-
1
-
-
84857421328
-
Hydration Shells of Molecules in Molecular Association: A Mechanism for Biomolecular Recognition
-
Lim, V. I.; Curran, J. F.; Garber, M. B. Hydration Shells of Molecules in Molecular Association: A Mechanism for Biomolecular Recognition J. Theor. Biol. 2012, 301, 42-48 10.1016/j.jtbi.2012.02.008
-
(2012)
J. Theor. Biol.
, vol.301
, pp. 42-48
-
-
Lim, V.I.1
Curran, J.F.2
Garber, M.B.3
-
2
-
-
84916623121
-
Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase
-
Mondal, J.; Friesner, R. A.; Berne, B. J. Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase J. Chem. Theory Comput. 2014, 10, 5696-5705 10.1021/ct500584n
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 5696-5705
-
-
Mondal, J.1
Friesner, R.A.2
Berne, B.J.3
-
3
-
-
0008863560
-
Some Factors in the Interpretation of Protein Denaturation
-
Kauzmann, W. Some Factors in the Interpretation of Protein Denaturation Adv. Protein Chem. 1959, 14, 1-63 10.1016/S0065-3233(08)60608-7
-
(1959)
Adv. Protein Chem.
, vol.14
, pp. 1-63
-
-
Kauzmann, W.1
-
4
-
-
67449084506
-
Dewetting and Hydrophobic Interaction in Physical and Biological Systems
-
Berne, B. J.; Weeks, J. D.; Zhou, R. Dewetting and Hydrophobic Interaction in Physical and Biological Systems Annu. Rev. Phys. Chem. 2009, 60, 85-103 10.1146/annurev.physchem.58.032806.104445
-
(2009)
Annu. Rev. Phys. Chem.
, vol.60
, pp. 85-103
-
-
Berne, B.J.1
Weeks, J.D.2
Zhou, R.3
-
5
-
-
34447108978
-
Water, Water Everywhere - Except Where It Matters?
-
Homans, S. W. Water, Water Everywhere-except Where It Matters? Drug Discovery Today 2007, 12, 534-539 10.1016/j.drudis.2007.05.004
-
(2007)
Drug Discovery Today
, vol.12
, pp. 534-539
-
-
Homans, S.W.1
-
6
-
-
10744231573
-
Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2-Methoxy-3-Isobutylpyrazine to the Major Urinary Protein
-
Bingham, R. J.; Findlay, J. B. C.; Hsieh, S.-Y.; Kalverda, A. P.; Kjellberg, A.; Perazzolo, C.; Phillips, S. E. V; Seshadri, K.; Trinh, C. H.; Turnbull, W. B.; Bodenhausen, G.; Homans, S. W. Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2-Methoxy-3-Isobutylpyrazine to the Major Urinary Protein J. Am. Chem. Soc. 2004, 126, 1675-1681 10.1021/ja038461i
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 1675-1681
-
-
Bingham, R.J.1
Findlay, J.B.C.2
Hsieh, S.-Y.3
Kalverda, A.P.4
Kjellberg, A.5
Perazzolo, C.6
Phillips, S.E.V.7
Seshadri, K.8
Trinh, C.H.9
Turnbull, W.B.10
Bodenhausen, G.11
Homans, S.W.12
-
7
-
-
81055130316
-
Mechanism of the Hydrophobic Effect in the Biomolecular Recognition of Arylsulfonamides by Carbonic Anhydrase
-
Snyder, P. W.; Mecinovic, J.; Moustakas, D. T.; Thomas, S. W.; Harder, M.; Mack, E. T.; Lockett, M. R.; Héroux, A.; Sherman, W.; Whitesides, G. M. Mechanism of the Hydrophobic Effect in the Biomolecular Recognition of Arylsulfonamides by Carbonic Anhydrase Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 17889-17894 10.1073/pnas.1114107108
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 17889-17894
-
-
Snyder, P.W.1
Mecinovic, J.2
Moustakas, D.T.3
Thomas, S.W.4
Harder, M.5
Mack, E.T.6
Lockett, M.R.7
Héroux, A.8
Sherman, W.9
Whitesides, G.M.10
-
8
-
-
77956583186
-
How Can Hydrophobic Association Be Enthalpy Driven?
-
Setny, P.; Baron, R.; McCammon, J. A. How Can Hydrophobic Association Be Enthalpy Driven? J. Chem. Theory Comput. 2010, 6, 2866-2871 10.1021/ct1003077
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2866-2871
-
-
Setny, P.1
Baron, R.2
McCammon, J.A.3
-
9
-
-
84985995059
-
Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces
-
Haider, K.; Wickstrom, L.; Ramsey, S.; Gilson, M. K.; Kurtzman, T. Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces J. Phys. Chem. B 2016, 120, 8743-8756 10.1021/acs.jpcb.6b01094
-
(2016)
J. Phys. Chem. B
, vol.120
, pp. 8743-8756
-
-
Haider, K.1
Wickstrom, L.2
Ramsey, S.3
Gilson, M.K.4
Kurtzman, T.5
-
10
-
-
84873351927
-
Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin
-
Biela, A.; Nasief, N. N.; Betz, M.; Heine, A.; Hangauer, D.; Klebe, G. Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin Angew. Chem., Int. Ed. 2013, 52, 1822-1828 10.1002/anie.201208561
-
(2013)
Angew. Chem., Int. Ed.
, vol.52
, pp. 1822-1828
-
-
Biela, A.1
Nasief, N.N.2
Betz, M.3
Heine, A.4
Hangauer, D.5
Klebe, G.6
-
11
-
-
84898006931
-
Methyl, Ethyl, Propyl, Butyl: Futile but Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors
-
Krimmer, S. G.; Betz, M.; Heine, A.; Klebe, G. Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors ChemMedChem 2014, 9, 833-846 10.1002/cmdc.201400013
-
(2014)
ChemMedChem
, vol.9
, pp. 833-846
-
-
Krimmer, S.G.1
Betz, M.2
Heine, A.3
Klebe, G.4
-
12
-
-
85003422164
-
Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands
-
Krimmer, S. G.; Cramer, J.; Betz, M.; Fridh, V.; Karlsson, R.; Heine, A.; Klebe, G. Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands J. Med. Chem. 2016, 59, 10530-10548 10.1021/acs.jmedchem.6b00998
-
(2016)
J. Med. Chem.
, vol.59
, pp. 10530-10548
-
-
Krimmer, S.G.1
Cramer, J.2
Betz, M.3
Fridh, V.4
Karlsson, R.5
Heine, A.6
Klebe, G.7
-
13
-
-
84867342383
-
Water Mediated Ligand Functional Group Cooperativity: The Contribution of a Methyl Group to Binding Affinity Is Enhanced by a COO- Group Through Changes in the Structure and Thermodynamics of the Hydration Waters of Ligand-Thermolysin Complexes
-
Nasief, N. N.; Tan, H.; Kong, J.; Hangauer, D. Water Mediated Ligand Functional Group Cooperativity: The Contribution of a Methyl Group to Binding Affinity Is Enhanced by a COO- Group Through Changes in the Structure and Thermodynamics of the Hydration Waters of Ligand-Thermolysin Complexes J. Med. Chem. 2012, 55, 8283-8302 10.1021/jm300472k
-
(2012)
J. Med. Chem.
, vol.55
, pp. 8283-8302
-
-
Nasief, N.N.1
Tan, H.2
Kong, J.3
Hangauer, D.4
-
14
-
-
84897471228
-
Influence of Neighboring Groups on the Thermodynamics of Hydrophobic Binding: An Added Complex Facet to the Hydrophobic Effect
-
Nasief, N. N.; Hangauer, D. Influence of Neighboring Groups on the Thermodynamics of Hydrophobic Binding: An Added Complex Facet to the Hydrophobic Effect J. Med. Chem. 2014, 57, 2315-2333 10.1021/jm401609a
-
(2014)
J. Med. Chem.
, vol.57
, pp. 2315-2333
-
-
Nasief, N.N.1
Hangauer, D.2
-
15
-
-
84900498772
-
Is It the Shape of the Cavity, or the Shape of the Water in the Cavity?
-
Snyder, P. W.; Lockett, M. R.; Moustakas, D. T.; Whitesides, G. M. Is It the Shape of the Cavity, or the Shape of the Water in the Cavity? Eur. Phys. J.: Spec. Top. 2014, 223, 853-891 10.1140/epjst/e2013-01818-y
-
(2014)
Eur. Phys. J.: Spec. Top.
, vol.223
, pp. 853-891
-
-
Snyder, P.W.1
Lockett, M.R.2
Moustakas, D.T.3
Whitesides, G.M.4
-
16
-
-
84940501243
-
Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip?
-
Geschwindner, S.; Ulander, J.; Johansson, P. Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip? J. Med. Chem. 2015, 58, 6321-6335 10.1021/jm501511f
-
(2015)
J. Med. Chem.
, vol.58
, pp. 6321-6335
-
-
Geschwindner, S.1
Ulander, J.2
Johansson, P.3
-
17
-
-
56549131177
-
The Thermodynamics of Protein-Ligand Interaction and Solvation: Insights for Ligand Design
-
Olsson, T. S. G.; Williams, M. A.; Pitt, W. R.; Ladbury, J. E. The Thermodynamics of Protein-Ligand Interaction and Solvation: Insights for Ligand Design J. Mol. Biol. 2008, 384, 1002-1017 10.1016/j.jmb.2008.09.073
-
(2008)
J. Mol. Biol.
, vol.384
, pp. 1002-1017
-
-
Olsson, T.S.G.1
Williams, M.A.2
Pitt, W.R.3
Ladbury, J.E.4
-
18
-
-
84944352692
-
Thermodynamics of Protein-Ligand Interactions as a Reference for Computational Analysis: How to Assess Accuracy, Reliability and Relevance of Experimental Data
-
Krimmer, S. G.; Klebe, G. Thermodynamics of Protein-Ligand Interactions as a Reference for Computational Analysis: How to Assess Accuracy, Reliability and Relevance of Experimental Data J. Comput.-Aided Mol. Des. 2015, 29, 867-883 10.1007/s10822-015-9867-y
-
(2015)
J. Comput.-Aided Mol. Des.
, vol.29
, pp. 867-883
-
-
Krimmer, S.G.1
Klebe, G.2
-
19
-
-
84904735461
-
Statistical Comparison of the Slopes of Two Regression Lines: A Tutorial
-
Andrade, J. M.; Estévez-Pérez, M. G. Statistical Comparison of the Slopes of Two Regression Lines: A Tutorial Anal. Chim. Acta 2014, 838, 1-12 10.1016/j.aca.2014.04.057
-
(2014)
Anal. Chim. Acta
, vol.838
, pp. 1-12
-
-
Andrade, J.M.1
Estévez-Pérez, M.G.2
-
20
-
-
85019607617
-
Elucidating the Origin of Long Residence Time Binding for Inhibitors of the Metalloprotease Thermolysin
-
Cramer, J.; Krimmer, S. G.; Fridh, V.; Wulsdorf, T.; Karlsson, R.; Heine, A.; Klebe, G. Elucidating the Origin of Long Residence Time Binding for Inhibitors of the Metalloprotease Thermolysin ACS Chem. Biol. 2017, 12, 225-233 10.1021/acschembio.6b00979
-
(2017)
ACS Chem. Biol.
, vol.12
, pp. 225-233
-
-
Cramer, J.1
Krimmer, S.G.2
Fridh, V.3
Wulsdorf, T.4
Karlsson, R.5
Heine, A.6
Klebe, G.7
-
21
-
-
84864400966
-
Water Makes the Difference: Rearrangement of Water Solvation Layer Triggers Non-Additivity of Functional Group Contributions in Protein-Ligand Binding
-
Biela, A.; Betz, M.; Heine, A.; Klebe, G. Water Makes the Difference: Rearrangement of Water Solvation Layer Triggers Non-Additivity of Functional Group Contributions in Protein-Ligand Binding ChemMedChem 2012, 7, 1423-1434 10.1002/cmdc.201200206
-
(2012)
ChemMedChem
, vol.7
, pp. 1423-1434
-
-
Biela, A.1
Betz, M.2
Heine, A.3
Klebe, G.4
-
22
-
-
36849117971
-
Free Volume and Entropy in Condensed Systems III. Entropy in Binary Liquid Mixtures; Partial Molal Entropy in Dilute Solutions; Structure and Thermodynamics in Aqueous Electrolytes
-
Frank, H. S.; Evans, M. W. Free Volume and Entropy in Condensed Systems III. Entropy in Binary Liquid Mixtures; Partial Molal Entropy in Dilute Solutions; Structure and Thermodynamics in Aqueous Electrolytes J. Chem. Phys. 1945, 13, 507-532 10.1063/1.1723985
-
(1945)
J. Chem. Phys.
, vol.13
, pp. 507-532
-
-
Frank, H.S.1
Evans, M.W.2
-
23
-
-
85009971479
-
An Allyl Protection and Improved Purification Strategy Enables the Synthesis of Functionalized Phosphonamidate Peptides
-
Cramer, J.; Klebe, G. An Allyl Protection and Improved Purification Strategy Enables the Synthesis of Functionalized Phosphonamidate Peptides Synthesis 2017, 49, 1857-1866 10.1055/s-0036-1588393
-
(2017)
Synthesis
, vol.49
, pp. 1857-1866
-
-
Cramer, J.1
Klebe, G.2
-
24
-
-
84861840835
-
High-Precision Isothermal Titration Calorimetry with Automated Peak Shape Analysis
-
Keller, S.; Vargas, C.; Zhao, H.; Piszczek, G.; Brautigam, C. A.; Schuck, P. High-Precision Isothermal Titration Calorimetry with Automated Peak Shape Analysis Anal. Chem. 2012, 84, 5066-5073 10.1021/ac3007522
-
(2012)
Anal. Chem.
, vol.84
, pp. 5066-5073
-
-
Keller, S.1
Vargas, C.2
Zhao, H.3
Piszczek, G.4
Brautigam, C.A.5
Schuck, P.6
-
25
-
-
84925455000
-
SEDPHAT - A Platform for Global ITC Analysis and Global Multi-Method Analysis of Molecular Interactions
-
Zhao, H.; Piszczek, G.; Schuck, P. SEDPHAT-A Platform for Global ITC Analysis and Global Multi-Method Analysis of Molecular Interactions Methods 2015, 76, 137-148 10.1016/j.ymeth.2014.11.012
-
(2015)
Methods
, vol.76
, pp. 137-148
-
-
Zhao, H.1
Piszczek, G.2
Schuck, P.3
-
26
-
-
76449106188
-
Integration, Scaling, Space-Group Assignment and Post-Refinement
-
Kabsch, W. Integration, Scaling, Space-Group Assignment and Post-Refinement Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66, 133-144 10.1107/S0907444909047374
-
(2010)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.66
, pp. 133-144
-
-
Kabsch, W.1
-
27
-
-
34447508216
-
Phaser Crystallographic Software
-
McCoy, A. J.; Grosse-Kunstleve, R. W.; Adams, P. D.; Winn, M. D.; Storoni, L. C.; Read, R. J. Phaser Crystallographic Software J. Appl. Crystallogr. 2007, 40, 658-674 10.1107/S0021889807021206
-
(2007)
J. Appl. Crystallogr.
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
28
-
-
76449098262
-
PHENIX: A Comprehensive Python-Based System for Macromolecular Structure Solution
-
Adams, P. D.; Afonine, P. V.; Bunkoczi, G.; Chen, V. B.; Davis, I. W.; Echols, N.; Headd, J. J.; Hung, L.-W.; Kapral, G. J.; Grosse-Kunstleve, R. W.; McCoy, A. J.; Moriarty, N. W.; Oeffner, R.; Read, R. J.; Richardson, D. C.; Richardson, J. S.; Terwilliger, T. C.; Zwart, P. H. PHENIX: A Comprehensive Python-Based System for Macromolecular Structure Solution Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66, 213-221 10.1107/S0907444909052925
-
(2010)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
Afonine, P.V.2
Bunkoczi, G.3
Chen, V.B.4
Davis, I.W.5
Echols, N.6
Headd, J.J.7
Hung, L.-W.8
Kapral, G.J.9
Grosse-Kunstleve, R.W.10
McCoy, A.J.11
Moriarty, N.W.12
Oeffner, R.13
Read, R.J.14
Richardson, D.C.15
Richardson, J.S.16
Terwilliger, T.C.17
Zwart, P.H.18
-
29
-
-
13244281317
-
Coot: Model-Building Tools for Molecular Graphics
-
Emsley, P.; Cowtan, K. Coot: Model-Building Tools for Molecular Graphics Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 2126-2132 10.1107/S0907444904019158
-
(2004)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.60
, pp. 2126-2132
-
-
Emsley, P.1
Cowtan, K.2
-
30
-
-
84855757480
-
-
Chemical Computing Group Inc. Montreal, QC, Canada
-
Molecular Operating Environment (MOE); Chemical Computing Group Inc.: Montreal, QC, Canada.
-
Molecular Operating Environment (MOE)
-
-
-
31
-
-
70349597601
-
Electronic Ligand Builder and Optimization Workbench (eLBOW): A Tool for Ligand Coordinate and Restraint Generation
-
Moriarty, N. W.; Grosse-Kunstleve, R. W.; Adams, P. D. Electronic Ligand Builder and Optimization Workbench (eLBOW): A Tool for Ligand Coordinate and Restraint Generation Acta Crystallogr., Sect. D: Biol. Crystallogr. 2009, 65, 1074-1080 10.1107/S0907444909029436
-
(2009)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.65
, pp. 1074-1080
-
-
Moriarty, N.W.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
-
32
-
-
0028103275
-
The CCP4 Suite: Programs for Protein Crystallography
-
CCP4
-
CCP4 The CCP4 Suite: Programs for Protein Crystallography Acta Crystallogr., Sect. D: Biol. Crystallogr. 1994, 50, 760-763 10.1107/S0907444994003112
-
(1994)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.50
, pp. 760-763
-
-
-
33
-
-
0000243829
-
PROCHECK: A Program to Check the Stereochemical Quality of Protein Structures
-
Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK: A Program to Check the Stereochemical Quality of Protein Structures J. Appl. Crystallogr. 1993, 26, 283-291 10.1107/S0021889892009944
-
(1993)
J. Appl. Crystallogr.
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
34
-
-
0000252066
-
The G Turn. Evidence for a New Folded Conformation in Proteins
-
Matthews, B. W. The G Turn. Evidence for a New Folded Conformation in Proteins Macromolecules 1972, 5, 818-819 10.1021/ma60030a031
-
(1972)
Macromolecules
, vol.5
, pp. 818-819
-
-
Matthews, B.W.1
-
35
-
-
85023768803
-
-
Unpublished Program; Uppsala University: Uppsala, Sweden
-
Kleywegt, G. J. MOLEMAN-Unpublished Program; Uppsala University: Uppsala, Sweden.
-
MOLEMAN
-
-
Kleywegt, G.J.1
-
36
-
-
0002906346
-
-
Rossmann, M. G. Arnold, E. Kluwer Academic Publishers: Dordrecht, The Netherlands
-
Kleywegt, G. J.; Zou, J. Y.; Kjeldgaard, M.; Jones, T. A. International Tables for Crystallography: Crystallography of Biological Macromolecules; Rossmann, M. G.; Arnold, E., Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 2001; Vol F.
-
(2001)
International Tables for Crystallography: Crystallography of Biological Macromolecules
-
-
Kleywegt, G.J.1
Zou, J.Y.2
Kjeldgaard, M.3
Jones, T.A.4
|