-
1
-
-
0026572775
-
Molecular-surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
-
Katchalskikatzir, E.; Shariv, I.; Eisenstein, M.; Friesem, A. A.; Aflalo, C.; Vakser, I. A. Molecular-surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 2195-2199
-
(1992)
Proc. Natl. Acad. Sci. U.S.A.
, vol.89
, pp. 2195-2199
-
-
Katchalskikatzir, E.1
Shariv, I.2
Eisenstein, M.3
Friesem, A.A.4
Aflalo, C.5
Vakser, I.A.6
-
2
-
-
0029430865
-
Surveying Molecular Interactions with DOT
-
San Diego, CA
-
Ten Eyck, L. F.; Mandell, J.; Roberts, V. A.; Pique, M. E. Surveying Molecular Interactions with DOT. In Proceedings of the 1995 ACM/IEEE Supercomputing Conference, San Diego, CA, 1995, pp 506-517.
-
(1995)
Proceedings of the 1995 ACM/IEEE Supercomputing Conference
, pp. 506-517
-
-
Ten Eyck, L.F.1
Mandell, J.2
Roberts, V.A.3
Pique, M.E.4
-
3
-
-
0031565730
-
Modelling protein docking using shape complementarity, electrostatics and biochemical information
-
Gabb, H. A.; Jackson, R. M.; Sternberg, M. J. E. Modelling protein docking using shape complementarity, electrostatics and biochemical information J. Mol. Biol. 1997, 272, 106-120
-
(1997)
J. Mol. Biol.
, vol.272
, pp. 106-120
-
-
Gabb, H.A.1
Jackson, R.M.2
Sternberg, M.J.E.3
-
4
-
-
0037093643
-
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
-
Chen, R.; Weng, Z. P. Docking unbound proteins using shape complementarity, desolvation, and electrostatics Proteins 2002, 47, 281-294
-
(2002)
Proteins
, vol.47
, pp. 281-294
-
-
Chen, R.1
Weng, Z.P.2
-
5
-
-
33747879307
-
SHARP(2): Protein-protein interaction predictions using patch analysis
-
Murakami, Y.; Jones, S. SHARP(2): Protein-protein interaction predictions using patch analysis Bioinformatics 2006, 22, 1794-1795
-
(2006)
Bioinformatics
, vol.22
, pp. 1794-1795
-
-
Murakami, Y.1
Jones, S.2
-
6
-
-
20444409186
-
Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes
-
Yang, L. W.; Bahar, I. Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes Structure 2005, 13, 893-904
-
(2005)
Structure
, vol.13
, pp. 893-904
-
-
Yang, L.W.1
Bahar, I.2
-
7
-
-
33744926664
-
Common mechanism of pore opening shared by five different potassium channels
-
Shrivastava, I. H.; Bahar, I. Common mechanism of pore opening shared by five different potassium channels Biophys. J. 2006, 90, 3929-3940
-
(2006)
Biophys. J.
, vol.90
, pp. 3929-3940
-
-
Shrivastava, I.H.1
Bahar, I.2
-
8
-
-
77956309711
-
Metal-binding sites are designed to achieve optimal mechanical and signaling properties
-
Dutta, A.; Bahar, I. Metal-binding sites are designed to achieve optimal mechanical and signaling properties Structure 2010, 18, 1140-1148
-
(2010)
Structure
, vol.18
, pp. 1140-1148
-
-
Dutta, A.1
Bahar, I.2
-
9
-
-
34147133371
-
Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation
-
Meirovitch, H. Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation Curr. Opin. Struct. Biol. 2007, 17, 181-186
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 181-186
-
-
Meirovitch, H.1
-
10
-
-
0035828630
-
On the calculation of entropy from covariance matrices of the atomic fluctuations
-
Andricioaei, I.; Karplus, M. On the calculation of entropy from covariance matrices of the atomic fluctuations J. Chem. Phys. 2001, 115, 6289-6292
-
(2001)
J. Chem. Phys.
, vol.115
, pp. 6289-6292
-
-
Andricioaei, I.1
Karplus, M.2
-
11
-
-
0001351515
-
Estimation of absolute and relative entropies of macromolecules using the covariance matrix
-
Schlitter, J. Estimation of absolute and relative entropies of macromolecules using the covariance matrix Chem. Phys. Lett. 1993, 215, 617-621
-
(1993)
Chem. Phys. Lett.
, vol.215
, pp. 617-621
-
-
Schlitter, J.1
-
12
-
-
0345973041
-
Gaussian dynamics of folded proteins
-
Haliloglu, T.; Bahar, I.; Erman, B. Gaussian dynamics of folded proteins Phys. Rev. Lett. 1997, 79, 3090-3093
-
(1997)
Phys. Rev. Lett.
, vol.79
, pp. 3090-3093
-
-
Haliloglu, T.1
Bahar, I.2
Erman, B.3
-
13
-
-
84862290983
-
Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking poses
-
Zimmermann, M. T.; Leelananda, S. P.; Kloczkowski, A.; Jernigan, R. L. Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking poses J. Phys. Chem. B 2012, 116, 6725-6731
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 6725-6731
-
-
Zimmermann, M.T.1
Leelananda, S.P.2
Kloczkowski, A.3
Jernigan, R.L.4
-
14
-
-
84888298806
-
Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI)
-
Huang, S.-Y.; Yan, C.; Grinter, S. Z.; Chang, S.; Jiang, L.; Zou, X. Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI) Proteins 2013, 81, 2183-2191
-
(2013)
Proteins
, vol.81
, pp. 2183-2191
-
-
Huang, S.-Y.1
Yan, C.2
Grinter, S.Z.3
Chang, S.4
Jiang, L.5
Zou, X.6
-
15
-
-
84873704422
-
Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation
-
Takemura, K.; Burri, R. R.; Ishikawa, T.; Ishikura, T.; Sakuraba, S.; Matubayasi, N.; Kuwata, K.; Kitao, A. Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation Chem. Phys. Lett. 2013, 559, 94-98
-
(2013)
Chem. Phys. Lett.
, vol.559
, pp. 94-98
-
-
Takemura, K.1
Burri, R.R.2
Ishikawa, T.3
Ishikura, T.4
Sakuraba, S.5
Matubayasi, N.6
Kuwata, K.7
Kitao, A.8
-
16
-
-
84870950733
-
Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation
-
Takemura, K.; Guo, H.; Sakuraba, S.; Matubayasi, N.; Kitao, A. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation J. Chem. Phys. 2012, 137, 215105
-
(2012)
J. Chem. Phys.
, vol.137
, pp. 215105
-
-
Takemura, K.1
Guo, H.2
Sakuraba, S.3
Matubayasi, N.4
Kitao, A.5
-
17
-
-
57349132441
-
Protein-protein docking benchmark version 3.0
-
Hwang, H.; Pierce, B.; Mintseris, J.; Janin, J.; Weng, Z. Protein-protein docking benchmark version 3.0 Proteins 2008, 73, 705-709
-
(2008)
Proteins
, vol.73
, pp. 705-709
-
-
Hwang, H.1
Pierce, B.2
Mintseris, J.3
Janin, J.4
Weng, Z.5
-
18
-
-
0038526303
-
ZDOCK: An initial-stage protein-docking algorithm
-
Chen, R.; Li, L.; Weng, Z. ZDOCK: An initial-stage protein-docking algorithm Proteins 2003, 52, 80-87
-
(2003)
Proteins
, vol.52
, pp. 80-87
-
-
Chen, R.1
Li, L.2
Weng, Z.3
-
19
-
-
21644480883
-
Protein-protein docking benchmark 2.0: An update
-
Mintseris, J.; Wiehe, K.; Pierce, B.; Anderson, R.; Chen, R.; Janin, J.; Weng, Z. Protein-protein docking benchmark 2.0: An update Proteins 2005, 60, 214-216
-
(2005)
Proteins
, vol.60
, pp. 214-216
-
-
Mintseris, J.1
Wiehe, K.2
Pierce, B.3
Anderson, R.4
Chen, R.5
Janin, J.6
Weng, Z.7
-
20
-
-
77957944014
-
Protein-protein docking benchmark version 4.0
-
Hwang, H.; Vreven, T.; Janin, J.; Weng, Z. Protein-protein docking benchmark version 4.0 Proteins 2010, 78, 3111-4
-
(2010)
Proteins
, vol.78
, pp. 3111-3114
-
-
Hwang, H.1
Vreven, T.2
Janin, J.3
Weng, Z.4
-
21
-
-
0345864027
-
The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
-
Porter, C. T.; Bartlett, G. J.; Thornton, J. M. The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data Nucleic Acids Res. 2004, 32, D129-33
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 129-133
-
-
Porter, C.T.1
Bartlett, G.J.2
Thornton, J.M.3
-
22
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel, E.; Henrick, K. Inference of macromolecular assemblies from crystalline state J. Mol. Biol. 2007, 372, 774-97
-
(2007)
J. Mol. Biol.
, vol.372
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
23
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein, F. C.; Koetzle, T. F.; Williams, G. J.; Meyer, E. F., Jr.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protein Data Bank: A computer-based archival file for macromolecular structures J. Mol. Biol. 1977, 112, 535-42
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.3
Meyer, Jr.E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
24
-
-
77952938726
-
Global dynamics of proteins: Bridging between structure and function
-
Bahar, I.; Lezon, T. R.; Yang, L. W.; Eyal, E. Global dynamics of proteins: Bridging between structure and function Annu. Rev. Biophys. 2010, 39, 23-42
-
(2010)
Annu. Rev. Biophys.
, vol.39
, pp. 23-42
-
-
Bahar, I.1
Lezon, T.R.2
Yang, L.W.3
Eyal, E.4
-
25
-
-
34147166490
-
Comment on elastic network models and proteins
-
Thorpe, M. F. Comment on elastic network models and proteins Phys. Biol. 2007, 4, 60-63
-
(2007)
Phys. Biol.
, vol.4
, pp. 60-63
-
-
Thorpe, M.F.1
-
26
-
-
79959666296
-
Models with energy penalty on interresidue rotation address insufficiencies of conventional elastic network models
-
Yang, L. W. Models with energy penalty on interresidue rotation address insufficiencies of conventional elastic network models Biophys. J. 2011, 100, 1784-1793
-
(2011)
Biophys. J.
, vol.100
, pp. 1784-1793
-
-
Yang, L.W.1
-
27
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan, A. R.; Durell, S. R.; Jernigan, R. L.; Demirel, M. C.; Keskin, O.; Bahar, I. Anisotropy of fluctuation dynamics of proteins with an elastic network model Biophys. J. 2001, 80, 505-515
-
(2001)
Biophys. J.
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
28
-
-
0030888546
-
Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme
-
Hayward, S.; Kitao, A.; Berendsen, H. J. C. Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme Proteins 1997, 27, 425-437
-
(1997)
Proteins
, vol.27
, pp. 425-437
-
-
Hayward, S.1
Kitao, A.2
Berendsen, H.J.C.3
-
29
-
-
0036888353
-
Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50
-
Hayward, S.; Lee, R. A. Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50 J. Mol. Graph. Model. 2002, 21, 181-183
-
(2002)
J. Mol. Graph. Model.
, vol.21
, pp. 181-183
-
-
Hayward, S.1
Lee, R.A.2
-
30
-
-
0033557178
-
Analysis of domain motions in large proteins
-
Hinsen, K.; Thomas, A.; Field, M. J. Analysis of domain motions in large proteins Proteins 1999, 34, 369-382
-
(1999)
Proteins
, vol.34
, pp. 369-382
-
-
Hinsen, K.1
Thomas, A.2
Field, M.J.3
-
31
-
-
33644517853
-
Functional modes of proteins are among the most robust
-
Nicolay, S.; Sanejouand, Y. H. Functional modes of proteins are among the most robust Phys. Rev. Lett. 2006, 96
-
(2006)
Phys. Rev. Lett.
, pp. 96
-
-
Nicolay, S.1
Sanejouand, Y.H.2
-
32
-
-
61449106774
-
Principal component analysis of native ensembles of biomolecular structures (PCA-NEST): Insights into functional dynamics
-
Yang, L. W.; Eyal, E.; Bahar, I.; Kitao, A. Principal component analysis of native ensembles of biomolecular structures (PCA-NEST): Insights into functional dynamics Bioinformatics 2009, 25, 606-14
-
(2009)
Bioinformatics
, vol.25
, pp. 606-614
-
-
Yang, L.W.1
Eyal, E.2
Bahar, I.3
Kitao, A.4
-
33
-
-
0000764772
-
The use of multiple measurements in taxonomic problems
-
Fisher, R. A. The use of multiple measurements in taxonomic problems Ann. Eugenic. 1936, 7, 179-188
-
(1936)
Ann. Eugenic.
, vol.7
, pp. 179-188
-
-
Fisher, R.A.1
-
34
-
-
84941871856
-
The Kolmogorov-Smirnov Test for goodness of fit
-
Massey, F. J. The Kolmogorov-Smirnov Test for goodness of fit J. Am. Stat. Assoc. 1951, 46, 68-78
-
(1951)
J. Am. Stat. Assoc.
, vol.46
, pp. 68-78
-
-
Massey, F.J.1
-
35
-
-
0002386913
-
On the interpretation of 2 from contingency tables, and the calculation of P
-
Fisher, R. A. On the interpretation of 2 from contingency tables, and the calculation of P J. R. Stat. Soc. 1922, 85, 87-94
-
(1922)
J. R. Stat. Soc.
, vol.85
, pp. 87-94
-
-
Fisher, R.A.1
-
36
-
-
0034556938
-
Thermodynamic parameters of specific and nonspecific protein-DNA binding
-
Jen-jacobson, L.; Engler, L. E.; Ames, J. T.; Kurpiewski, M. R.; Grigorescu, A. Thermodynamic parameters of specific and nonspecific protein-DNA binding Supramol. Chem. 2000, 12, 143-160
-
(2000)
Supramol. Chem.
, vol.12
, pp. 143-160
-
-
Jen-Jacobson, L.1
Engler, L.E.2
Ames, J.T.3
Kurpiewski, M.R.4
Grigorescu, A.5
-
37
-
-
84906539214
-
-
University Science Books: Herndon, VA, Chapter 8
-
McQuarrie, D. A. Statistical Mechanics; University Science Books: Herndon, VA, 2000; Chapter 8, pp 134-136.
-
(2000)
Statistical Mechanics
, pp. 134-136
-
-
McQuarrie, D.A.1
-
38
-
-
0032570266
-
Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model
-
Bahar, I.; Wallqvist, A.; Covell, D. G.; Jernigan, R. L. Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model Biochemistry 1998, 37, 1067-75
-
(1998)
Biochemistry
, vol.37
, pp. 1067-1075
-
-
Bahar, I.1
Wallqvist, A.2
Covell, D.G.3
Jernigan, R.L.4
-
39
-
-
0028247281
-
Side-chain entropy and packing in proteins
-
Bromberg, S.; Dill, K. A. Side-chain entropy and packing in proteins Protein Sci. 1994, 3, 997-1009
-
(1994)
Protein Sci.
, vol.3
, pp. 997-1009
-
-
Bromberg, S.1
Dill, K.A.2
-
40
-
-
0036821028
-
The consequences of translational and rotational entropy lost by small molecules on binding to proteins
-
Murray, C.; Verdonk, M. The consequences of translational and rotational entropy lost by small molecules on binding to proteins J. Comput.-Aided Mol. Des. 2002, 16, 741-753
-
(2002)
J. Comput.-Aided Mol. Des.
, vol.16
, pp. 741-753
-
-
Murray, C.1
Verdonk, M.2
-
41
-
-
25844507555
-
The entropic cost of protein-protein association: A case study on acetylcholinesterase binding to fasciculin-2
-
Minh, D. D. L.; Bui, J. M.; Chang, C.-e.; Jain, T.; Swanson, J. M. J.; McCammon, J. A. The entropic cost of protein-protein association: A case study on acetylcholinesterase binding to fasciculin-2 Biophys. J. 2005, 89, L25-L27
-
(2005)
Biophys. J.
, vol.89
-
-
Minh, D.D.L.1
Bui, J.M.2
Chang, C.-E.3
Jain, T.4
Swanson, J.M.J.5
McCammon, J.A.6
-
42
-
-
34447503697
-
Conformational entropy in molecular recognition by proteins
-
Frederick, K. K.; Marlow, M. S.; Valentine, K. G.; Wand, A. J. Conformational entropy in molecular recognition by proteins Nature 2007, 448, 325-329
-
(2007)
Nature
, vol.448
, pp. 325-329
-
-
Frederick, K.K.1
Marlow, M.S.2
Valentine, K.G.3
Wand, A.J.4
-
43
-
-
33745832658
-
Flexibility and conformational entropy in protein-protein binding
-
Grünberg, R.; Nilges, M.; Leckner, J. Flexibility and conformational entropy in protein-protein binding Structure 2006, 14, 1205
-
(2006)
Structure
, vol.14
, pp. 1205
-
-
Grünberg, R.1
Nilges, M.2
Leckner, J.3
-
44
-
-
34248579768
-
A simple shape characteristic of protein-protein recognition
-
Nicola, G.; Vakser, I. A. A simple shape characteristic of protein-protein recognition Bioinformatics 2007, 23, 789-92
-
(2007)
Bioinformatics
, vol.23
, pp. 789-792
-
-
Nicola, G.1
Vakser, I.A.2
-
45
-
-
0033967490
-
A relation between the principal axes of inertia and ligand binding
-
Foote, J.; Raman, A. A relation between the principal axes of inertia and ligand binding Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 978-83
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 978-983
-
-
Foote, J.1
Raman, A.2
|