cassou, M. Statistical mechanics approach to lock-key supramolecular chemistry interactions. Phys. Rev. Lett. 2013, 110, 105701. [CrossRef] [PubMed]
-
(2013)
Phys. Rev. Lett
, vol.110
-
-
Odriozola, G.1
Lozada-Cassou, M.2
-
75
-
-
33645999511
-
On interaction between two bodies immersed in a solution of macromolecules
-
Asakura, S.; Oosawa, F. On interaction between two bodies immersed in a solution of macromolecules. J. Chem. Phys. 1954, 22, 1255–1256.
-
(1954)
J. Chem. Phys
, vol.22
, pp. 1255-1256
-
-
Asakura, S.1
Oosawa, F.2
-
76
-
-
80955158478
-
Entropy effects in self-assembling mechanisms: Also a view from the information theory
-
[CrossRef]
-
Jiménez-Ángeles, F.; Odriozola, G.; Lozada-Cassou, M. Entropy effects in self-assembling mechanisms: Also a view from the information theory. J. Mol. Liq. 2011, 164, 87–100. [CrossRef]
-
(2011)
J. Mol. Liq
, vol.164
, pp. 87-100
-
-
Jiménez-Ángeles, F.1
Odriozola, G.2
Lozada-Cassou, M.3
-
77
-
-
78649875544
-
Assembly of shape-controlled nanocrystals by depletion attraction
-
[CrossRef] [PubMed]
-
Zanella, M.; Bertoni, G.; Franchini, I.R.; Brescia, R.; Baranov, D.; Manna, L. Assembly of shape-controlled nanocrystals by depletion attraction. Chem. Commun. 2011, 47, 203–205. [CrossRef] [PubMed]
-
(2011)
Chem. Commun
, vol.47
, pp. 203-205
-
-
Zanella, M.1
Bertoni, G.2
Franchini, I.R.3
Brescia, R.4
Baranov, D.5
Manna, L.6
-
78
-
-
84863564456
-
Surface roughness directed self-assembly of patchy particles into colloidal micelles
-
[CrossRef] [PubMed]
-
Kraft, D.J.; Ni, R.; Smallenburg, F.; Hermes, M.; Yoon, K.; Weitz, D.A.; van Blaaderen, A.; Groenewold, J.; Dijkstra, M.; Kegel, W.K. Surface roughness directed self-assembly of patchy particles into colloidal micelles. Proc. Natl. Acad. Sci. USA 2012, 109, 10787–10792. [CrossRef] [PubMed]
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 10787-10792
-
-
Kraft, D.J.1
Ni, R.2
Smallenburg, F.3
Hermes, M.4
Yoon, K.5
Weitz, D.A.6
Van Blaaderen, A.7
Groenewold, J.8
Dijkstra, M.9
Kegel, W.K.10
-
79
-
-
13444250015
-
Formation of spanning water networks on protein surfaces via 2D percolation transition
-
[CrossRef] [PubMed]
-
Oleinikova, A.; Smolin, N.; Brovchenko, I.A.G.; Winter, R. Formation of spanning water networks on protein surfaces via 2D percolation transition. J. Phys. Chem. B 2005, 109, 1988–1998. [CrossRef] [PubMed]
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 1988-1998
-
-
Oleinikova, A.1
Smolin, N.2
Brovchenko, I.A.G.3
Winter, R.4
-
80
-
-
84925866707
-
Limitations and extensions of the lock-and-key principle: Differences between gas state, solution and solid state structures
-
[CrossRef] [PubMed]
-
Schneider, H.J. Limitations and extensions of the lock-and-key principle: Differences between gas state, solution and solid state structures. Int. J. Mol. Sci. 2015, 16, 6694–6717. [CrossRef] [PubMed]
-
(2015)
Int. J. Mol. Sci
, vol.16
, pp. 6694-6717
-
-
Schneider, H.J.1
-
81
-
-
21244499277
-
Diastereoselective amplification of an induced-fit receptor from a dynamic combinatorial library
-
[CrossRef] [PubMed]
-
Corbett, P.T.; Tong, L.H.; Sanders, J.K.; Otto, S. Diastereoselective amplification of an induced-fit receptor from a dynamic combinatorial library. J. Am. Chem. Soc. 2005, 127, 8902–8903. [CrossRef] [PubMed]
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 8902-8903
-
-
Corbett, P.T.1
Tong, L.H.2
Sanders, J.K.3
Otto, S.4
-
82
-
-
0037473066
-
Calculation of molecular configuration integrals
-
[CrossRef]
-
Chang, C.E.; Potter, M.J.; Gilson, M.K. Calculation of molecular configuration integrals. J. Phys. Chem. B 2003, 107, 1048–1055. [CrossRef]
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 1048-1055
-
-
Chang, C.E.1
Potter, M.J.2
Gilson, M.K.3
-
83
-
-
84893445590
-
Structure of sugar-bound LacY
-
[CrossRef] [PubMed]
-
Kumar, H.; Kasho, V.; Smirnova, I.; Finer-Moore, J.S.; Kaback, H.R.; Stroud, R.M. Structure of sugar-bound LacY. Proc. Natl. Acad. Sci. USA 2014, 111, 1784–1788. [CrossRef] [PubMed]
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 1784-1788
-
-
Kumar, H.1
Kasho, V.2
Smirnova, I.3
Finer-Moore, J.S.4
Kaback, H.R.5
Stroud, R.M.6
-
84
-
-
33645320817
-
Structural evidence for induced fit and a mechanism for sugar/H+ symport in LacY
-
[CrossRef] [PubMed]
-
Mirza, O.; Guan, L.; Verner, G.; Iwata, S.; Kaback, H.R. Structural evidence for induced fit and a mechanism for sugar/H+ symport in LacY. EMBO J. 2006, 25, 1177–1183. [CrossRef] [PubMed]
-
(2006)
EMBO J
, vol.25
, pp. 1177-1183
-
-
Mirza, O.1
Guan, L.2
Verner, G.3
Iwata, S.4
Kaback, H.R.5
-
85
-
-
79959349280
-
Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition
-
[CrossRef] [PubMed]
-
Chaptal, V.; Kwon, S.; Sawaya, M.R.; Guan, L.; Kaback, H.R.; Abramson, J. Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition. Proc. Natl. Acad. Sci. USA 2011, 108, 9361–9366. [CrossRef] [PubMed]
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 9361-9366
-
-
Chaptal, V.1
Kwon, S.2
Sawaya, M.R.3
Guan, L.4
Kaback, H.R.5
Abramson, J.6
-
86
-
-
84911443461
-
Insights into the inhibitory mechanisms of the regulatory protein IIA(Glc) on melibiose permease activity
-
[CrossRef] [PubMed]
-
Hariharan, P.; Guan, L. Insights into the inhibitory mechanisms of the regulatory protein IIA(Glc) on melibiose permease activity. J. Biol. Chem. 2014, 289, 33012–33019. [CrossRef] [PubMed]
-
(2014)
J. Biol. Chem
, vol.289
, pp. 33012-33019
-
-
Hariharan, P.1
Guan, L.2
-
87
-
-
0035432947
-
Molecular recognition by induced fit: How fit is the concept?
-
[PubMed]
-
Bosshard, H.R. Molecular recognition by induced fit: How fit is the concept? News Physiol. Sci. 2001, 16, 171–173. [PubMed]
-
(2001)
News Physiol. Sci
, vol.16
, pp. 171-173
-
-
Bosshard, H.R.1
-
88
-
-
0027943261
-
Conformational isomerism and the diversity of antibodies
-
[CrossRef] [PubMed]
-
Foote, J.; Milstein, C. Conformational isomerism and the diversity of antibodies. Proc. Natl. Acad. Sci. USA 1994, 91, 10370–10374. [CrossRef] [PubMed]
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 10370-10374
-
-
Foote, J.1
Milstein, C.2
-
89
-
-
0033970020
-
Folding and binding cascades: Dynamic landscapes and population shifts
-
[CrossRef] [PubMed]
-
Kumar, S.; Ma, B.; Tsai, C.J.; Sinha, N.; Nussinov, R. Folding and binding cascades: Dynamic landscapes and population shifts. Protein Sci. 2000, 9, 10–19. [CrossRef] [PubMed]
-
(2000)
Protein Sci
, vol.9
, pp. 10-19
-
-
Kumar, S.1
Ma, B.2
Tsai, C.J.3
Sinha, N.4
Nussinov, R.5
-
90
-
-
73349117207
-
Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin
-
[CrossRef] [PubMed]
-
Wlodarski, T.; Zagrovic, B. Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin. Proc. Natl. Acad. Sci. USA 2009, 106, 19346–19351. [CrossRef] [PubMed]
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 19346-19351
-
-
Wlodarski, T.1
Zagrovic, B.2
-
91
-
-
9944237833
-
Complementarity of structure ensembles in protein-protein binding
-
[CrossRef] [PubMed]
-
Grünberg, R.; Leckner, J.; Nilges, M. Complementarity of structure ensembles in protein-protein binding. Structure 2004, 12, 2125–2136. [CrossRef] [PubMed]
-
(2004)
Structure
, vol.12
, pp. 2125-2136
-
-
Grünberg, R.1
Leckner, J.2
Nilges, M.3
-
92
-
-
33748781457
-
The dynamic energy landscape of dihydrofolate reductase catalysis
-
[CrossRef] [PubMed]
-
Boehr, D.D.; McElheny, D.; Dyson, H.J.; Wright, P.E. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 2006, 313, 1638–1642. [CrossRef] [PubMed]
-
(2006)
Science
, vol.313
, pp. 1638-1642
-
-
Boehr, D.D.1
McElheny, D.2
Dyson, H.J.3
Wright, P.E.4
-
93
-
-
42949129270
-
A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction
-
[CrossRef] [PubMed]
-
Gsponer, J.; Christodoulou, J.; Cavalli, A.; Bui, J.M.; Richter, B.; Dobson, C.M.; Vendruscolo, M. A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction. Structure 2008, 16, 736–746. [CrossRef] [PubMed]
-
(2008)
Structure
, vol.16
, pp. 736-746
-
-
Gsponer, J.1
Christodoulou, J.2
Cavalli, A.3
Bui, J.M.4
Richter, B.5
Dobson, C.M.6
Vendruscolo, M.7
-
94
-
-
59149096062
-
Ligand-dependent equilibrium fluctuations of single calmodulin molecules
-
[CrossRef] [PubMed]
-
Junker, J.P.; Ziegler, F.; Rief, M. Ligand-dependent equilibrium fluctuations of single calmodulin molecules. Science 2009, 323, 633–637. [CrossRef] [PubMed]
-
(2009)
Science
, vol.323
, pp. 633-637
-
-
Junker, J.P.1
Ziegler, F.2
Rief, M.3
-
95
-
-
0035366379
-
Protein functional epitopes: Hot spots, dynamics and combinatorial libraries
-
[CrossRef]
-
Ma, B.; Wolfson, H.J.; Nussinov, R. Protein functional epitopes: Hot spots, dynamics and combinatorial libraries. Curr. Opin. Struct. Biol. 2001, 11, 364–369. [CrossRef]
-
(2001)
Curr. Opin. Struct. Biol
, vol.11
, pp. 364-369
-
-
Ma, B.1
Wolfson, H.J.2
Nussinov, R.3
-
96
-
-
84864462749
-
Conformational selection or induced fit? A critical appraisal of the kinetic mechanism
-
[CrossRef] [PubMed]
-
Vogt, A.D.; di Cera, E. Conformational selection or induced fit? A critical appraisal of the kinetic mechanism. Biochemistry 2012, 51, 5894–5902. [CrossRef] [PubMed]
-
(2012)
Biochemistry
, vol.51
, pp. 5894-5902
-
-
Vogt, A.D.1
Di Cera, E.2
-
97
-
-
69549120472
-
Conformational selection or induced fit: A flux description of reaction mechanism
-
[CrossRef] [PubMed]
-
Hammes, G.G.; Chang, Y.C.; Oas, T.G. Conformational selection or induced fit: A flux description of reaction mechanism. Proc. Natl. Acad. Sci. USA 2009, 106, 13737–13741. [CrossRef] [PubMed]
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 13737-13741
-
-
Hammes, G.G.1
Chang, Y.C.2
Oas, T.G.3
-
98
-
-
84904291286
-
Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit
-
[CrossRef] [PubMed]
-
Greives, N.; Zhou, H.X. Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit. Proc. Natl. Acad. Sci. USA 2014, 111, 10197–10202. [CrossRef] [PubMed]
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 10197-10202
-
-
Greives, N.1
Zhou, H.X.2
-
99
-
-
77949587817
-
From induced fit to conformational selection: A continuum of binding mechanism controlled by the timescale of conformational transitions
-
[CrossRef] [PubMed]
-
Zhou, H.X. From induced fit to conformational selection: A continuum of binding mechanism controlled by the timescale of conformational transitions. Biophys. J. 2010, 98, L15–L17. [CrossRef] [PubMed]
-
(2010)
Biophys. J
, vol.98
, pp. L15-L17
-
-
Zhou, H.X.1
-
100
-
-
84872225092
-
On the binding affinity of macromolecular interactions: Daring to ask why proteins interact
-
[CrossRef] [PubMed]
-
Kastritis, P.L.; Bonvin, A.M. On the binding affinity of macromolecular interactions: Daring to ask why proteins interact. J. R. Soc. Interface 2012, 10, 20120835. [CrossRef] [PubMed]
-
(2012)
J. R. Soc. Interface
, vol.10
-
-
Kastritis, P.L.1
Bonvin, A.M.2
-
101
-
-
33645834303
-
New tools provide new insights in NMR studies of protein dynamics
-
[CrossRef] [PubMed]
-
Mittermaier, A.; Kay, L.E. New tools provide new insights in NMR studies of protein dynamics. Science 2006, 312, 224–228. [CrossRef] [PubMed]
-
(2006)
Science
, vol.312
, pp. 224-228
-
-
Mittermaier, A.1
Kay, L.E.2
-
102
-
-
0037463033
-
NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors
-
[CrossRef] [PubMed]
-
Meyer, B.; Peters, T. NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angew. Chem. Int. Ed. Engl. 2003, 42, 864–890. [CrossRef] [PubMed]
-
(2003)
Angew. Chem. Int. Ed. Engl
, vol.42
, pp. 864-890
-
-
Meyer, B.1
Peters, T.2
-
103
-
-
25844521524
-
Advances in kinetic protein crystallography
-
[CrossRef] [PubMed]
-
Bourgeois, D.; Royant, A. Advances in kinetic protein crystallography. Curr. Opin. Struct. Biol. 2005, 15, 538–547. [CrossRef] [PubMed]
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 538-547
-
-
Bourgeois, D.1
Royant, A.2
-
104
-
-
0033813064
-
Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy
-
[CrossRef] [PubMed]
-
Weiss, S. Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy. Nat. Struct. Biol. 2000, 7, 724–729. [CrossRef] [PubMed]
-
(2000)
Nat. Struct. Biol
, vol.7
, pp. 724-729
-
-
Weiss, S.1
-
105
-
-
62049084010
-
Spatially and kinetically resolved changes in the conformational dynamics of the Hsp90 chaperone machine
-
[CrossRef] [PubMed]
-
Graf, C.; Stankiewicz, M.; Kramer, G.; Mayer, M.P. Spatially and kinetically resolved changes in the conformational dynamics of the Hsp90 chaperone machine. EMBO J. 2009, 28, 602–613. [CrossRef] [PubMed]
-
(2009)
EMBO J
, vol.28
, pp. 602-613
-
-
Graf, C.1
Stankiewicz, M.2
Kramer, G.3
Mayer, M.P.4
-
106
-
-
70350759905
-
Analysis of biomolecules using surface plasmons
-
[PubMed]
-
Willander, M.; Al-Hilli, S. Analysis of biomolecules using surface plasmons. Methods Mol. Biol. 2009, 544, 201–229. [PubMed]
-
(2009)
Methods Mol. Biol
, vol.544
, pp. 201-229
-
-
Willander, M.1
Al-Hilli, S.2
-
107
-
-
77954675167
-
Optical methods in the study of protein-protein interactions
-
[PubMed]
-
Masi, A.; Cicchi, R.; Carloni, A.; Pavone, F.S.; Arcangeli, A. Optical methods in the study of protein-protein interactions. Adv. Exp. Med. Biol. 2010, 674, 33–42. [PubMed]
-
(2010)
Adv. Exp. Med. Biol
, vol.674
, pp. 33-42
-
-
Masi, A.1
Cicchi, R.2
Carloni, A.3
Pavone, F.S.4
Arcangeli, A.5
-
108
-
-
0000826487
-
Biochemical applications of differential scanning calorimetry
-
[CrossRef]
-
Sturtevant, M. Biochemical applications of differential scanning calorimetry. Annu. Rev. Phys. Chem. 1987, 38, 463–488. [CrossRef]
-
(1987)
Annu. Rev. Phys. Chem
, vol.38
, pp. 463-488
-
-
Sturtevant, M.1
-
109
-
-
33644675826
-
Differential scanning calorimetry as a tool to estimate binding parameters in multiligand binding proteins
-
[CrossRef] [PubMed]
-
Celej, M.S.; Dassie, S.A.; González, M.; Bianconi, M.L.; Fidelio, G.D. Differential scanning calorimetry as a tool to estimate binding parameters in multiligand binding proteins. Anal. Biochem. 2006, 350, 277–284. [CrossRef] [PubMed]
-
(2006)
Anal. Biochem
, vol.350
, pp. 277-284
-
-
Celej, M.S.1
Dassie, S.A.2
González, M.3
Bianconi, M.L.4
Fidelio, G.D.5
-
110
-
-
0032720338
-
Isothermal titration calorimetry of protein-protein interactions
-
[CrossRef] [PubMed]
-
Pierce, M.M.; Raman, C.S.; Nall, B.T. Isothermal titration calorimetry of protein-protein interactions. Methods 1999, 19, 213–221. [CrossRef] [PubMed]
-
(1999)
Methods
, vol.19
, pp. 213-221
-
-
Pierce, M.M.1
Raman, C.S.2
Nall, B.T.3
-
111
-
-
0029112951
-
Calorimetric methods for interpreting protein-ligand interactions
-
[PubMed]
-
Fisher, H.F.; Singh, N. Calorimetric methods for interpreting protein-ligand interactions. Methods Enzymol. 1995, 259, 194–221. [PubMed]
-
(1995)
Methods Enzymol
, vol.259
, pp. 194-221
-
-
Fisher, H.F.1
Singh, N.2
-
112
-
-
21244442969
-
Heat capacity in proteins
-
[CrossRef] [PubMed]
-
Prabhu, N.V.; Sharp, K.A. Heat capacity in proteins. Annu. Rev. Phys. Chem. 2005, 56, 521–548. [CrossRef] [PubMed]
-
(2005)
Annu. Rev. Phys. Chem
, vol.56
, pp. 521-548
-
-
Prabhu, N.V.1
Sharp, K.A.2
-
113
-
-
34548742806
-
Origin of heat capacity changes in a “nonclassical” hydrophobic interaction
-
[CrossRef] [PubMed]
-
Syme, N.R.; Dennis, C.; Phillips, S.E.; Homans, S.W. Origin of heat capacity changes in a “nonclassical” hydrophobic interaction. Chembiochem 2007, 8, 1509–1511. [CrossRef] [PubMed]
-
(2007)
Chembiochem
, vol.8
, pp. 1509-1511
-
-
Syme, N.R.1
Dennis, C.2
Phillips, S.E.3
Homans, S.W.4
-
114
-
-
54049157385
-
New challenges for pharmaceutical formulations and drug delivery systems characterization using isothermal titration calorimetry
-
[CrossRef] [PubMed]
-
Bouchemal, K. New challenges for pharmaceutical formulations and drug delivery systems characterization using isothermal titration calorimetry. Drug Discov. Today 2008, 13, 960–972. [CrossRef] [PubMed]
-
(2008)
Drug Discov. Today
, vol.13
, pp. 960-972
-
-
Bouchemal, K.1
-
115
-
-
56949106817
-
Microcalorimetry: A response to challenges in modern biotechnology
-
[CrossRef] [PubMed]
-
Krell, T. Microcalorimetry: A response to challenges in modern biotechnology. Microb. Biotechnol. 2008, 1, 126–136. [CrossRef] [PubMed]
-
(2008)
Microb. Biotechnol
, vol.1
, pp. 126-136
-
-
Krell, T.1
-
116
-
-
35448962899
-
Isothermal titration calorimetry: Experimental design, data analysis, and probing macromolecule/ligand binding and kinetic interactions
-
[PubMed]
-
Freyer, M.W.; Lewis, E.A. Isothermal titration calorimetry: Experimental design, data analysis, and probing macromolecule/ligand binding and kinetic interactions. Methods Cell Biol. 2008, 84, 79–113. [PubMed]
-
(2008)
Methods Cell Biol
, vol.84
, pp. 79-113
-
-
Freyer, M.W.1
Lewis, E.A.2
-
117
-
-
84888318270
-
Isothermal titration calorimetry of membrane proteins—Progress and challenges
-
[CrossRef] [PubMed]
-
Rajarathnam, K.; Rösgen, J. Isothermal titration calorimetry of membrane proteins—Progress and challenges. Biochim. Biophys. Acta. 2014, 1838, 69–77. [CrossRef] [PubMed]
-
(2014)
Biochim. Biophys. Acta
, vol.1838
, pp. 69-77
-
-
Rajarathnam, K.1
Rösgen, J.2
-
118
-
-
0029131539
-
Tight binding affinities determined from thermodynamic linkage to protons by titration calorimetry
-
Doyle, M.L.; Louie, G.; Dal Monte, P.R.; Sokoloski, T.D. Tight binding affinities determined from thermodynamic linkage to protons by titration calorimetry. Method Enzymol. 1995, 259, 183–194.
-
(1995)
Method Enzymol
, vol.259
, pp. 183-194
-
-
Doyle, M.L.1
Louie, G.2
Dal Monte, P.R.3
Sokoloski, T.D.4
-
119
-
-
84855269204
-
Applications of isothermal titration calorimetry in pure and applied research - survey of the literature from 2010
-
[CrossRef] [PubMed]
-
Ghai, R.; Falconer, R.J.; Collins, B.M. Applications of isothermal titration calorimetry in pure and applied research - survey of the literature from 2010. J. Mol. Recognit. 2012, 25, 32–52. [CrossRef] [PubMed]
-
(2012)
J. Mol. Recognit
, vol.25
, pp. 32-52
-
-
Ghai, R.1
Falconer, R.J.2
Collins, B.M.3
-
120
-
-
78650894342
-
Survey of the year 2009: Applications of isothermal titration calorimetry
-
[CrossRef] [PubMed]
-
Falconer, R.J.; Collins, B.M. Survey of the year 2009: Applications of isothermal titration calorimetry. J. Mol. Recognit. 2011, 24, 1–16. [CrossRef] [PubMed]
-
J. Mol. Recognit
, Issue.24
, pp. 2011
-
-
Falconer, R.J.1
Collins, B.M.2
-
121
-
-
77956404669
-
Survey of the year 2008: Applications of isothermal titration calorimetry
-
[CrossRef] [PubMed]
-
Falconer, R.J.; Penkova, A.; Jelesarov, I.; Collins, B.M. Survey of the year 2008: Applications of isothermal titration calorimetry. J. Mol. Recognit. 2010, 23, 395–413. [CrossRef] [PubMed]
-
(2010)
J. Mol. Recognit
, vol.23
, pp. 395-413
-
-
Falconer, R.J.1
Penkova, A.2
Jelesarov, I.3
Collins, B.M.4
-
122
-
-
84979718358
-
The binding thermodynamics of drug candidate
-
Keserü, G.M., Swinney, D.C., Eds.; Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Germany
-
Freire, E. The binding thermodynamics of drug candidate. In Thermodynamics and Kinetics of Drug Binding; Keserü, G.M., Swinney, D.C., Eds.; Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Germany, 2015; pp. 1–13.
-
(2015)
Thermodynamics and Kinetics of Drug Binding
, pp. 1-13
-
-
Freire, E.1
-
123
-
-
0033815251
-
Thermodynamic dissection of the binding energetics of KNI-272, a potent HIV-1 protease inhibitor
-
[CrossRef] [PubMed]
-
Velazquez-Campoy, A.; Luque, I.; Todd, M.J.; Milutinovich, M.; Kiso, Y.; Freire, E. Thermodynamic dissection of the binding energetics of KNI-272, a potent HIV-1 protease inhibitor. Protein Sci. 2000, 9, 1801–1809. [CrossRef] [PubMed]
-
(2000)
Protein Sci
, vol.9
, pp. 1801-1809
-
-
Velazquez-Campoy, A.1
Luque, I.2
Todd, M.J.3
Milutinovich, M.4
Kiso, Y.5
Freire, E.6
-
124
-
-
0034093758
-
HIV-1 protease inhibitors: Enthalpic versus entropic optimization of the binding affinity
-
[CrossRef] [PubMed]
-
Velazquez-Campoy, A.; Todd, M.J.; Freire, E. HIV-1 protease inhibitors: Enthalpic versus entropic optimization of the binding affinity. Biochemistry 2000, 39, 2201–2207. [CrossRef] [PubMed]
-
(2000)
Biochemistry
, vol.39
, pp. 2201-2207
-
-
Velazquez-Campoy, A.1
Todd, M.J.2
Freire, E.3
-
125
-
-
2942557079
-
Thermodynamic rules for the design of high affinity HIV-1 protease inhibitors with adaptability to mutations and high selectivity towards unwanted targets
-
[CrossRef] [PubMed]
-
Ohtaka, H.; Muzammil, S.; Schon, A.; Velazquez-Campoy, A.; Vega, S.; Freire, E. Thermodynamic rules for the design of high affinity HIV-1 protease inhibitors with adaptability to mutations and high selectivity towards unwanted targets. Int. J. Biochem. Cell Biol. 2004, 36, 1787–1799. [CrossRef] [PubMed]
-
(2004)
Int. J. Biochem. Cell Biol
, vol.36
, pp. 1787-1799
-
-
Ohtaka, H.1
Muzammil, S.2
Schon, A.3
Velazquez-Campoy, A.4
Vega, S.5
Freire, E.6
-
126
-
-
9644257332
-
Adaptive inhibitors of the HIV-1 protease
-
[CrossRef] [PubMed]
-
Ohtaka, H.; Freire, E. Adaptive inhibitors of the HIV-1 protease. Prog. Biophys. Mol. Biol. 2005, 88, 193–208. [CrossRef] [PubMed]
-
(2005)
Prog. Biophys. Mol. Biol
, vol.88
, pp. 193-208
-
-
Ohtaka, H.1
Freire, E.2
-
127
-
-
34250745809
-
Compensating enthalpic and entropic changes hinder binding affinity optimization
-
[CrossRef] [PubMed]
-
Lafont, V.; Armstrong, A.A.; Ohtaka, H.; Kiso, Y.; Mario Amzel, L.; Freire, E. Compensating enthalpic and entropic changes hinder binding affinity optimization. Chem. Biol. Drug Des. 2007, 69, 413–422. [CrossRef] [PubMed]
-
(2007)
Chem. Biol. Drug Des
, vol.69
, pp. 413-422
-
-
Lafont, V.1
Armstrong, A.A.2
Ohtaka, H.3
Kiso, Y.4
Mario Amzel, L.5
Freire, E.6
-
128
-
-
80255126234
-
Finding a better path to drug selectivity
-
[CrossRef] [PubMed]
-
Kawasaki, Y.; Freire, E. Finding a better path to drug selectivity. Drug Discov. Today 2011, 16, 985–990. [CrossRef] [PubMed]
-
(2011)
Drug Discov. Today
, vol.16
, pp. 985-990
-
-
Kawasaki, Y.1
Freire, E.2
-
129
-
-
84921525079
-
Is there a link between selectivity and binding thermodynamics profiles?
-
[CrossRef] [PubMed]
-
Tarcsay, Á.; Keserű, G.M. Is there a link between selectivity and binding thermodynamics profiles? Drug Discov. Today 2015, 20, 86–94. [CrossRef] [PubMed]
-
(2015)
Drug Discov. Today
, vol.20
, pp. 86-94
-
-
Tarcsay, Á.1
Keserű, G.M.2
-
130
-
-
84888364004
-
Surface plasmon resonance spectroscopy for characterisation of membrane protein-ligand interactions and its potential for drug discovery
-
[CrossRef] [PubMed]
-
Patching, S.G. Surface plasmon resonance spectroscopy for characterisation of membrane protein-ligand interactions and its potential for drug discovery. Biochim. Biophys. Acta 2014, 1838, 43–55. [CrossRef] [PubMed]
-
(2014)
Biochim. Biophys. Acta
, vol.1838
, pp. 43-55
-
-
Patching, S.G.1
-
131
-
-
0029644480
-
BIAcore: A microchip-based system for analyzing the formation of macromolecular complexes
-
[CrossRef]
-
Raghavan, M.; Bjorkman, P.J. BIAcore: A microchip-based system for analyzing the formation of macromolecular complexes. Structure 1995, 3, 331–333. [CrossRef]
-
(1995)
Structure
, vol.3
, pp. 331-333
-
-
Raghavan, M.1
Bjorkman, P.J.2
-
132
-
-
0034824017
-
BIACORE J: A new platform for routine biomolecular interaction analysis
-
[CrossRef] [PubMed]
-
Rich, R.L.; Myszka, D.G. BIACORE J: A new platform for routine biomolecular interaction analysis. J. Mol. Recognit. 2001, 14, 223–228. [CrossRef] [PubMed]
-
(2001)
J. Mol. Recognit
, vol.14
, pp. 223-228
-
-
Rich, R.L.1
Myszka, D.G.2
-
133
-
-
84942850829
-
Surface plasmon resonance method to evaluate anti-citrullinated protein/peptide antibody affinity to citrullinated peptides
-
[PubMed]
-
Real-Fernández, F.; Rossi, G.; Panza, F.; Pratesi, F.; Migliorini, P.; Rovero, P. Surface plasmon resonance method to evaluate anti-citrullinated protein/peptide antibody affinity to citrullinated peptides. Methods Mol. Biol. 2015, 1348, 267–274. [PubMed]
-
(2015)
Methods Mol. Biol
, vol.1348
, pp. 267-274
-
-
Real-Fernández, F.1
Rossi, G.2
Panza, F.3
Pratesi, F.4
Migliorini, P.5
Rovero, P.6
-
134
-
-
78649769725
-
Surface plasmon resonance
-
Hydrodynamics and Calorimetry; Harding, S., Chowdhry, P.Z., Eds.; Oxford University Press: Bath, UK
-
Van der Merwe, P.A. Surface plasmon resonance. In Protein-Ligand Interactions: Hydrodynamics and Calorimetry; Harding, S., Chowdhry, P.Z., Eds.; Oxford University Press: Bath, UK, 2001; pp. 137–170.
-
(2001)
Protein-Ligand Interactions
, pp. 137-170
-
-
Van Der Merwe, P.A.1
-
135
-
-
84897857251
-
-
Isha Books: Dehli, India
-
Joshi, R. Biosensors; Isha Books: Dehli, India, 2006.
-
(2006)
Biosensors
-
-
Joshi, R.1
-
136
-
-
84955611669
-
-
(accessed on 6 December 2015)
-
Affinity Measurement with Biomolecular Interaction Analysis. Available online: www.iib.unibe.ch/ wiki/files/biacore_slides.ppt (accessed on 6 December 2015).
-
-
-
-
137
-
-
0033103834
-
TCR binding to peptide-MHC stabilizes a flexible recognition interface
-
[CrossRef]
-
Willcox, B.E.; Gao, G.F.; Wyer, J.R.; Ladbury, J.E.; Bell, J.I.; Jakobsen, B.K.; van der Merwe, P.A. TCR binding to peptide-MHC stabilizes a flexible recognition interface. Immunity 1999, 10, 357–365. [CrossRef]
-
(1999)
Immunity
, vol.10
, pp. 357-365
-
-
Willcox, B.E.1
Gao, G.F.2
Wyer, J.R.3
Ladbury, J.E.4
Bell, J.I.5
Jakobsen, B.K.6
van der Merwe, P.A.7
-
138
-
-
73449109166
-
Surface plasmon resonance for high-throughput ligand screening of membrane-bound proteins
-
[CrossRef] [PubMed]
-
Maynard, J.A.; Lindquist, N.C.; Sutherland, J.N.; Lesuffleur, A.; Warrington, A.E.; Rodriguez, M.; Oh, S.H. Surface plasmon resonance for high-throughput ligand screening of membrane-bound proteins. Biotechnol. J. 2009, 4, 1542–1558. [CrossRef] [PubMed]
-
(2009)
Biotechnol. J
, vol.4
, pp. 1542-1558
-
-
Maynard, J.A.1
Lindquist, N.C.2
Sutherland, J.N.3
Lesuffleur, A.4
Warrington, A.E.5
Rodriguez, M.6
Oh, S.H.7
-
139
-
-
0033773937
-
Fluorescence polarization and anisotropy in high throughput screening: Perspectives and primer
-
[CrossRef] [PubMed]
-
Owicki, J.C. Fluorescence polarization and anisotropy in high throughput screening: Perspectives and primer. J. Biomol. Screen. 2000, 5, 297–306. [CrossRef] [PubMed]
-
(2000)
J. Biomol. Screen
, vol.5
, pp. 297-306
-
-
Owicki, J.C.1
-
140
-
-
0242385316
-
Ligand-receptor kinetics measured by total internal reflection with fluorescence correlation spectroscopy
-
[CrossRef]
-
Lieto, A.; Cush, R.; Thompson, N. Ligand-receptor kinetics measured by total internal reflection with fluorescence correlation spectroscopy. Biophys. J. 2003, 85, 3294–3302. [CrossRef]
-
(2003)
Biophys. J
, vol.85
, pp. 3294-3302
-
-
Lieto, A.1
Cush, R.2
Thompson, N.3
-
141
-
-
19344375930
-
Lanthanide-based luminescent assays for ligand-receptor interactions
-
[CrossRef] [PubMed]
-
Handl, H.; Gillies, R. Lanthanide-based luminescent assays for ligand-receptor interactions. Life Sci. 2005, 77, 361–371. [CrossRef] [PubMed]
-
(2005)
Life Sci
, vol.77
, pp. 361-371
-
-
Handl, H.1
Gillies, R.2
-
143
-
-
78650630819
-
Fluorescence polarization assays in small molecule screening
-
[CrossRef] [PubMed]
-
Lea, W.A.; Simeonov, A. Fluorescence polarization assays in small molecule screening. Expert Opin. Drug Discov. 2011, 6, 17–32. [CrossRef] [PubMed]
-
(2011)
Expert Opin. Drug Discov
, vol.6
, pp. 17-32
-
-
Lea, W.A.1
Simeonov, A.2
-
144
-
-
0015861774
-
Relationship between the inhibition constant (KI) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction
-
[PubMed]
-
Cheng, Y.; Prusoff, W.H. Relationship between the inhibition constant (KI) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction. Biochem. Pharmacol. 1973, 22, 3099–3108. [PubMed]
-
(1973)
Biochem. Pharmacol
, vol.22
, pp. 3099-3108
-
-
Cheng, Y.1
Prusoff, W.H.2
-
145
-
-
0023918636
-
An exact correction to the”Cheng-Prusoff” correction
-
[CrossRef] [PubMed]
-
Munson, P.J.; Rodbard, D. An exact correction to the”Cheng-Prusoff” correction. J. Recept. Res. 1988, 8, 533–546. [CrossRef] [PubMed]
-
(1988)
J. Recept. Res
, vol.8
, pp. 533-546
-
-
Munson, P.J.1
Rodbard, D.2
-
146
-
-
3242663695
-
Quantitative analysis of protein-protein interactions
-
[PubMed]
-
Wilkinson, K.D. Quantitative analysis of protein-protein interactions. Methods Mol. Biol. 2004, 261, 15–32. [PubMed]
-
(2004)
Methods Mol. Biol
, vol.261
, pp. 15-32
-
-
Wilkinson, K.D.1
-
147
-
-
79952177781
-
A structure-based benchmark for protein-protein binding affinity
-
[CrossRef] [PubMed]
-
Kastritis, P.L.; Moal, I.H.; Hwang, H.; Weng, Z.; Bates, P.A.; Bonvin, A.M.; Janin, J. A structure-based benchmark for protein-protein binding affinity. Protein Sci. 2011, 20, 482–491. [CrossRef] [PubMed]
-
(2011)
Protein Sci
, vol.20
, pp. 482-491
-
-
Kastritis, P.L.1
Moal, I.H.2
Hwang, H.3
Weng, Z.4
Bates, P.A.5
Bonvin, A.M.6
Janin, J.7
-
148
-
-
0032880709
-
Homogeneous fluorescence readouts for miniaturized high-throughput screening: Theory and practice
-
[CrossRef]
-
Pope, A.J.; Haupts, U.M.; Moore, K.J. Homogeneous fluorescence readouts for miniaturized high-throughput screening: Theory and practice. Drug Discov. Today 1999, 4, 350–362. [CrossRef]
-
(1999)
Drug Discov. Today
, vol.4
, pp. 350-362
-
-
Pope, A.J.1
Haupts, U.M.2
Moore, K.J.3
-
149
-
-
77955563247
-
A fluorescence polarization-based assay for the identification and evaluation of calmodulin antagonists
-
[CrossRef] [PubMed]
-
Arai, T.; Yatabe, M.; Furui, M.; Akatsuka, H.; Uehata, M.; Kamiyama, T. A fluorescence polarization-based assay for the identification and evaluation of calmodulin antagonists. Anal. Biochem. 2010, 405, 147–152. [CrossRef] [PubMed]
-
(2010)
Anal. Biochem
, vol.405
, pp. 147-152
-
-
Arai, T.1
Yatabe, M.2
Furui, M.3
Akatsuka, H.4
Uehata, M.5
Kamiyama, T.6
-
150
-
-
39149087067
-
Strategies and tactics for optimizing the Hit-to-Lead process and beyond—A computational chemistry perspective
-
[CrossRef] [PubMed]
-
Manly, C.J.; Chandrasekhar, J.; Ochterski, J.W.; Hammer, J.D.; Warfield, B.B. Strategies and tactics for optimizing the Hit-to-Lead process and beyond—A computational chemistry perspective. Drug Discov. Today 2008, 13, 99–109. [CrossRef] [PubMed]
-
(2008)
Drug Discov. Today
, vol.13
, pp. 99-109
-
-
Manly, C.J.1
Chandrasekhar, J.2
Ochterski, J.W.3
Hammer, J.D.4
Warfield, B.B.5
-
151
-
-
77957899529
-
Advances and challenges in protein-ligand docking
-
[CrossRef] [PubMed]
-
Huang, S.Y.; Zou, X. Advances and challenges in protein-ligand docking. Int. J. Mol. Sci. 2010, 11, 3016–3034. [CrossRef] [PubMed]
-
(2010)
Int. J. Mol. Sci
, vol.11
, pp. 3016-3034
-
-
Huang, S.Y.1
Zou, X.2
-
152
-
-
77955767207
-
Virtual screening in drug design and development
-
[CrossRef] [PubMed]
-
Sousa, S.F.; Cerqueira, N.M.; Fernandes, P.A.; Ramos, M.J. Virtual screening in drug design and development. Comb. Chem. High Throughput Screen. 2010, 13, 442–453. [CrossRef] [PubMed]
-
(2010)
Comb. Chem. High Throughput Screen
, vol.13
, pp. 442-453
-
-
Sousa, S.F.1
Cerqueira, N.M.2
Fernandes, P.A.3
Ramos, M.J.4
-
153
-
-
70349932423
-
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
-
[CrossRef] [PubMed]
-
Morris, G.M.; Huey, R.; Lindstrom, W.; Sanner, M.F.; Belew, R.K.; Goodsell, D.S.; Olson, A.J. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 2009, 30, 2785–2791. [CrossRef] [PubMed]
-
(2009)
J. Comput. Chem
, vol.30
, pp. 2785-2791
-
-
Morris, G.M.1
Huey, R.2
Lindstrom, W.3
Sanner, M.F.4
Belew, R.K.5
Goodsell, D.S.6
Olson, A.J.7
-
154
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
[CrossRef] [PubMed]
-
Jones, G.; Willett, P.; Glen, R.C.; Leach, A.R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727–748. [CrossRef] [PubMed]
-
(1997)
J. Mol. Biol
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
155
-
-
78649505687
-
Docking validation resources: Protein family and ligand flexibility experiments
-
[CrossRef] [PubMed]
-
Mukherjee, S.; Balius, T.E.; Rizzo, R.C. Docking validation resources: Protein family and ligand flexibility experiments. J. Chem. Inf. Model. 2010, 50, 1986–2000. [CrossRef] [PubMed]
-
(2010)
J. Chem. Inf. Model
, vol.50
, pp. 1986-2000
-
-
Mukherjee, S.1
Balius, T.E.2
Rizzo, R.C.3
-
156
-
-
0035025191
-
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
[CrossRef] [PubMed]
-
Ewing, T.J.; Makino, S.; Skillman, A.G.; Kuntz, I.D. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aided Mol. Des. 2001, 15, 411–428. [CrossRef] [PubMed]
-
(2001)
J. Comput. Aided Mol. Des
, vol.15
, pp. 411-428
-
-
Ewing, T.J.1
Makino, S.2
Skillman, A.G.3
Kuntz, I.D.4
-
157
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
[CrossRef] [PubMed]
-
Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470–489. [CrossRef] [PubMed]
-
(1996)
J. Mol. Biol
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
158
-
-
33750124980
-
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes
-
[CrossRef] [PubMed]
-
Friesner, R.A.; Murphy, R.B.; Repasky, M.P.; Frye, L.L.; Greenwood, J.R.; Halgren, T.A.; Sanschagrin, P.C.; Mainz, D.T. Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes. J. Med. Chem. 2006, 49, 6177–6196. [CrossRef] [PubMed]
-
(2006)
J. Med. Chem
, vol.49
, pp. 6177-6196
-
-
Friesner, R.A.1
Murphy, R.B.2
Repasky, M.P.3
Frye, L.L.4
Greenwood, J.R.5
Halgren, T.A.6
Sanschagrin, P.C.7
Mainz, D.T.8
-
159
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
[CrossRef] [PubMed]
-
Halperin, I.; Ma, B.; Wolfson, H.; Nussinov, R. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 2002, 47, 409–443. [CrossRef] [PubMed]
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
160
-
-
33748276474
-
Protein-ligand docking: Current status and future challenges
-
[CrossRef] [PubMed]
-
Sousa, S.F.; Fernandes, P.A.; Ramos, M.J. Protein-ligand docking: Current status and future challenges. Proteins 2006, 65, 15–26. [CrossRef] [PubMed]
-
(2006)
Proteins
, vol.65
, pp. 15-26
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
161
-
-
0038526303
-
ZDOCK: An initial-stage protein-docking algorithm
-
[CrossRef] [PubMed]
-
Chen, R.; Li, L.; Weng, Z. ZDOCK: An initial-stage protein-docking algorithm. Proteins 2003, 52, 80–87. [CrossRef] [PubMed]
-
(2003)
Proteins
, vol.52
, pp. 80-87
-
-
Chen, R.1
Li, L.2
Weng, Z.3
-
162
-
-
33750555073
-
An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials
-
[CrossRef] [PubMed]
-
Huang, S.Y.; Zou, X. An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. J. Comput. Chem. 2006, 27, 1866–1875. [CrossRef] [PubMed]
-
(2006)
J. Comput. Chem
, vol.27
, pp. 1866-1875
-
-
Huang, S.Y.1
Zou, X.2
-
163
-
-
33750574927
-
An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function
-
[CrossRef] [PubMed]
-
Huang, S.Y.; Zou, X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J. Comput. Chem. 2006, 27, 1876–1882. [CrossRef] [PubMed]
-
(2006)
J. Comput. Chem
, vol.27
, pp. 1876-1882
-
-
Huang, S.Y.1
Zou, X.2
-
164
-
-
84986518987
-
Molecular docking using shape descriptors
-
[CrossRef]
-
Shoichet, B.K.; Kuntz, I.D.; Bodian, D.L. Molecular docking using shape descriptors. J. Comput. Chem. 1992, 13, 380–397. [CrossRef]
-
(1992)
J. Comput. Chem
, vol.13
, pp. 380-397
-
-
Shoichet, B.K.1
Kuntz, I.D.2
Bodian, D.L.3
-
165
-
-
0028522982
-
Flexibases: A way to enhance the use of molecular docking methods
-
[CrossRef] [PubMed]
-
Kearsley, S.K.; Underwood, D.J.; Sheridan, R.P.; Miller, M.D. Flexibases: A way to enhance the use of molecular docking methods. J. Comput. Aided Mol. Des. 1994, 8, 565–582. [CrossRef] [PubMed]
-
(1994)
J. Comput. Aided Mol. Des
, vol.8
, pp. 565-582
-
-
Kearsley, S.K.1
Underwood, D.J.2
Sheridan, R.P.3
Miller, M.D.4
-
166
-
-
84986467005
-
Conformational analysis of flexible ligands in macromolecular receptor sites
-
[CrossRef]
-
Leach, A.R.; Kuntz, I.D. Conformational analysis of flexible ligands in macromolecular receptor sites. J. Comput. Chem. 1992, 13, 730–748. [CrossRef]
-
(1992)
J. Comput. Chem
, vol.13
, pp. 730-748
-
-
Leach, A.R.1
Kuntz, I.D.2
-
167
-
-
0026813925
-
The computer program LUDI: A new method for the de novo design of enzyme inhibitors
-
[CrossRef] [PubMed]
-
Böhm, H.J. The computer program LUDI: A new method for the de novo design of enzyme inhibitors. J. Comput. Aided Mol. Des. 1992, 6, 61–78. [CrossRef] [PubMed]
-
(1992)
J. Comput. Aided Mol. Des
, vol.6
, pp. 61-78
-
-
Böhm, H.J.1
-
168
-
-
0028522365
-
A fast and efficient method to generate biologically relevant conformations
-
[CrossRef] [PubMed]
-
Klebe, G.; Mietzner, T. A fast and efficient method to generate biologically relevant conformations. J. Comput. Aided Mol. Des. 1994, 8, 583–606. [CrossRef] [PubMed]
-
(1994)
J. Comput. Aided Mol. Des
, vol.8
, pp. 583-606
-
-
Klebe, G.1
Mietzner, T.2
-
169
-
-
23844444239
-
Hierarchical docking of databases of multiple ligand conformations
-
[CrossRef] [PubMed]
-
Lorber, D.M.; Shoichet, B.K. Hierarchical docking of databases of multiple ligand conformations. Curr. Top. Med. Chem. 2005, 5, 739–749. [CrossRef] [PubMed]
-
(2005)
Curr. Top. Med. Chem
, vol.5
, pp. 739-749
-
-
Lorber, D.M.1
Shoichet, B.K.2
-
170
-
-
40749129010
-
Preference of small molecules for local minimum conformations when binding to proteins
-
[CrossRef] [PubMed]
-
Wang, Q.; Pang, Y.P. Preference of small molecules for local minimum conformations when binding to proteins. PLoS ONE 2007, 2, e820. [CrossRef] [PubMed]
-
(2007)
Plos ONE
, vol.2
-
-
Wang, Q.1
Pang, Y.P.2
-
171
-
-
41949132916
-
Flexible ligand docking to multiple receptor conformations: A practical alternative
-
[CrossRef] [PubMed]
-
Totrov, M.; Abagyan, R. Flexible ligand docking to multiple receptor conformations: A practical alternative. Curr. Opin. Struct. Biol. 2008, 18, 178–184. [CrossRef] [PubMed]
-
(2008)
Curr. Opin. Struct. Biol
, vol.18
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
172
-
-
0002833057
-
Docking small ligands in flexible binding sites
-
[CrossRef]
-
Apostolakis, J.; Plückthun, A.; Caflisch, A. Docking small ligands in flexible binding sites. J. Comput. Chem. 1998, 19, 21–37. [CrossRef]
-
(1998)
J. Comput. Chem
, vol.19
, pp. 21-37
-
-
Apostolakis, J.1
Plückthun, A.2
Caflisch, A.3
-
173
-
-
0029283717
-
Flexible ligand docking using a genetic algorithm
-
Dixon, J.S.; Oshiro, C.M. Flexible ligand docking using a genetic algorithm. J. Comput. Aided Mol. Des. 1995, 9, 113–130.
-
(1995)
J. Comput. Aided Mol. Des
, vol.9
, pp. 113-130
-
-
Dixon, J.S.1
Oshiro, C.M.2
-
174
-
-
0026589733
-
The dead end eliminatino theorem and its use in protein side-chain positioning
-
[CrossRef] [PubMed]
-
Desmet, J.; Maeyer, M.D.; Hazes, B.; Lasters, I. The dead end eliminatino theorem and its use in protein side-chain positioning. Nature 1992, 356, 539–542. [CrossRef] [PubMed]
-
(1992)
Nature
, vol.356
, pp. 539-542
-
-
Desmet, J.1
Maeyer, M.D.2
Hazes, B.3
Lasters, I.4
-
175
-
-
59849126340
-
Docking and scoring with alternative side-chain conformations
-
[CrossRef] [PubMed]
-
Hartmann, C.; Antes, I.; Lengauer, T. Docking and scoring with alternative side-chain conformations. Proteins 2009, 74, 712–726. [CrossRef] [PubMed]
-
(2009)
Proteins
, vol.74
, pp. 712-726
-
-
Hartmann, C.1
Antes, I.2
Lengauer, T.3
-
176
-
-
77950207644
-
Tackling the challenges posed by target flexibility in drug design
-
[CrossRef] [PubMed]
-
Beier, C.; Zacharias, M. Tackling the challenges posed by target flexibility in drug design. Exp. Opin. Drug Discov. 2010, 5, 347–359. [CrossRef] [PubMed]
-
(2010)
Exp. Opin. Drug Discov
, vol.5
, pp. 347-359
-
-
Beier, C.1
Zacharias, M.2
-
177
-
-
33244490820
-
Physics-based scoring of protein-ligand complexes: Enrichment of known inhibitors in large-scale virtual screening
-
[CrossRef] [PubMed]
-
Huang, N.; Kalyanaraman, C.; Irwin, J.J.; Jacobson, M.P. Physics-based scoring of protein-ligand complexes: Enrichment of known inhibitors in large-scale virtual screening. J. Chem. Inf. Model. 2006, 46, 243–253. [CrossRef] [PubMed]
-
(2006)
J. Chem. Inf. Model
, vol.46
, pp. 243-253
-
-
Huang, N.1
Kalyanaraman, C.2
Irwin, J.J.3
Jacobson, M.P.4
-
178
-
-
0037080244
-
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
-
[CrossRef] [PubMed]
-
Rocchia, W.; Sridharan, S.; Nicholls, A.; Alexov, E.; Chiabrera, A.; Honig, B. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. J. Comput. Chem. 2002, 23, 128–137. [CrossRef] [PubMed]
-
(2002)
J. Comput. Chem
, vol.23
, pp. 128-137
-
-
Rocchia, W.1
Sridharan, S.2
Nicholls, A.3
Alexov, E.4
Chiabrera, A.5
Honig, B.6
-
179
-
-
0034811498
-
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
-
[CrossRef] [PubMed]
-
Wang, J.; Morin, P.; Wang, W.; Kollman, P.A. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J. Am. Chem. Soc. 2001, 123, 5221–5230. [CrossRef] [PubMed]
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 5221-5230
-
-
Wang, J.1
Morin, P.2
Wang, W.3
Kollman, P.A.4
-
180
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
[CrossRef]
-
Still, W.C.; Tempczyk, A.; Hawley, R.C.; Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 1990, 112, 6127–6129. [CrossRef]
-
(1990)
J. Am. Chem. Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
181
-
-
0002636134
-
Pairwise solute descreening of solute charges from a dielectric medium
-
[CrossRef]
-
Hawkins, G.D.; Cramer, C.J.; Truhlar, D.G. Pairwise solute descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 1995, 246, 122–129. [CrossRef]
-
(1995)
Chem. Phys. Lett
, vol.246
, pp. 122-129
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
182
-
-
0031226772
-
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
[CrossRef] [PubMed]
-
Eldridge, M.D.; Murray, C.W.; Auton, T.R.; Paolini, G.V.; Mee, R.P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput. Aided Mol. Des. 1997, 11, 425–445. [CrossRef] [PubMed]
-
(1997)
J. Comput. Aided Mol. Des
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
183
-
-
77957898063
-
Scoring functions and their evaluation methods for protein-ligand docking: Recent advances and future directions
-
[CrossRef] [PubMed]
-
Huang, S.Y.; Grinter, S.Z.; Zou, X. Scoring functions and their evaluation methods for protein-ligand docking: Recent advances and future directions. Phys. Chem. Chem. Phys. 2010, 12, 12899–12908. [CrossRef] [PubMed]
-
(2010)
Phys. Chem. Chem. Phys
, vol.12
, pp. 12899-12908
-
-
Huang, S.Y.1
Grinter, S.Z.2
Zou, X.3
-
184
-
-
33749242403
-
PMF scoring revisited
-
[CrossRef] [PubMed]
-
Muegge, I. PMF scoring revisited. J. Med. Chem. 2006, 49, 5895–5902. [CrossRef] [PubMed]
-
(2006)
J. Med. Chem
, vol.49
, pp. 5895-5902
-
-
Muegge, I.1
-
185
-
-
0033576680
-
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
-
[CrossRef] [PubMed]
-
Charifson, P.S.; Corkery, J.J.; Murcko, M.A.; Walters, W.P. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem. 1999, 42, 5100–5109. [CrossRef] [PubMed]
-
(1999)
J. Med. Chem
, vol.42
, pp. 5100-5109
-
-
Charifson, P.S.1
Corkery, J.J.2
Murcko, M.A.3
Walters, W.P.4
-
186
-
-
0033670301
-
Deciphering common failures in molecular docking of ligand-protein complexes
-
[CrossRef] [PubMed]
-
Verkhivker, G.M.; Bouzida, D.; Gehlhaar, D.K.; Rejto, P.A.; Arthurs, S.; Colson, A.B.; Freer, S.T.; Larson, V.; Luty, B.A.; Marrone, T.; et al. Deciphering common failures in molecular docking of ligand-protein complexes. J. Comput. Aided Mol. Des. 2000, 14, 731–751. [CrossRef] [PubMed]
-
(2000)
J. Comput. Aided Mol. Des
, vol.14
, pp. 731-751
-
-
Verkhivker, G.M.1
Bouzida, D.2
Gehlhaar, D.K.3
Rejto, P.A.4
Arthurs, S.5
Colson, A.B.6
Freer, S.T.7
Larson, V.8
Luty, B.A.9
Marrone, T.10
-
187
-
-
79960998152
-
Free energy calculations of protein-ligand interactions
-
[CrossRef] [PubMed]
-
De Ruiter, A.; Oostenbrink, C. Free energy calculations of protein-ligand interactions. Curr. Opin. Chem. Biol. 2011, 15, 547–552. [CrossRef] [PubMed]
-
(2011)
Curr. Opin. Chem. Biol
, vol.15
, pp. 547-552
-
-
De Ruiter, A.1
Oostenbrink, C.2
-
188
-
-
84904130280
-
Practical aspects of free-energy calculations: A review
-
[CrossRef] [PubMed]
-
Hansen, N.; van Gunsteren, W.F. Practical aspects of free-energy calculations: A review. J. Chem. Theory Comput. 2014, 10, 2632–2647. [CrossRef] [PubMed]
-
(2014)
J. Chem. Theory Comput
, vol.10
, pp. 2632-2647
-
-
Hansen, N.1
Van Gunsteren, W.F.2
-
189
-
-
34548703110
-
Chapter 4 alchemical free energy calculations: Ready for prime Time?
-
Spellmeyer, D.C., Wheeler, R., Eds.; Elsevier: Amsterdam, The Netherlands, 2007
-
Shirts, M.R.; Mobley, D.L.; Chodera, J.D. Chapter 4 alchemical free energy calculations: Ready for prime Time? In Annual Reports in Computational Chemistry; Spellmeyer, D.C., Wheeler, R., Eds.; Elsevier: Amsterdam, The Netherlands, 2007; Volume 3, pp. 41–59.
-
Annual Reports in Computational Chemistry
, vol.3
, pp. 41-59
-
-
Shirts, M.R.1
Mobley, D.L.2
Chodera, J.D.3
-
190
-
-
0242696091
-
Free energy calculations and ligand binding
-
Brandsdal, B.O.; Österberg, F.; Almlöf, M.; Feierberg, I.; Luzhkov, V.B.; Åqvist, J. Free energy calculations and ligand binding. Adv. Prot. Chem. 2003, 66, 123–158.
-
(2003)
Adv. Prot. Chem
, vol.66
, pp. 123-158
-
-
Brandsdal, B.O.1
Österberg, F.2
Almlöf, M.3
Feierberg, I.4
Luzhkov, V.B.5
Åqvist, J.6
-
191
-
-
77952390528
-
Basic ingredients of free energy calculations: A review
-
[CrossRef] [PubMed]
-
Christ, C.D.; Mark, A.E.; van Gunsteren, W.F. Basic ingredients of free energy calculations: A review. J. Comput. Chem. 2010, 31, 1569–1582. [CrossRef] [PubMed]
-
(2010)
J. Comput. Chem
, vol.31
, pp. 1569-1582
-
-
Christ, C.D.1
Mark, A.E.2
Van Gunsteren, W.F.3
-
192
-
-
79953075221
-
Alchemical free energy methods for drug discovery: Progress and challenges
-
[CrossRef] [PubMed]
-
Chodera, J.D.; Mobley, D.L.; Shirts, M.R.; Dixon, R.W.; Branson, K.; Pande, V.S. Alchemical free energy methods for drug discovery: Progress and challenges. Curr. Opin. Struct. Biol. 2011, 21, 150–160. [CrossRef] [PubMed]
-
(2011)
Curr. Opin. Struct. Biol
, vol.21
, pp. 150-160
-
-
Chodera, J.D.1
Mobley, D.L.2
Shirts, M.R.3
Dixon, R.W.4
Branson, K.5
Pande, V.S.6
-
193
-
-
0021582448
-
Ligand-receptor interactions
-
[CrossRef]
-
Tembe, B.L.; McCammon, J.A. Ligand-receptor interactions. Comput. Chem. 1984, 8, 281–283. [CrossRef]
-
(1984)
Comput. Chem
, vol.8
, pp. 281-283
-
-
Tembe, B.L.1
McCammon, J.A.2
-
194
-
-
65249124122
-
Computations of standard binding free energies with molecular dynamics simulations
-
[CrossRef] [PubMed]
-
Deng, Y.; Roux, B. Computations of standard binding free energies with molecular dynamics simulations. J. Phys. Chem. B 2009, 113, 2234–2246. [CrossRef] [PubMed]
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 2234-2246
-
-
Deng, Y.1
Roux, B.2
-
195
-
-
76649086691
-
Alchemical free energy simulations for biological complexes: Powerful but temperamental
-
[CrossRef] [PubMed]
-
Aleksandrov, A.; Thompson, D.; Simonson, T. Alchemical free energy simulations for biological complexes: Powerful but temperamental. J. Mol. Recognit. 2009, 23, 117–127. [CrossRef] [PubMed]
-
(2009)
J. Mol. Recognit
, vol.23
, pp. 117-127
-
-
Aleksandrov, A.1
Thompson, D.2
Simonson, T.3
-
196
-
-
36549092795
-
Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water
-
[CrossRef]
-
Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water. J. Chem. Phys. 1988, 89, 3742–3746. [CrossRef]
-
(1988)
J. Chem. Phys
, vol.89
, pp. 3742-3746
-
-
Jorgensen, W.L.1
Buckner, J.K.2
Boudon, S.3
Tirado-Rives, J.4
-
197
-
-
36849122972
-
High temperature equation of state by a perturbation method. I. Nonpolar gases
-
Zwanzig, R.W. High temperature equation of state by a perturbation method. I. Nonpolar gases. J. Chem. Phys. 1954, 22, 1420–1426.
-
(1954)
J. Chem. Phys
, vol.22
, pp. 1420-1426
-
-
Zwanzig, R.W.1
-
198
-
-
33646471468
-
Statistical mechanics of fluid mixtures
-
[CrossRef]
-
Kirkwood, J.G. Statistical mechanics of fluid mixtures. J. Chem. Phys. 1935, 3, 300–313. [CrossRef]
-
(1935)
J. Chem. Phys
, vol.3
, pp. 300-313
-
-
Kirkwood, J.G.1
-
199
-
-
5244304444
-
Efficient estimation of free energy differences from Monte Carlo data
-
[CrossRef]
-
Bennett, C.H. Efficient estimation of free energy differences from Monte Carlo data. J. Comput. Phys. 1976, 22, 245–268. [CrossRef]
-
(1976)
J. Comput. Phys
, vol.22
, pp. 245-268
-
-
Bennett, C.H.1
-
200
-
-
42149194240
-
Adaptive biasing force method for scalar and vector free energy calculations
-
[CrossRef] [PubMed]
-
Darve, E.; Rodríguez-Gómez, D.; Pohorille, A. Adaptive biasing force method for scalar and vector free energy calculations. J. Chem. Phys. 2008, 128, 144120. [CrossRef] [PubMed]
-
(2008)
J. Chem. Phys
, vol.128
-
-
Darve, E.1
Rodríguez-Gómez, D.2
Pohorille, A.3
-
201
-
-
33745762636
-
A temperature-accelerated method for sampling free energy and determining reaction pathways in rare events simulations
-
[CrossRef]
-
Maragliano, L.; Vanden-Eijnden, E. A temperature-accelerated method for sampling free energy and determining reaction pathways in rare events simulations. Chem. Phys. Lett. 2006, 426, 168–175. [CrossRef]
-
(2006)
Chem. Phys. Lett
, vol.426
, pp. 168-175
-
-
Maragliano, L.1
Vanden-Eijnden, E.2
-
202
-
-
79959236502
-
Use of umbrella sampling to calculate the entrance/exit pathway for Z-Pro-Prolinal inhibitor in prolyl oligopeptidase
-
[CrossRef] [PubMed]
-
St-Pierre, J.-F.; Karttunen, M.; Mousseau, N.; Róg, T.; Bunker, A. Use of umbrella sampling to calculate the entrance/exit pathway for Z-Pro-Prolinal inhibitor in prolyl oligopeptidase. J. Chem. Theory Comput. 2011, 7, 1583–1594. [CrossRef] [PubMed]
-
(2011)
J. Chem. Theory Comput
, vol.7
, pp. 1583-1594
-
-
St-Pierre, J.-F.1
Karttunen, M.2
Mousseau, N.3
Róg, T.4
Bunker, A.5
-
203
-
-
0036790894
-
Escaping free-energy minima
-
[CrossRef] [PubMed]
-
Laio, A.; Parrinello, M. Escaping free-energy minima. Proc. Natl. Acad. Sci. USA 2002, 99, 12562–12566. [CrossRef] [PubMed]
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12562-12566
-
-
Laio, A.1
Parrinello, M.2
-
204
-
-
58149159707
-
Replica-exchange accelerated molecular dynamics (REXAMD) applied to thermodynamic integration
-
[CrossRef] [PubMed]
-
Fajer, M.; Hamelberg, D.; McCammon, J.A. Replica-exchange accelerated molecular dynamics (REXAMD) applied to thermodynamic integration. J. Chem. Theory Comput. 2008, 4, 1565–1569. [CrossRef] [PubMed]
-
(2008)
J. Chem. Theory Comput
, vol.4
, pp. 1565-1569
-
-
Fajer, M.1
Hamelberg, D.2
McCammon, J.A.3
-
205
-
-
69549138254
-
Protein-ligand binding free energy calculation by the smooth reaction path generation (SRPG) method
-
[CrossRef] [PubMed]
-
Fukunishi, Y.; Mitomo, D.; Nakamura, H. Protein-ligand binding free energy calculation by the smooth reaction path generation (SRPG) method. J. Chem. Inf. Model. 2009, 49, 1944–1951. [CrossRef] [PubMed]
-
(2009)
J. Chem. Inf. Model
, vol.49
, pp. 1944-1951
-
-
Fukunishi, Y.1
Mitomo, D.2
Nakamura, H.3
-
206
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: A critical review
-
[CrossRef]
-
Gilson, M.K.; Given, J.A.; Bush, B.L.; McCammon, J.A. The statistical-thermodynamic basis for computation of binding affinities: A critical review. Biophys. J. 1997, 72, 1047–1769. [CrossRef]
-
(1997)
Biophys. J
, vol.72
, pp. 1047-1769
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
207
-
-
85005687495
-
The free energy of xenon binding to myoglobin from molecular dynamics simulation
-
[CrossRef]
-
Hermans, J.; Shankar, S. The free energy of xenon binding to myoglobin from molecular dynamics simulation. Isr. J. Chem. 1986, 27, 225–227. [CrossRef]
-
(1986)
Isr. J. Chem
, vol.27
, pp. 225-227
-
-
Hermans, J.1
Shankar, S.2
-
208
-
-
18744372751
-
Calculation of absolute protein-ligand binding free energy from computer simulations
-
[CrossRef] [PubMed]
-
Woo, H.J.; Roux, B. Calculation of absolute protein-ligand binding free energy from computer simulations. Proc. Natl. Acad. Sci. USA 2005, 102, 6825–6830. [CrossRef] [PubMed]
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 6825-6830
-
-
Woo, H.J.1
Roux, B.2
-
209
-
-
4243754128
-
Nonequilibrium equality for free energy differences
-
[CrossRef]
-
Jarzynski, C. Nonequilibrium equality for free energy differences. Phys. Rev. Lett. 1997, 78, 2690–2693. [CrossRef]
-
(1997)
Phys. Rev. Lett
, vol.78
, pp. 2690-2693
-
-
Jarzynski, C.1
-
210
-
-
57449107299
-
Protein-ligand binding affinity by nonequilibrium free energy methods
-
[CrossRef] [PubMed]
-
Cossins, B.P.; Foucher, S.; Edge, C.M.; Essex, J.W. Protein-ligand binding affinity by nonequilibrium free energy methods. J. Phys. Chem. B 2008, 112, 14985–14992. [CrossRef] [PubMed]
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 14985-14992
-
-
Cossins, B.P.1
Foucher, S.2
Edge, C.M.3
Essex, J.W.4
-
211
-
-
56549110295
-
Polyelectrolyte adsorption on a charged surface. Free energy calculation from Monte Carlo simulations using Jarzynski equality
-
[CrossRef]
-
Narambuena, C.F.; Beltramo, D.M.; Leiva, E.P.M. Polyelectrolyte adsorption on a charged surface. Free energy calculation from Monte Carlo simulations using Jarzynski equality. Macromolecules 2008, 41, 8267–8274. [CrossRef]
-
(2008)
Macromolecules
, vol.41
, pp. 8267-8274
-
-
Narambuena, C.F.1
Beltramo, D.M.2
Leiva, E.P.M.3
-
212
-
-
78751518467
-
Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes: Theory and application to free energies, moments, and thermodynamic length in singlemolecule pulling experiments
-
[CrossRef] [PubMed]
-
Minh, D.D.L.; Chodera, J.D. Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes: Theory and application to free energies, moments, and thermodynamic length in singlemolecule pulling experiments. J. Chem. Phys. 2011, 134, 024111. [CrossRef] [PubMed]
-
(2011)
J. Chem. Phys
, vol.134
-
-
Minh, D.D.L.1
Chodera, J.D.2
-
213
-
-
66349099077
-
Assessment of nonequilibrium free energy methods
-
[CrossRef] [PubMed]
-
Cossins, B.P.; Foucher, S.; Edge, C.M.; Essex, J.W. Assessment of nonequilibrium free energy methods. J. Phys. Chem. B 2009, 113, 5508–5519. [CrossRef] [PubMed]
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 5508-5519
-
-
Cossins, B.P.1
Foucher, S.2
Edge, C.M.3
Essex, J.W.4
-
214
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
[CrossRef] [PubMed]
-
Åqvist, J.; Medina, C.; Samuelsson, J.E. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 1994, 7, 385–391. [CrossRef] [PubMed]
-
(1994)
Protein Eng
, vol.7
, pp. 385-391
-
-
Åqvist, J.1
Medina, C.2
Samuelsson, J.E.3
-
215
-
-
33745799052
-
Continuum solvation models in the linear interaction energy method
-
[CrossRef] [PubMed]
-
Carlsson, J.; Ander, M.; Nervall, M.; Åqvist, J. Continuum solvation models in the linear interaction energy method. J. Phys. Chem. B 2006, 110, 12034–12041. [CrossRef] [PubMed]
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 12034-12041
-
-
Carlsson, J.1
Ander, M.2
Nervall, M.3
Åqvist, J.4
-
216
-
-
0033557303
-
What determines the van der Waals coefficient beta in the LIE (Linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?
-
[CrossRef]
-
Wang, W.; Wang, J.; Kollman, P.A. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Proteins 1999, 34, 395–402. [CrossRef]
-
(1999)
Proteins
, vol.34
, pp. 395-402
-
-
Wang, W.1
Wang, J.2
Kollman, P.A.3
-
217
-
-
78149423058
-
New parameterization approaches of the LIE method to improve free energy calculations of PlmII-inhibitors complexes
-
[CrossRef] [PubMed]
-
Valiente, P.A.; Gil, A.; Batista, P.R.; Caffarena, E.R.; Pons, T.; Pascutti, P.G. New parameterization approaches of the LIE method to improve free energy calculations of PlmII-inhibitors complexes. J. Comput. Chem. 2010, 31, 2723–2734. [CrossRef] [PubMed]
-
(2010)
J. Comput. Chem
, vol.31
, pp. 2723-2734
-
-
Valiente, P.A.1
Gil, A.2
Batista, P.R.3
Caffarena, E.R.4
Pons, T.5
Pascutti, P.G.6
-
218
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
-
[CrossRef]
-
Srinivasan, J.; Cheatham, T.E.; Cieplak, P.; Kollman, P.A.; Case, D.A. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J. Am. Chem. Soc. 1998, 120, 9401–9409. [CrossRef]
-
(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.A.5
-
219
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
[CrossRef] [PubMed]
-
Kollman, P.A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; et al. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33, 889–897. [CrossRef] [PubMed]
-
(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
-
220
-
-
0347949637
-
Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
-
[CrossRef]
-
Swanson, J.M.; Henchman, R.H.; McCammon, J.A. Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys. J. 2004, 86, 67–74. [CrossRef]
-
(2004)
Biophys. J
, vol.86
, pp. 67-74
-
-
Swanson, J.M.1
Henchman, R.H.2
McCammon, J.A.3
-
221
-
-
33745405015
-
High-throughput calculation of protein-ligand binding affinities: Modification and adaptation of the MM-PBSA protocol to enterprise grid computing
-
[CrossRef] [PubMed]
-
Brown, S.P.; Muchmore, S.W. High-throughput calculation of protein-ligand binding affinities: Modification and adaptation of the MM-PBSA protocol to enterprise grid computing. J. Chem. Inf. Model. 2006, 46, 999–1005. [CrossRef] [PubMed]
-
(2006)
J. Chem. Inf. Model
, vol.46
, pp. 999-1005
-
-
Brown, S.P.1
Muchmore, S.W.2
-
222
-
-
79952588669
-
Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations
-
[CrossRef] [PubMed]
-
Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J. Chem. Inf. Model. 2011, 51, 69–82. [CrossRef] [PubMed]
-
(2011)
J. Chem. Inf. Model
, vol.51
, pp. 69-82
-
-
Hou, T.1
Wang, J.2
Li, Y.3
Wang, W.4
-
223
-
-
0000127140
-
Method for estimating the configurational entropy of macromolecules
-
[CrossRef]
-
Karplus, M.; Kushick, J. Method for estimating the configurational entropy of macromolecules. Macromolecules 1981, 14, 325–332. [CrossRef]
-
(1981)
Macromolecules
, vol.14
, pp. 325-332
-
-
Karplus, M.1
Kushick, J.2
-
224
-
-
0347602124
-
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
-
[CrossRef] [PubMed]
-
Gohlke, H.; Case, D.A. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J. Comput. Chem. 2004, 25, 238–250. [CrossRef] [PubMed]
-
(2004)
J. Comput. Chem
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
225
-
-
84928313330
-
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
-
[CrossRef] [PubMed]
-
Genheden, S.; Ryde, U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin. Drug Discov. 2015, 10, 449–461. [CrossRef] [PubMed]
-
(2015)
Expert Opin. Drug Discov
, vol.10
, pp. 449-461
-
-
Genheden, S.1
Ryde, U.2
|