-
1
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: Methods and applications
-
Kitchen, D.B.; Decornez, H.; Furr, J.R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nat. Rev. Drug Discov. 2004, 3, 935-949.
-
(2004)
Nat. Rev. Drug Discov.
, vol.3
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
2
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz, I.D.; Blaney, J.M.; Oatley, S.J.; Langridge, R.; Ferrin, T.E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 1982, 161, 269-288.
-
(1982)
J. Mol. Biol.
, vol.161
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
3
-
-
0037413558
-
Homology modeling of rat and human cytochrome p450 2d (cyp2d) isoforms and computational rationalization of experimental ligand-binding specificities
-
Venhorst, J.; ter Laak, A.M.; Commandeur, J.N.; Funae, Y.; Hiroi, T.; Vermeulen, N.P. Homology modeling of rat and human cytochrome p450 2d (cyp2d) isoforms and computational rationalization of experimental ligand-binding specificities. J. Med. Chem. 2003, 46, 74-86.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 74-86
-
-
Venhorst, J.1
Ter Laak, A.M.2
Commandeur, J.N.3
Funae, Y.4
Hiroi, T.5
Vermeulen, N.P.6
-
5
-
-
48049090902
-
Lead generation: Reality check on commonly held views
-
Fotouhi, N.; Gillespie, P.; Goodnow, R., Jr. Lead generation: Reality check on commonly held views. Expert Opin. Drug Discov. 2008, 3, 733-744.
-
(2008)
Expert Opin. Drug Discov.
, vol.3
, pp. 733-744
-
-
Fotouhi, N.1
Gillespie, P.2
Goodnow, R.3
-
6
-
-
84860390112
-
Demythologizing the high costs of pharmaceutical research
-
Light, D.W.; Warburton, R. Demythologizing the high costs of pharmaceutical research. BioSocieties 2011, 6, 34-50.
-
(2011)
BioSocieties
, vol.6
, pp. 34-50
-
-
Light, D.W.1
Warburton, R.2
-
7
-
-
77950503976
-
Virtual screening: An endless staircase?
-
Schneider, G. Virtual screening: An endless staircase? Nat. Rev. Drug Discov. 2010, 9, 273-276.
-
(2010)
Nat. Rev. Drug Discov.
, vol.9
, pp. 273-276
-
-
Schneider, G.1
-
8
-
-
84927719289
-
Recent advances in virtual screening for drug discovery
-
Leung, C.H.; Ma, D.L. Recent advances in virtual screening for drug discovery. Methods 2015, 71, 1-3.
-
(2015)
Methods
, vol.71
, pp. 1-3
-
-
Leung, C.H.1
Ma, D.L.2
-
9
-
-
23844449940
-
Computer-based de novo design of drug-like molecules
-
Schneider, G.; Fechner, U. Computer-based de novo design of drug-like molecules. Nat. Rev. Drug Discov. 2005, 4, 649-663.
-
(2005)
Nat. Rev. Drug Discov.
, vol.4
, pp. 649-663
-
-
Schneider, G.1
Fechner, U.2
-
10
-
-
33749245117
-
Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps
-
Leach, A.R.; Shoichet, B.K.; Peishoff, C.E. Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps. J. Med. Chem. 2006, 49, 5851-5855.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5851-5855
-
-
Leach, A.R.1
Shoichet, B.K.2
Peishoff, C.E.3
-
11
-
-
40349087133
-
Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go
-
Suppl. 1
-
Moitessier, N.; Englebienne, P.; Lee, D.; Lawandi, J.; Corbeil, C.R. Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go. Br. J. Pharmacol. 2008, 153 (Suppl. 1), S7-S26.
-
(2008)
Br. J. Pharmacol.
, vol.153
, pp. S7-S26
-
-
Moitessier, N.1
Englebienne, P.2
Lee, D.3
Lawandi, J.4
Corbeil, C.R.5
-
12
-
-
84904819424
-
Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design
-
Grinter, S.Z.; Zou, X. Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design. Molecules 2014, 19, 10150-10176.
-
(2014)
Molecules
, vol.19
, pp. 10150-10176
-
-
Grinter, S.Z.1
Zou, X.2
-
13
-
-
3042806401
-
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
-
Perola, E.; Walters, W.P.; Charifson, P.S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 2004, 56, 235-249.
-
(2004)
Proteins
, vol.56
, pp. 235-249
-
-
Perola, E.1
Walters, W.P.2
Charifson, P.S.3
-
14
-
-
84857509304
-
Small-molecule stabilization of protein-protein interactions: An underestimated concept in drug discovery?
-
Thiel, P.; Kaiser, M.; Ottmann, C. Small-molecule stabilization of protein-protein interactions: An underestimated concept in drug discovery? Angew. Chem. 2012, 51, 2012-2018.
-
(2012)
Angew. Chem.
, vol.51
, pp. 2012-2018
-
-
Thiel, P.1
Kaiser, M.2
Ottmann, C.3
-
15
-
-
44349113144
-
Estimating the size of the human interactome
-
Stumpf, M.P.; Thorne, T.; de Silva, E.; Stewart, R.; An, H.J.; Lappe, M.; Wiuf, C. Estimating the size of the human interactome. Proc. Natl. Acad. Sci. USA 2008, 105, 6959-6964.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 6959-6964
-
-
Stumpf, M.P.1
Thorne, T.2
De Silva, E.3
Stewart, R.4
An, H.J.5
Lappe, M.6
Wiuf, C.7
-
16
-
-
50249154886
-
Small-molecule inhibitors of protein-protein interactions
-
Berg, T. Small-molecule inhibitors of protein-protein interactions. Curr. Opin. Drug Discov. Dev. 2008, 11, 666-674.
-
(2008)
Curr. Opin. Drug Discov. Dev.
, vol.11
, pp. 666-674
-
-
Berg, T.1
-
17
-
-
47349109056
-
Drug-like inhibitors of protein-protein interactions: A structural examination of effective protein mimicry
-
Fry, D.C. Drug-like inhibitors of protein-protein interactions: A structural examination of effective protein mimicry. Curr. Protein Pept. Sci. 2008, 9, 240-247.
-
(2008)
Curr. Protein Pept. Sci.
, vol.9
, pp. 240-247
-
-
Fry, D.C.1
-
18
-
-
58849145512
-
Predicting druggable binding sites at the protein-protein interface
-
Fuller, J.C.; Burgoyne, N.J.; Jackson, R.M. Predicting druggable binding sites at the protein-protein interface. Drug Discov. Today 2009, 14, 155-161.
-
(2009)
Drug Discov. Today
, vol.14
, pp. 155-161
-
-
Fuller, J.C.1
Burgoyne, N.J.2
Jackson, R.M.3
-
19
-
-
84878306995
-
Protein-protein interactions: General trends in the relationship between binding affinity and interfacial buried surface area
-
Chen, J.; Sawyer, N.; Regan, L. Protein-protein interactions: General trends in the relationship between binding affinity and interfacial buried surface area. Protein Sci. 2013, 22, 510-515.
-
(2013)
Protein Sci.
, vol.22
, pp. 510-515
-
-
Chen, J.1
Sawyer, N.2
Regan, L.3
-
20
-
-
33846925964
-
The molecular architecture of protein-protein binding sites
-
Reichmann, D.; Rahat, O.; Cohen, M.; Neuvirth, H.; Schreiber, G. The molecular architecture of protein-protein binding sites. Curr. Opin. Struct. Biol. 2007, 17, 67-76.
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 67-76
-
-
Reichmann, D.1
Rahat, O.2
Cohen, M.3
Neuvirth, H.4
Schreiber, G.5
-
21
-
-
34548779127
-
Hot spots-A review of the protein-protein interface determinant amino-acid residues
-
Moreira, I.S.; Fernandes, P.A.; Ramos, M.J. Hot spots-A review of the protein-protein interface determinant amino-acid residues. Proteins 2007, 68, 803-812.
-
(2007)
Proteins
, vol.68
, pp. 803-812
-
-
Moreira, I.S.1
Fernandes, P.A.2
Ramos, M.J.3
-
22
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Lo Conte, L.; Chothia, C.; Janin, J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 1999, 285, 2177-2198.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 2177-2198
-
-
Lo Conte, L.1
Chothia, C.2
Janin, J.3
-
23
-
-
33846155913
-
Structure-based maximal affinity model predicts small-molecule druggability
-
Cheng, A.C.; Coleman, R.G.; Smyth, K.T.; Cao, Q.; Soulard, P.; Caffrey, D.R.; Salzberg, A.C.; Huang, E.S. Structure-based maximal affinity model predicts small-molecule druggability. Nat. Biotechnol. 2007, 25, 71-75.
-
(2007)
Nat. Biotechnol.
, vol.25
, pp. 71-75
-
-
Cheng, A.C.1
Coleman, R.G.2
Smyth, K.T.3
Cao, Q.4
Soulard, P.5
Caffrey, D.R.6
Salzberg, A.C.7
Huang, E.S.8
-
25
-
-
33645886036
-
Exploring protein-ligand recognition with binding moad
-
Smith, R.D.; Hu, L.; Falkner, J.A.; Benson, M.L.; Nerothin, J.P.; Carlson, H.A. Exploring protein-ligand recognition with binding moad. J. Mol. Graph. Model. 2006, 24, 414-425.
-
(2006)
J. Mol. Graph. Model.
, vol.24
, pp. 414-425
-
-
Smith, R.D.1
Hu, L.2
Falkner, J.A.3
Benson, M.L.4
Nerothin, J.P.5
Carlson, H.A.6
-
26
-
-
37249004920
-
Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
-
Wells, J.A.; McClendon, C.L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007, 450, 1001-1009.
-
(2007)
Nature
, vol.450
, pp. 1001-1009
-
-
Wells, J.A.1
McClendon, C.L.2
-
27
-
-
38549151817
-
Drugbank: A knowledgebase for drugs, drug actions and drug targets
-
Wishart, D.S.; Knox, C.; Guo, A.C.; Cheng, D.; Shrivastava, S.; Tzur, D.; Gautam, B.; Hassanali, M. Drugbank: A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2008, 36, D901-D906.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. D901-D906
-
-
Wishart, D.S.1
Knox, C.2
Guo, A.C.3
Cheng, D.4
Shrivastava, S.5
Tzur, D.6
Gautam, B.7
Hassanali, M.8
-
28
-
-
84907172237
-
Chemokine receptor ccr5 antagonist maraviroc: Medicinal chemistry and clinical applications
-
Xu, G.G.; Guo, J.; Wu, Y. Chemokine receptor ccr5 antagonist maraviroc: Medicinal chemistry and clinical applications. Curr. Top. Med. Chem. 2014, 14, 1504-1514.
-
(2014)
Curr. Top. Med. Chem.
, vol.14
, pp. 1504-1514
-
-
Xu, G.G.1
Guo, J.2
Wu, Y.3
-
29
-
-
44949154279
-
Small molecular weight protein-protein interaction antagonists: An insurmountable challenge?
-
Domling, A. Small molecular weight protein-protein interaction antagonists: An insurmountable challenge? Curr. Opin. Chem. Biol. 2008, 12, 281-291.
-
(2008)
Curr. Opin. Chem. Biol.
, vol.12
, pp. 281-291
-
-
Domling, A.1
-
30
-
-
0028916599
-
A hot spot of binding energy in a hormone-receptor interface
-
Clackson, T.; Wells, J.A. A hot spot of binding energy in a hormone-receptor interface. Science 1995, 267, 383-386.
-
(1995)
Science
, vol.267
, pp. 383-386
-
-
Clackson, T.1
Wells, J.A.2
-
31
-
-
0037093645
-
Dissecting protein-protein recognition sites
-
Chakrabarti, P.; Janin, J. Dissecting protein-protein recognition sites. Proteins 2002, 47, 334-343.
-
(2002)
Proteins
, vol.47
, pp. 334-343
-
-
Chakrabarti, P.1
Janin, J.2
-
32
-
-
33750610998
-
Drugs targeting protein-protein interactions
-
Chene, P. Drugs targeting protein-protein interactions. ChemMedChem 2006, 1, 400-411.
-
(2006)
ChemMedChem
, vol.1
, pp. 400-411
-
-
Chene, P.1
-
33
-
-
0036469060
-
Unraveling hot spots in binding interfaces: Progress and challenges
-
DeLano, W.L. Unraveling hot spots in binding interfaces: Progress and challenges. Curr. Opin. Struct. Biol. 2002, 12, 14-20.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 14-20
-
-
DeLano, W.L.1
-
34
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan, A.A.; Thorn, K.S. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 1998, 280, 1-9.
-
(1998)
J. Mol. Biol.
, vol.280
, pp. 1-9
-
-
Bogan, A.A.1
Thorn, K.S.2
-
35
-
-
78650947751
-
Discovery of modulators of protein-protein interactions: Current approaches and limitations
-
Meireles, L.M.; Mustata, G. Discovery of modulators of protein-protein interactions: Current approaches and limitations. Curr. Top. Med. Chem. 2011, 11, 248-257.
-
(2011)
Curr. Top. Med. Chem.
, vol.11
, pp. 248-257
-
-
Meireles, L.M.1
Mustata, G.2
-
36
-
-
79951960238
-
Small-molecule protein-protein interaction inhibitors: Therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations
-
Buchwald, P. Small-molecule protein-protein interaction inhibitors: Therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations. IUBMB Life 2010, 62, 724-731.
-
(2010)
IUBMB Life
, vol.62
, pp. 724-731
-
-
Buchwald, P.1
-
37
-
-
33748578600
-
Targeting protein-protein interactions with small molecules: Challenges and perspectives for computational binding epitope detection and ligand finding
-
Gonzalez-Ruiz, D.; Gohlke, H. Targeting protein-protein interactions with small molecules: Challenges and perspectives for computational binding epitope detection and ligand finding. Curr. Med. Chem. 2006, 13, 2607-2625.
-
(2006)
Curr. Med. Chem.
, vol.13
, pp. 2607-2625
-
-
Gonzalez-Ruiz, D.1
Gohlke, H.2
-
38
-
-
77649233664
-
Rationalizing the chemical space of protein-protein interaction inhibitors
-
Sperandio, O.; Reynes, C.H.; Camproux, A.C.; Villoutreix, B.O. Rationalizing the chemical space of protein-protein interaction inhibitors. Drug Discov. Today 2010, 15, 220-229.
-
(2010)
Drug Discov. Today
, vol.15
, pp. 220-229
-
-
Sperandio, O.1
Reynes, C.H.2
Camproux, A.C.3
Villoutreix, B.O.4
-
39
-
-
84897443073
-
Oncogenic protein interfaces: Small molecules, big challenges
-
Nero, T.L.; Morton, C.J.; Holien, J.K.; Wielens, J.; Parker, M.W. Oncogenic protein interfaces: Small molecules, big challenges. Nat. Rev. Cancer 2014, 14, 248-262.
-
(2014)
Nat. Rev. Cancer
, vol.14
, pp. 248-262
-
-
Nero, T.L.1
Morton, C.J.2
Holien, J.K.3
Wielens, J.4
Parker, M.W.5
-
40
-
-
70450169243
-
Inhibition of protein-protein interactions using designed molecules
-
Wilson, A.J. Inhibition of protein-protein interactions using designed molecules. Chem. Soc. Rev. 2009, 38, 3289-3300.
-
(2009)
Chem. Soc. Rev.
, vol.38
, pp. 3289-3300
-
-
Wilson, A.J.1
-
41
-
-
84928645682
-
Alternative modulation of protein-protein interactions by small molecules
-
Fischer, G.; Rossmann, M.; Hyvonen, M. Alternative modulation of protein-protein interactions by small molecules. Curr. Opin. Biotechnol. 2015, 35, 78-85.
-
(2015)
Curr. Opin. Biotechnol.
, vol.35
, pp. 78-85
-
-
Fischer, G.1
Rossmann, M.2
Hyvonen, M.3
-
42
-
-
84892581838
-
Is nmr fragment screening fine-tuned to assess druggability of protein-protein interactions?
-
Dias, D.M.; Van Molle, I.; Baud, M.G.; Galdeano, C.; Geraldes, C.F.; Ciulli, A. Is nmr fragment screening fine-tuned to assess druggability of protein-protein interactions? ACS Med. Chem. Lett. 2014, 5, 23-28.
-
(2014)
ACS Med. Chem. Lett.
, vol.5
, pp. 23-28
-
-
Dias, D.M.1
Van Molle, I.2
Baud, M.G.3
Galdeano, C.4
Geraldes, C.F.5
Ciulli, A.6
-
43
-
-
84940891441
-
In silico design of low molecular weight protein-protein interaction inhibitors: Overall concept and recent advances
-
Kuenemann, M.A.; Sperandio, O.; Labbe, C.M.; Lagorce, D.; Miteva, M.A.; Villoutreix, B.O. In silico design of low molecular weight protein-protein interaction inhibitors: Overall concept and recent advances. Prog. Biophys. Mol. Biol. 2015, doi:10.1016/j.pbiomolbio.2015.02.006.
-
(2015)
Prog. Biophys. Mol. Biol.
-
-
Kuenemann, M.A.1
Sperandio, O.2
Labbe, C.M.3
Lagorce, D.4
Miteva, M.A.5
Villoutreix, B.O.6
-
44
-
-
84940893103
-
Flexibility and small pockets at protein-protein interfaces: New insights into druggability
-
Jubb, H.; Blundell, T.L.; Ascher, D.B. Flexibility and small pockets at protein-protein interfaces: New insights into druggability. Prog. Biophys. Mol. Biol. 2015, doi:10.1016/j.pbiomolbio.2015.01.009.
-
(2015)
Prog. Biophys. Mol. Biol.
-
-
Jubb, H.1
Blundell, T.L.2
Ascher, D.B.3
-
45
-
-
84922813362
-
Small-molecule inhibitors of the MDM2-p53 protein-protein interaction (MDM2 inhibitors) in clinical trials for cancer treatment
-
Zhao, Y.; Aguilar, A.; Bernard, D.; Wang, S. Small-molecule inhibitors of the MDM2-p53 protein-protein interaction (MDM2 inhibitors) in clinical trials for cancer treatment. J. Med. Chem. 2015, 58, 1038-1052.
-
(2015)
J. Med. Chem.
, vol.58
, pp. 1038-1052
-
-
Zhao, Y.1
Aguilar, A.2
Bernard, D.3
Wang, S.4
-
46
-
-
84896987501
-
Challenges and opportunities in targeting the menin-mll interaction
-
Cierpicki, T.; Grembecka, J. Challenges and opportunities in targeting the menin-mll interaction. Future Med. Chem. 2014, 6, 447-462.
-
(2014)
Future Med. Chem.
, vol.6
, pp. 447-462
-
-
Cierpicki, T.1
Grembecka, J.2
-
47
-
-
84895491357
-
Structure-based design of small-molecule protein-protein interaction modulators: The story so far
-
Falchi, F.; Caporuscio, F.; Recanatini, M. Structure-based design of small-molecule protein-protein interaction modulators: The story so far. Future Med. Chem. 2014, 6, 343-357.
-
(2014)
Future Med. Chem.
, vol.6
, pp. 343-357
-
-
Falchi, F.1
Caporuscio, F.2
Recanatini, M.3
-
48
-
-
84886315105
-
Small molecules modulation of 14-3-3 protein-protein interactions
-
Mori, M.; Vignaroli, G.; Botta, M. Small molecules modulation of 14-3-3 protein-protein interactions. Drug Discov. Today Technol. 2013, 10, e541-e547.
-
(2013)
Drug Discov. Today Technol.
, vol.10
, pp. e541-e547
-
-
Mori, M.1
Vignaroli, G.2
Botta, M.3
-
49
-
-
84886286398
-
Inhibitors of protein-protein interactions: New methodologies to tackle this challenge
-
Silvian, L.; Enyedy, I.; Kumaravel, G. Inhibitors of protein-protein interactions: New methodologies to tackle this challenge. Drug Discov. Today Technol. 2013, 10, e509-e515.
-
(2013)
Drug Discov. Today Technol.
, vol.10
, pp. e509-e515
-
-
Silvian, L.1
Enyedy, I.2
Kumaravel, G.3
-
50
-
-
84891850975
-
Targeting protein-protein interaction by small molecules
-
Jin, L.; Wang, W.; Fang, G. Targeting protein-protein interaction by small molecules. Annu. Rev. Pharmacol. Toxicol. 2014, 54, 435-456.
-
(2014)
Annu. Rev. Pharmacol. Toxicol.
, vol.54
, pp. 435-456
-
-
Jin, L.1
Wang, W.2
Fang, G.3
-
51
-
-
84878589163
-
From protein-protein interactions to rational drug design: Are computational methods up to the challenge?
-
Coelho, E.D.; Arrais, J.P.; Oliveira, J.L. From protein-protein interactions to rational drug design: Are computational methods up to the challenge? Curr. Top. Med. Chem. 2013, 13, 602-618.
-
(2013)
Curr. Top. Med. Chem.
, vol.13
, pp. 602-618
-
-
Coelho, E.D.1
Arrais, J.P.2
Oliveira, J.L.3
-
52
-
-
84874614807
-
Structure prediction of protein complexes
-
Xu, Y., Xu, D., Liang, J. Springer: New York, NY, USA
-
Pierce, B.; Phillips, A.T.; Weng, Z. Structure prediction of protein complexes. In Computational Methods for Protein Structure Prediction and Modeling; Xu, Y., Xu, D., Liang, J., Eds.; Springer: New York, NY, USA, 2007; Volume 2, pp. 109-134.
-
(2007)
Computational Methods for Protein Structure Prediction and Modeling
, vol.VOLUME 2
, pp. 109-134
-
-
Pierce, B.1
Phillips, A.T.2
Weng, Z.3
-
53
-
-
33645453254
-
Global landscape of protein complexes in the yeast saccharomyces cerevisiae
-
Krogan, N.J.; Cagney, G.; Yu, H.; Zhong, G.; Guo, X.; Ignatchenko, A.; Li, J.; Pu, S.; Datta, N.; Tikuisis, A.P.; et al. Global landscape of protein complexes in the yeast saccharomyces cerevisiae. Nature 2006, 440, 637-643.
-
(2006)
Nature
, vol.440
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
Ignatchenko, A.6
Li, J.7
Pu, S.8
Datta, N.9
Tikuisis, A.P.10
-
54
-
-
33645983211
-
Efficient algorithms for detecting signaling pathways in protein interaction networks
-
Scott, J.; Ideker, T.; Karp, R.M.; Sharan, R. Efficient algorithms for detecting signaling pathways in protein interaction networks. J. Comput. Biol. 2006, 13, 133-144.
-
(2006)
J. Comput. Biol.
, vol.13
, pp. 133-144
-
-
Scott, J.1
Ideker, T.2
Karp, R.M.3
Sharan, R.4
-
55
-
-
33947252154
-
Network-based prediction of protein function
-
Sharan, R.; Ulitsky, I.; Shamir, R. Network-based prediction of protein function. Mol. Syst. Biol. 2007, 3, 88.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 88
-
-
Sharan, R.1
Ulitsky, I.2
Shamir, R.3
-
56
-
-
79952674000
-
Interactome networks and human disease
-
Vidal, M.; Cusick, M.E.; Barabasi, A.L. Interactome networks and human disease. Cell 2011, 144, 986-998.
-
(2011)
Cell
, vol.144
, pp. 986-998
-
-
Vidal, M.1
Cusick, M.E.2
Barabasi, A.L.3
-
57
-
-
84888829614
-
Protein-protein interaction networks: The puzzling riches
-
Wodak, S.J.; Vlasblom, J.; Turinsky, A.L.; Pu, S. Protein-protein interaction networks: The puzzling riches. Curr. Opin. Struct. Biol. 2013, 23, 941-953.
-
(2013)
Curr. Opin. Struct. Biol.
, vol.23
, pp. 941-953
-
-
Wodak, S.J.1
Vlasblom, J.2
Turinsky, A.L.3
Pu, S.4
-
58
-
-
84876546810
-
2p2idb: A structural database dedicated to orthosteric modulation of protein-protein interactions
-
Basse, M.J.; Betzi, S.; Bourgeas, R.; Bouzidi, S.; Chetrit, B.; Hamon, V.; Morelli, X.; Roche, P. 2p2idb: A structural database dedicated to orthosteric modulation of protein-protein interactions. Nucleic Acids Res. 2013, 41, D824-D827.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D824-D827
-
-
Basse, M.J.1
Betzi, S.2
Bourgeas, R.3
Bouzidi, S.4
Chetrit, B.5
Hamon, V.6
Morelli, X.7
Roche, P.8
-
59
-
-
79960990847
-
Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2p2i)
-
Morelli, X.; Bourgeas, R.; Roche, P. Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2p2i). Curr. Opin. Chem. Biol. 2011, 15, 475-481.
-
(2011)
Curr. Opin. Chem. Biol.
, vol.15
, pp. 475-481
-
-
Morelli, X.1
Bourgeas, R.2
Roche, P.3
-
60
-
-
84867881743
-
Structure-based prediction of protein-protein interactions on a genome-wide scale
-
Zhang, Q.C.; Petrey, D.; Deng, L.; Qiang, L.; Shi, Y.; Thu, C.A.; Bisikirska, B.; Lefebvre, C.; Accili, D.; Hunter, T.; et al. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 2012, 490, 556-560.
-
(2012)
Nature
, vol.490
, pp. 556-560
-
-
Zhang, Q.C.1
Petrey, D.2
Deng, L.3
Qiang, L.4
Shi, Y.5
Thu, C.A.6
Bisikirska, B.7
Lefebvre, C.8
Accili, D.9
Hunter, T.10
-
61
-
-
84876515907
-
String v9.1: Protein-protein interaction networks, with increased coverage and integration
-
Franceschini, A.; Szklarczyk, D.; Frankild, S.; Kuhn, M.; Simonovic, M.; Roth, A.; Lin, J.; Minguez, P.; Bork, P.; von Mering, C.; et al. String v9.1: Protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013, 41, D808-D815.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D808-D815
-
-
Franceschini, A.1
Szklarczyk, D.2
Frankild, S.3
Kuhn, M.4
Simonovic, M.5
Roth, A.6
Lin, J.7
Minguez, P.8
Bork, P.9
Von Mering, C.10
-
62
-
-
78651324347
-
The string database in 2011: Functional interaction networks of proteins, globally integrated and scored
-
Szklarczyk, D.; Franceschini, A.; Kuhn, M.; Simonovic, M.; Roth, A.; Minguez, P.; Doerks, T.; Stark, M.; Muller, J.; Bork, P.; et al. The string database in 2011: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011, 39, D561-D568.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D561-D568
-
-
Szklarczyk, D.1
Franceschini, A.2
Kuhn, M.3
Simonovic, M.4
Roth, A.5
Minguez, P.6
Doerks, T.7
Stark, M.8
Muller, J.9
Bork, P.10
-
63
-
-
84857784008
-
Ibis (inferred biomolecular interaction server) reports, predicts and integrates multiple types of conserved interactions for proteins
-
Shoemaker, B.A.; Zhang, D.; Tyagi, M.; Thangudu, R.R.; Fong, J.H.; Marchler-Bauer, A.; Bryant, S.H.; Madej, T.; Panchenko, A.R. Ibis (inferred biomolecular interaction server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Res. 2012, 40, D834-D840.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D834-D840
-
-
Shoemaker, B.A.1
Zhang, D.2
Tyagi, M.3
Thangudu, R.R.4
Fong, J.H.5
Marchler-Bauer, A.6
Bryant, S.H.7
Madej, T.8
Panchenko, A.R.9
-
64
-
-
75549083885
-
Inferred biomolecular interaction server-A web server to analyze and predict protein interacting partners and binding sites
-
Shoemaker, B.A.; Zhang, D.; Thangudu, R.R.; Tyagi, M.; Fong, J.H.; Marchler-Bauer, A.; Bryant, S.H.; Madej, T.; Panchenko, A.R. Inferred biomolecular interaction server-A web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res. 2010, 38, D518-D524.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. D518-D524
-
-
Shoemaker, B.A.1
Zhang, D.2
Thangudu, R.R.3
Tyagi, M.4
Fong, J.H.5
Marchler-Bauer, A.6
Bryant, S.H.7
Madej, T.8
Panchenko, A.R.9
-
65
-
-
58149178567
-
Pips: Human protein-protein interaction prediction database
-
McDowall, M.D.; Scott, M.S.; Barton, G.J. Pips: Human protein-protein interaction prediction database. Nucleic Acids Res. 2009, 37, D651-D656.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D651-D656
-
-
McDowall, M.D.1
Scott, M.S.2
Barton, G.J.3
-
66
-
-
34547693013
-
Probabilistic prediction and ranking of human protein-protein interactions
-
Scott, M.S.; Barton, G.J. Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinform. 2007, 8, doi:10.1186/1471-2105-8-239.
-
(2007)
BMC Bioinform.
, vol.8
-
-
Scott, M.S.1
Barton, G.J.2
-
67
-
-
77954636479
-
Protein interface conservation across structure space
-
Zhang, Q.C.; Petrey, D.; Norel, R.; Honig, B.H. Protein interface conservation across structure space. Proc. Natl. Acad. Sci. USA 2010, 107, 10896-10901.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 10896-10901
-
-
Zhang, Q.C.1
Petrey, D.2
Norel, R.3
Honig, B.H.4
-
68
-
-
79960027319
-
Markus: A server to navigate sequence-structure-function space
-
Fischer, M.; Zhang, Q.C.; Dey, F.; Chen, B.Y.; Honig, B.; Petrey, D. Markus: A server to navigate sequence-structure-function space. Nucleic Acids Res. 2011, 39, W357-W361.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W357-W361
-
-
Fischer, M.1
Zhang, Q.C.2
Dey, F.3
Chen, B.Y.4
Honig, B.5
Petrey, D.6
-
69
-
-
0036463402
-
Describing biological protein interactions in terms of protein states and state transitions: The livedip database
-
Duan, X.J.; Xenarios, I.; Eisenberg, D. Describing biological protein interactions in terms of protein states and state transitions: The livedip database. Mol. Cell. Proteomics MCP 2002, 1, 104-116.
-
(2002)
Mol. Cell. Proteomics MCP
, vol.1
, pp. 104-116
-
-
Duan, X.J.1
Xenarios, I.2
Eisenberg, D.3
-
70
-
-
0037245913
-
Bind: The biomolecular interaction network database
-
Bader, G.D.; Betel, D.; Hogue, C.W. Bind: The biomolecular interaction network database. Nucleic Acids Res. 2003, 31, 248-250.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.W.3
-
71
-
-
33644878150
-
Mpact: The mips protein interaction resource on yeast
-
Guldener, U.; Munsterkotter, M.; Oesterheld, M.; Pagel, P.; Ruepp, A.; Mewes, H.W.; Stumpflen, V. Mpact: The mips protein interaction resource on yeast. Nucleic Acids Res. 2006, 34, D436-D441.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D436-D441
-
-
Guldener, U.1
Munsterkotter, M.2
Oesterheld, M.3
Pagel, P.4
Ruepp, A.5
Mewes, H.W.6
Stumpflen, V.7
-
72
-
-
0034747024
-
Ypd, pombepd and wormpd: Model organism volumes of the bioknowledge library, an integrated resource for protein information
-
Costanzo, M.C.; Crawford, M.E.; Hirschman, J.E.; Kranz, J.E.; Olsen, P.; Robertson, L.S.; Skrzypek, M.S.; Braun, B.R.; Hopkins, K.L.; Kondu, P.; et al. Ypd, pombepd and wormpd: Model organism volumes of the bioknowledge library, an integrated resource for protein information. Nucleic Acids Res. 2001, 29, 75-79.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 75-79
-
-
Costanzo, M.C.1
Crawford, M.E.2
Hirschman, J.E.3
Kranz, J.E.4
Olsen, P.5
Robertson, L.S.6
Skrzypek, M.S.7
Braun, B.R.8
Hopkins, K.L.9
Kondu, P.10
-
73
-
-
0033968614
-
The yeast proteome database (YPD) and caenorhabditis elegans proteome database (WormPD): Comprehensive resources for the organization and comparison of model organism protein information
-
Costanzo, M.C.; Hogan, J.D.; Cusick, M.E.; Davis, B.P.; Fancher, A.M.; Hodges, P.E.; Kondu, P.; Lengieza, C.; Lew-Smith, J.E.; Lingner, C.; et al. The yeast proteome database (YPD) and caenorhabditis elegans proteome database (WormPD): Comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res. 2000, 28, 73-76.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 73-76
-
-
Costanzo, M.C.1
Hogan, J.D.2
Cusick, M.E.3
Davis, B.P.4
Fancher, A.M.5
Hodges, P.E.6
Kondu, P.7
Lengieza, C.8
Lew-Smith, J.E.9
Lingner, C.10
-
75
-
-
0037138406
-
Mint: A molecular interaction database
-
Zanzoni, A.; Montecchi-Palazzi, L.; Quondam, M.; Ausiello, G.; Helmer-Citterich, M.; Cesareni, G. Mint: A molecular interaction database. FEBS Lett. 2002, 513, 135-140.
-
(2002)
FEBS Lett.
, vol.513
, pp. 135-140
-
-
Zanzoni, A.1
Montecchi-Palazzi, L.2
Quondam, M.3
Ausiello, G.4
Helmer-Citterich, M.5
Cesareni, G.6
-
76
-
-
84891799734
-
The mintact project-Intact as a common curation platform for 11 molecular interaction databases
-
Orchard, S.; Ammari, M.; Aranda, B.; Breuza, L.; Briganti, L.; Broackes-Carter, F.; Campbell, N.H.; Chavali, G.; Chen, C.; del-Toro, N.; et al. The mintact project-Intact as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 2014, 42, D358-D363.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D358-D363
-
-
Orchard, S.1
Ammari, M.2
Aranda, B.3
Breuza, L.4
Briganti, L.5
Broackes-Carter, F.6
Campbell, N.H.7
Chavali, G.8
Chen, C.9
Del-Toro, N.10
-
77
-
-
84941145210
-
The biogrid interaction database: 2015 update
-
Chatr-Aryamontri, A.; Breitkreutz, B.J.; Oughtred, R.; Boucher, L.; Heinicke, S.; Chen, D.; Stark, C.; Breitkreutz, A.; Kolas, N.; O'Donnell, L.; et al. The biogrid interaction database: 2015 update. Nucleic Acids Res. 2015, 43, D470-D478.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D470-D478
-
-
Chatr-Aryamontri, A.1
Breitkreutz, B.J.2
Oughtred, R.3
Boucher, L.4
Heinicke, S.5
Chen, D.6
Stark, C.7
Breitkreutz, A.8
Kolas, N.9
O'Donnell, L.10
-
78
-
-
58149193222
-
Human protein reference database-2009 update
-
Keshava Prasad, T.S.; Goel, R.; Kandasamy, K.; Keerthikumar, S.; Kumar, S.; Mathivanan, S.; Telikicherla, D.; Raju, R.; Shafreen, B.; Venugopal, A.; et al. Human protein reference database-2009 update. Nucleic Acids Res. 2009, 37, D767-D772.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D767-D772
-
-
Keshava Prasad, T.S.1
Goel, R.2
Kandasamy, K.3
Keerthikumar, S.4
Kumar, S.5
Mathivanan, S.6
Telikicherla, D.7
Raju, R.8
Shafreen, B.9
Venugopal, A.10
-
79
-
-
83455224806
-
An overview of human protein databases and their application to functional proteomics in health and disease
-
Zhang, Y.; Zhu, Y.; He, F. An overview of human protein databases and their application to functional proteomics in health and disease. Sci. China Life Sci. 2011, 54, 988-998.
-
(2011)
Sci. China Life Sci.
, vol.54
, pp. 988-998
-
-
Zhang, Y.1
Zhu, Y.2
He, F.3
-
80
-
-
33846077881
-
Protcom: Searchable database of protein complexes enhanced with domain-domain structures
-
Kundrotas, P.J.; Alexov, E. Protcom: Searchable database of protein complexes enhanced with domain-domain structures. Nucleic Acids Res. 2007, 35, D575-D579.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D575-D579
-
-
Kundrotas, P.J.1
Alexov, E.2
-
81
-
-
68949089840
-
On the electrostatic component of protein-protein binding free energy
-
Talley, K.; Ng, C.; Shoppell, M.; Kundrotas, P.; Alexov, E. On the electrostatic component of protein-protein binding free energy. PMC Biophys. 2008, 1, 2, doi:10.1186/1757-5036-1-2.
-
(2008)
PMC Biophys.
, vol.1
, pp. 2
-
-
Talley, K.1
Ng, C.2
Shoppell, M.3
Kundrotas, P.4
Alexov, E.5
-
82
-
-
84891779335
-
3did: A catalog of domain-based interactions of known three-dimensional structure
-
Mosca, R.; Ceol, A.; Stein, A.; Olivella, R.; Aloy, P. 3did: A catalog of domain-based interactions of known three-dimensional structure. Nucleic Acids Res. 2014, 42, D374-D379.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D374-D379
-
-
Mosca, R.1
Ceol, A.2
Stein, A.3
Olivella, R.4
Aloy, P.5
-
83
-
-
78651344377
-
3did: Identification and classification of domain-based interactions of known three-dimensional structure
-
Stein, A.; Ceol, A.; Aloy, P. 3did: Identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res. 2011, 39, D718-D723.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D718-D723
-
-
Stein, A.1
Ceol, A.2
Aloy, P.3
-
84
-
-
18744382508
-
Pibase: A comprehensive database of structurally defined protein interfaces
-
Davis, F.P.; Sali, A. Pibase: A comprehensive database of structurally defined protein interfaces. Bioinformatics 2005, 21, 1901-1907.
-
(2005)
Bioinformatics
, vol.21
, pp. 1901-1907
-
-
Davis, F.P.1
Sali, A.2
-
85
-
-
84871757599
-
From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: The pibase software
-
Forster, M.; Forster, P.; Elsharawy, A.; Hemmrich, G.; Kreck, B.; Wittig, M.; Thomsen, I.; Stade, B.; Barann, M.; Ellinghaus, D.; et al. From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: The pibase software. Nucleic Acids Res. 2013, 41, e16, doi:10.1093/nar/gks836.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. e16
-
-
Forster, M.1
Forster, P.2
Elsharawy, A.3
Hemmrich, G.4
Kreck, B.5
Wittig, M.6
Thomsen, I.7
Stade, B.8
Barann, M.9
Ellinghaus, D.10
-
86
-
-
4744368323
-
Carbohydrate-binding modules: Fine tuning polysaccharide recognition
-
Boraston, A.B.; Bolam, D.N.; Gilbert, H.J.; Davies, G.J. Carbohydrate-binding modules: Fine tuning polysaccharide recognition. Biochem. J. 2004, 382, 769-781.
-
(2004)
Biochem. J.
, vol.382
, pp. 769-781
-
-
Boraston, A.B.1
Bolam, D.N.2
Gilbert, H.J.3
Davies, G.J.4
-
87
-
-
33846113064
-
Recent structural studies of carbohydrate-binding modules
-
Hashimoto, H. Recent structural studies of carbohydrate-binding modules. Cell. Mol. Life Sci. 2006, 63, 2954-2967.
-
(2006)
Cell. Mol. Life Sci.
, vol.63
, pp. 2954-2967
-
-
Hashimoto, H.1
-
88
-
-
33644876493
-
SCOPPI: A structural classification of protein-protein interfaces
-
Winter, C.; Henschel, A.; Kim, W.K.; Schroeder, M. SCOPPI: A structural classification of protein-protein interfaces. Nucleic Acids Res. 2006, 34, D310-D314.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D310-D314
-
-
Winter, C.1
Henschel, A.2
Kim, W.K.3
Schroeder, M.4
-
89
-
-
28644448657
-
Survey of the geometric association of domain-domain interfaces
-
Kim, W.K.; Ison, J.C. Survey of the geometric association of domain-domain interfaces. Proteins 2005, 61, 1075-1088.
-
(2005)
Proteins
, vol.61
, pp. 1075-1088
-
-
Kim, W.K.1
Ison, J.C.2
-
90
-
-
84891796273
-
Ipfam: A database of protein family and domain interactions found in the protein data bank
-
Finn, R.D.; Miller, B.L.; Clements, J.; Bateman, A. Ipfam: A database of protein family and domain interactions found in the protein data bank. Nucleic Acids Res. 2014, 42, D364-D373.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D364-D373
-
-
Finn, R.D.1
Miller, B.L.2
Clements, J.3
Bateman, A.4
-
91
-
-
84938249876
-
In silico identification of protein-protein interactions in silkworm, bombyx mori
-
Sumathy, R.; Rao, A.S.; Chandrakanth, N.; Gopalakrishnan, V.K. In silico identification of protein-protein interactions in silkworm, bombyx mori. Bioinformation 2014, 10, 56-62.
-
(2014)
Bioinformation
, vol.10
, pp. 56-62
-
-
Sumathy, R.1
Rao, A.S.2
Chandrakanth, N.3
Gopalakrishnan, V.K.4
-
92
-
-
0037250151
-
Interdom: A database of putative interacting protein domains for validating predicted protein interactions and complexes
-
Ng, S.K.; Zhang, Z.; Tan, S.H.; Lin, K. Interdom: A database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res. 2003, 31, 251-254.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 251-254
-
-
Ng, S.K.1
Zhang, Z.2
Tan, S.H.3
Lin, K.4
-
93
-
-
78651334820
-
Dima 3.0: Domain interaction map
-
Luo, Q.; Pagel, P.; Vilne, B.; Frishman, D. Dima 3.0: Domain interaction map. Nucleic Acids Res. 2011, 39, D724-D729.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D724-D729
-
-
Luo, Q.1
Pagel, P.2
Vilne, B.3
Frishman, D.4
-
94
-
-
4644231028
-
Prolinks: A database of protein functional linkages derived from coevolution
-
Bowers, P.M.; Pellegrini, M.; Thompson, M.J.; Fierro, J.; Yeates, T.O.; Eisenberg, D. Prolinks: A database of protein functional linkages derived from coevolution. Genome Biol. 2004, 5, R35.
-
(2004)
Genome Biol.
, vol.5
, pp. R35
-
-
Bowers, P.M.1
Pellegrini, M.2
Thompson, M.J.3
Fierro, J.4
Yeates, T.O.5
Eisenberg, D.6
-
95
-
-
84897007440
-
Haddock(2p2i): A biophysical model for predicting the binding affinity of protein-protein interaction inhibitors
-
Kastritis, P.L.; Rodrigues, J.P.; Bonvin, A.M. Haddock(2p2i): A biophysical model for predicting the binding affinity of protein-protein interaction inhibitors. J. Chem. Inf. Model. 2014, 54, 826-836.
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 826-836
-
-
Kastritis, P.L.1
Rodrigues, J.P.2
Bonvin, A.M.3
-
96
-
-
84879916282
-
Pydockweb: A web server for rigid-body protein-protein docking using electrostatics and desolvation scoring
-
Jimenez-Garcia, B.; Pons, C.; Fernandez-Recio, J. Pydockweb: A web server for rigid-body protein-protein docking using electrostatics and desolvation scoring. Bioinformatics 2013, 29, 1698-1699.
-
(2013)
Bioinformatics
, vol.29
, pp. 1698-1699
-
-
Jimenez-Garcia, B.1
Pons, C.2
Fernandez-Recio, J.3
-
97
-
-
84866454213
-
Cell-dock: High-performance protein-protein docking
-
Pons, C.; Jimenez-Gonzalez, D.; Gonzalez-Alvarez, C.; Servat, H.; Cabrera-Benitez, D.; Aguilar, X.; Fernandez-Recio, J. Cell-dock: High-performance protein-protein docking. Bioinformatics 2012, 28, 2394-2396.
-
(2012)
Bioinformatics
, vol.28
, pp. 2394-2396
-
-
Pons, C.1
Jimenez-Gonzalez, D.2
Gonzalez-Alvarez, C.3
Servat, H.4
Cabrera-Benitez, D.5
Aguilar, X.6
Fernandez-Recio, J.7
-
98
-
-
84891818638
-
Kbdock 2013: A spatial classification of 3d protein domain family interactions
-
Ghoorah, A.W.; Devignes, M.D.; Smail-Tabbone, M.; Ritchie, D.W. Kbdock 2013: A spatial classification of 3d protein domain family interactions. Nucleic Acids Res. 2014, 42, D389-D395.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D389-D395
-
-
Ghoorah, A.W.1
Devignes, M.D.2
Smail-Tabbone, M.3
Ritchie, D.W.4
-
99
-
-
78449292668
-
F2dock: Fast fourier protein-protein docking
-
Bajaj, C.; Chowdhury, R.; Siddavanahalli, V. F2dock: Fast fourier protein-protein docking. IEEEACM Trans. Comput. Biol. Bioinform. 2011, 8, 45-58.
-
(2011)
IEEEACM Trans. Comput. Biol. Bioinform.
, vol.8
, pp. 45-58
-
-
Bajaj, C.1
Chowdhury, R.2
Siddavanahalli, V.3
-
100
-
-
0034212826
-
Bigger: A new (soft) docking algorithm for predicting protein interactions
-
Palma, P.N.; Krippahl, L.; Wampler, J.E.; Moura, J.J. Bigger: A new (soft) docking algorithm for predicting protein interactions. Proteins 2000, 39, 372-384.
-
(2000)
Proteins
, vol.39
, pp. 372-384
-
-
Palma, P.N.1
Krippahl, L.2
Wampler, J.E.3
Moura, J.J.4
-
101
-
-
70349882144
-
Frodock: A new approach for fast rotational protein-protein docking
-
Garzon, J.I.; Lopez-Blanco, J.R.; Pons, C.; Kovacs, J.; Abagyan, R.; Fernandez-Recio, J.; Chacon, P. Frodock: A new approach for fast rotational protein-protein docking. Bioinformatics 2009, 25, 2544-2551.
-
(2009)
Bioinformatics
, vol.25
, pp. 2544-2551
-
-
Garzon, J.I.1
Lopez-Blanco, J.R.2
Pons, C.3
Kovacs, J.4
Abagyan, R.5
Fernandez-Recio, J.6
Chacon, P.7
-
102
-
-
84907874609
-
Dock/pierr: Web server for structure prediction of protein-protein complexes
-
Viswanath, S.; Ravikant, D.V.; Elber, R. Dock/pierr: Web server for structure prediction of protein-protein complexes. Methods Mol. Biol. 2014, 1137, 199-207.
-
(2014)
Methods Mol. Biol.
, vol.1137
, pp. 199-207
-
-
Viswanath, S.1
Ravikant, D.V.2
Elber, R.3
-
103
-
-
80052903046
-
Accelerating protein docking in zdock using an advanced 3d convolution library
-
Pierce, B.G.; Hourai, Y.; Weng, Z. Accelerating protein docking in zdock using an advanced 3d convolution library. PLoS ONE 2011, 6, e24657.
-
(2011)
PLoS ONE
, vol.6
, pp. e24657
-
-
Pierce, B.G.1
Hourai, Y.2
Weng, Z.3
-
104
-
-
84897980054
-
Zdock server: Interactive docking prediction of protein-protein complexes and symmetric multimers
-
Pierce, B.G.; Wiehe, K.; Hwang, H.; Kim, B.H.; Vreven, T.; Weng, Z. Zdock server: Interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics 2014, 30, 1771-1773.
-
(2014)
Bioinformatics
, vol.30
, pp. 1771-1773
-
-
Pierce, B.G.1
Wiehe, K.2
Hwang, H.3
Kim, B.H.4
Vreven, T.5
Weng, Z.6
-
105
-
-
74049092313
-
Protein-protein docking using region-based 3D Zernike descriptors
-
Venkatraman, V.; Yang, Y.D.; Sael, L.; Kihara, D. Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinform. 2009, 10, doi:10.1186/1471-2105-10-407.
-
(2009)
BMC Bioinform.
, vol.10
-
-
Venkatraman, V.1
Yang, Y.D.2
Sael, L.3
Kihara, D.4
-
106
-
-
84855964607
-
Attract and ptools: Open source programs for protein-protein docking
-
Schneider, S.; Saladin, A.; Fiorucci, S.; Prevost, C.; Zacharias, M. Attract and ptools: Open source programs for protein-protein docking. Methods Mol. Biol. 2012, 819, 221-232.
-
(2012)
Methods Mol. Biol.
, vol.819
, pp. 221-232
-
-
Schneider, S.1
Saladin, A.2
Fiorucci, S.3
Prevost, C.4
Zacharias, M.5
-
107
-
-
84875151263
-
Swarmdock: A server for flexible protein-protein docking
-
Torchala, M.; Moal, I.H.; Chaleil, R.A.; Fernandez-Recio, J.; Bates, P.A. Swarmdock: A server for flexible protein-protein docking. Bioinformatics 2013, 29, 807-809.
-
(2013)
Bioinformatics
, vol.29
, pp. 807-809
-
-
Torchala, M.1
Moal, I.H.2
Chaleil, R.A.3
Fernandez-Recio, J.4
Bates, P.A.5
-
108
-
-
79959948212
-
Prune and probe-Two modular web services for protein-protein docking
-
Mitra, P.; Pal, D. Prune and probe-Two modular web services for protein-protein docking. Nucleic Acids Res. 2011, 39, W229-W234.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W229-W234
-
-
Mitra, P.1
Pal, D.2
-
109
-
-
42649122289
-
3D-garden: A system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm
-
Lesk, V.I.; Sternberg, M.J. 3D-garden: A system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. Bioinformatics 2008, 24, 1137-1144.
-
(2008)
Bioinformatics
, vol.24
, pp. 1137-1144
-
-
Lesk, V.I.1
Sternberg, M.J.2
-
110
-
-
0031296899
-
CASP2 molecular docking predictions with the LIGIN software
-
Sobolev, V.; Moallem, T.M.; Wade, R.C.; Vriend, G.; Edelman, M. CASP2 molecular docking predictions with the LIGIN software. Proteins 1997, 1, 210-214.
-
(1997)
Proteins
, vol.1
, pp. 210-214
-
-
Sobolev, V.1
Moallem, T.M.2
Wade, R.C.3
Vriend, G.4
Edelman, M.5
-
111
-
-
0038359596
-
Sucessful discrimination of protein interactions
-
Camacho, C.J.; Gatchell, D.W. Sucessful discrimination of protein interactions. Proteins 2003, 52, 92-97.
-
(2003)
Proteins
, vol.52
, pp. 92-97
-
-
Camacho, C.J.1
Gatchell, D.W.2
-
112
-
-
84879461612
-
Dot2: Macromolecular docking with improved biophysical models
-
Roberts, V.A.; Thompson, E.E.; Pique, M.E.; Perez, M.S.; Ten Eyck, L.F. Dot2: Macromolecular docking with improved biophysical models. J. Comput. Chem. 2013, 34, 1743-1758.
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 1743-1758
-
-
Roberts, V.A.1
Thompson, E.E.2
Pique, M.E.3
Perez, M.S.4
Ten Eyck, L.F.5
-
113
-
-
48449105393
-
The rosettadock server for local protein-protein docking
-
Lyskov, S.; Gray, J.J. The rosettadock server for local protein-protein docking. Nucleic Acids Res. 2008, 36, W233-W238.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. W233-W238
-
-
Lyskov, S.1
Gray, J.J.2
-
114
-
-
33847317318
-
Inherent limitations in protein-protein docking procedures
-
Kowalsman, N.; Eisenstein, M. Inherent limitations in protein-protein docking procedures. Bioinformatics 2007, 23, 421-426.
-
(2007)
Bioinformatics
, vol.23
, pp. 421-426
-
-
Kowalsman, N.1
Eisenstein, M.2
-
115
-
-
77957242885
-
Ultra-fast fft protein docking on graphics processors
-
Ritchie, D.W.; Venkatraman, V. Ultra-fast fft protein docking on graphics processors. Bioinformatics 2010, 26, 2398-2405.
-
(2010)
Bioinformatics
, vol.26
, pp. 2398-2405
-
-
Ritchie, D.W.1
Venkatraman, V.2
-
116
-
-
21644458085
-
Development and testing of an automated approach to protein docking
-
Tovchigrechko, A.; Vakser, I.A. Development and testing of an automated approach to protein docking. Proteins 2005, 60, 296-301.
-
(2005)
Proteins
, vol.60
, pp. 296-301
-
-
Tovchigrechko, A.1
Vakser, I.A.2
-
117
-
-
84888295075
-
How good is automated protein docking?
-
Kozakov, D.; Beglov, D.; Bohnuud, T.; Mottarella, S.E.; Xia, B.; Hall, D.R.; Vajda, S. How good is automated protein docking? Proteins 2013, 81, 2159-2166.
-
(2013)
Proteins
, vol.81
, pp. 2159-2166
-
-
Kozakov, D.1
Beglov, D.2
Bohnuud, T.3
Mottarella, S.E.4
Xia, B.5
Hall, D.R.6
Vajda, S.7
-
118
-
-
0345832301
-
Cluspro: An automated docking and discrimination method for the prediction of protein complexes
-
Comeau, S.R.; Gatchell, D.W.; Vajda, S.; Camacho, C.J. Cluspro: An automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 2004, 20, 45-50.
-
(2004)
Bioinformatics
, vol.20
, pp. 45-50
-
-
Comeau, S.R.1
Gatchell, D.W.2
Vajda, S.3
Camacho, C.J.4
-
119
-
-
77952068704
-
Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark
-
Kastritis, P.L.; Bonvin, A.M. Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J. Proteome Res. 2010, 9, 2216-2225.
-
(2010)
J. Proteome Res.
, vol.9
, pp. 2216-2225
-
-
Kastritis, P.L.1
Bonvin, A.M.2
-
120
-
-
84892698856
-
Protein-protein interactions in a crowded environment: An analysis via cross-docking simulations and evolutionary information
-
Lopes, A.; Sacquin-Mora, S.; Dimitrova, V.; Laine, E.; Ponty, Y.; Carbone, A. Protein-protein interactions in a crowded environment: An analysis via cross-docking simulations and evolutionary information. PLoS Comput. Biol. 2013, 9, e1003369.
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1003369
-
-
Lopes, A.1
Sacquin-Mora, S.2
Dimitrova, V.3
Laine, E.4
Ponty, Y.5
Carbone, A.6
-
121
-
-
84908098529
-
Udock, the interactive docking entertainment system
-
Levieux, G.; Tiger, G.; Mader, S.; Zagury, J.F.; Natkin, S.; Montes, M. Udock, the interactive docking entertainment system. Faraday Discuss. 2014, 169, 425-441.
-
(2014)
Faraday Discuss.
, vol.169
, pp. 425-441
-
-
Levieux, G.1
Tiger, G.2
Mader, S.3
Zagury, J.F.4
Natkin, S.5
Montes, M.6
-
122
-
-
34548317146
-
Firedock: Fast interaction refinement in molecular docking
-
Andrusier, N.; Nussinov, R.; Wolfson, H.J. Firedock: Fast interaction refinement in molecular docking. Proteins 2007, 69, 139-159.
-
(2007)
Proteins
, vol.69
, pp. 139-159
-
-
Andrusier, N.1
Nussinov, R.2
Wolfson, H.J.3
-
123
-
-
48449092207
-
Firedock: A web server for fast interaction refinement in molecular docking
-
Mashiach, E.; Schneidman-Duhovny, D.; Andrusier, N.; Nussinov, R.; Wolfson, H.J. Firedock: A web server for fast interaction refinement in molecular docking. Nucleic Acids Res. 2008, 36, W229-W232.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. W229-W232
-
-
Mashiach, E.1
Schneidman-Duhovny, D.2
Andrusier, N.3
Nussinov, R.4
Wolfson, H.J.5
-
124
-
-
0031565730
-
Modelling protein docking using shape complementarity, electrostatics and biochemical information
-
Gabb, H.A.; Jackson, R.M.; Sternberg, M.J. 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.3
-
125
-
-
39749202824
-
Hingeprot: Automated prediction of hinges in protein structures
-
Emekli, U.; Schneidman-Duhovny, D.; Wolfson, H.J.; Nussinov, R.; Haliloglu, T. Hingeprot: Automated prediction of hinges in protein structures. Proteins 2008, 70, 1219-1227.
-
(2008)
Proteins
, vol.70
, pp. 1219-1227
-
-
Emekli, U.1
Schneidman-Duhovny, D.2
Wolfson, H.J.3
Nussinov, R.4
Haliloglu, T.5
-
126
-
-
84865265287
-
Docking and scoring with icm: The benchmarking results and strategies for improvement
-
Neves, M.A.; Totrov, M.; Abagyan, R. Docking and scoring with icm: The benchmarking results and strategies for improvement. J. Comput. Aided Mol. Des. 2012, 26, 675-686.
-
(2012)
J. Comput. Aided Mol. Des.
, vol.26
, pp. 675-686
-
-
Neves, M.A.1
Totrov, M.2
Abagyan, R.3
-
127
-
-
21644476468
-
Patchdock and symmdock: Servers for rigid and symmetric docking
-
Schneidman-Duhovny, D.; Inbar, Y.; Nussinov, R.; Wolfson, H.J. Patchdock and symmdock: Servers for rigid and symmetric docking. Nucleic Acids Res. 2005, 33, W363-W367.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. W363-W367
-
-
Schneidman-Duhovny, D.1
Inbar, Y.2
Nussinov, R.3
Wolfson, H.J.4
-
128
-
-
59149107086
-
Funhunt: Model selection based on energy landscape characteristics
-
London, N.; Schueler-Furman, O. Funhunt: Model selection based on energy landscape characteristics. Biochem. Soc. Trans. 2008, 36, 1418-1421.
-
(2008)
Biochem. Soc. Trans.
, vol.36
, pp. 1418-1421
-
-
London, N.1
Schueler-Furman, O.2
-
129
-
-
77951232176
-
Fiberdock: Flexible induced-fit backbone refinement in molecular docking
-
Mashiach, E.; Nussinov, R.; Wolfson, H.J. Fiberdock: Flexible induced-fit backbone refinement in molecular docking. Proteins 2010, 78, 1503-1519.
-
(2010)
Proteins
, vol.78
, pp. 1503-1519
-
-
Mashiach, E.1
Nussinov, R.2
Wolfson, H.J.3
-
130
-
-
77954267296
-
Fiberdock: A web server for flexible induced-fit backbone refinement in molecular docking
-
Mashiach, E.; Nussinov, R.; Wolfson, H.J. Fiberdock: A web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Res. 2010, 38, W457-W461.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W457-W461
-
-
Mashiach, E.1
Nussinov, R.2
Wolfson, H.J.3
-
131
-
-
79960164372
-
Protein-protein complex structure predictions by multimeric threading and template recombination
-
Mukherjee, S.; Zhang, Y. Protein-protein complex structure predictions by multimeric threading and template recombination. Structure 2011, 19, 955-966.
-
(2011)
Structure
, vol.19
, pp. 955-966
-
-
Mukherjee, S.1
Zhang, Y.2
-
132
-
-
84885686923
-
Specificity and affinity quantification of protein-protein interactions
-
Yan, Z.; Guo, L.; Hu, L.; Wang, J. Specificity and affinity quantification of protein-protein interactions. Bioinformatics 2013, 29, 1127-1133.
-
(2013)
Bioinformatics
, vol.29
, pp. 1127-1133
-
-
Yan, Z.1
Guo, L.2
Hu, L.3
Wang, J.4
-
133
-
-
18844462557
-
Fastcontact: Rapid estimate of contact and binding free energies
-
Camacho, C.J.; Zhang, C. Fastcontact: Rapid estimate of contact and binding free energies. Bioinformatics 2005, 21, 2534-2536.
-
(2005)
Bioinformatics
, vol.21
, pp. 2534-2536
-
-
Camacho, C.J.1
Zhang, C.2
-
134
-
-
84938253300
-
Consrank: A server for the analysis, comparison and ranking of docking models based on inter-residue contacts
-
Chermak, E.; Petta, A.; Serra, L.; Vangone, A.; Scarano, V.; Cavallo, L.; Oliva, R. Consrank: A server for the analysis, comparison and ranking of docking models based on inter-residue contacts. Bioinformatics 2015, 31, 1481-1483.
-
(2015)
Bioinformatics
, vol.31
, pp. 1481-1483
-
-
Chermak, E.1
Petta, A.2
Serra, L.3
Vangone, A.4
Scarano, V.5
Cavallo, L.6
Oliva, R.7
-
135
-
-
78449278402
-
Filtrest3d: Discrimination of structural models using restraints from experimental data
-
Gajda, M.J.; Tuszynska, I.; Kaczor, M.; Bakulina, A.Y.; Bujnicki, J.M. Filtrest3d: Discrimination of structural models using restraints from experimental data. Bioinformatics 2010, 26, 2986-2987.
-
(2010)
Bioinformatics
, vol.26
, pp. 2986-2987
-
-
Gajda, M.J.1
Tuszynska, I.2
Kaczor, M.3
Bakulina, A.Y.4
Bujnicki, J.M.5
-
136
-
-
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
-
137
-
-
35449008122
-
Integrating statistical pair potentials into protein complex prediction
-
Mintseris, J.; Pierce, B.; Wiehe, K.; Anderson, R.; Chen, R.; Weng, Z. Integrating statistical pair potentials into protein complex prediction. Proteins 2007, 69, 511-520.
-
(2007)
Proteins
, vol.69
, pp. 511-520
-
-
Mintseris, J.1
Pierce, B.2
Wiehe, K.3
Anderson, R.4
Chen, R.5
Weng, Z.6
-
138
-
-
70049112107
-
Pushing structural information into the yeast interactome by high-throughput protein docking experiments
-
Mosca, R.; Pons, C.; Fernandez-Recio, J.; Aloy, P. Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PLoS Comput. Biol. 2009, 5, e1000490.
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. e1000490
-
-
Mosca, R.1
Pons, C.2
Fernandez-Recio, J.3
Aloy, P.4
-
139
-
-
34248513078
-
Zrank: Reranking protein docking predictions with an optimized energy function
-
Pierce, B.; Weng, Z. Zrank: Reranking protein docking predictions with an optimized energy function. Proteins 2007, 67, 1078-1086.
-
(2007)
Proteins
, vol.67
, pp. 1078-1086
-
-
Pierce, B.1
Weng, Z.2
-
140
-
-
0037442962
-
Haddock: A protein-protein docking approach based on biochemical or biophysical information
-
Dominguez, C.; Boelens, R.; Bonvin, A.M. Haddock: A protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 2003, 125, 1731-1737.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.3
-
141
-
-
36748998784
-
Haddock versus haddock: New features and performance of haddock2.0 on the capri targets
-
De Vries, S.J.; van Dijk, A.D.; Krzeminski, M.; van Dijk, M.; Thureau, A.; Hsu, V.; Wassenaar, T.; Bonvin, A.M. Haddock versus haddock: New features and performance of haddock2.0 on the capri targets. Proteins 2007, 69, 726-733.
-
(2007)
Proteins
, vol.69
, pp. 726-733
-
-
De Vries, S.J.1
Van Dijk, A.D.2
Krzeminski, M.3
Van Dijk, M.4
Thureau, A.5
Hsu, V.6
Wassenaar, T.7
Bonvin, A.M.8
-
142
-
-
84871327327
-
Attract-em: A new method for the computational assembly of large molecular machines using cryo-em maps
-
De Vries, S.J.; Zacharias, M. Attract-em: A new method for the computational assembly of large molecular machines using cryo-em maps. PLoS ONE 2012, 7, e49733.
-
(2012)
PLoS ONE
, vol.7
, pp. e49733
-
-
De Vries, S.J.1
Zacharias, M.2
-
143
-
-
29144485503
-
Accounting for global protein deformability during protein-protein and protein-ligand docking
-
May, A.; Zacharias, M. Accounting for global protein deformability during protein-protein and protein-ligand docking. Biochim. Biophys. Acta 2005, 1754, 225-231.
-
(2005)
Biochim. Biophys. Acta
, vol.1754
, pp. 225-231
-
-
May, A.1
Zacharias, M.2
-
144
-
-
0038583687
-
Protein-protein docking with a reduced protein model accounting for side-chain flexibility
-
Zacharias, M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci. 2003, 12, 1271-1282.
-
(2003)
Protein Sci.
, vol.12
, pp. 1271-1282
-
-
Zacharias, M.1
-
145
-
-
34447286908
-
The Third Capri Assessment Meeting Toronto, Canada, 20-21
-
April 2007.
-
Janin, J.; Wodak, S. The Third Capri Assessment Meeting Toronto, Canada, 20-21 April 2007. Structure 2007, 15, 755-759.
-
(2007)
Structure
, vol.15
, pp. 755-759
-
-
Janin, J.1
Wodak, S.2
-
146
-
-
84927695321
-
Protein models docking benchmark 2
-
Anishchenko, I.; Kundrotas, P.J.; Tuzikov, A.V.; Vakser, I.A. Protein models docking benchmark 2. Proteins 2015, 83, 891-897.
-
(2015)
Proteins
, vol.83
, pp. 891-897
-
-
Anishchenko, I.1
Kundrotas, P.J.2
Tuzikov, A.V.3
Vakser, I.A.4
-
147
-
-
84902387512
-
Scoring docking conformations using predicted protein interfaces
-
Esmaielbeiki, R.; Nebel, J.C. Scoring docking conformations using predicted protein interfaces. BMC Bioinform. 2014, 15, doi:10.1186/1471-2105-15-171.
-
(2014)
BMC Bioinform.
, vol.15
-
-
Esmaielbeiki, R.1
Nebel, J.C.2
-
148
-
-
80054899738
-
Community-wide assessment of protein-interface modeling suggests improvements to design methodology
-
Fleishman, S.J.; Whitehead, T.A.; Strauch, E.M.; Corn, J.E.; Qin, S.; Zhou, H.X.; Mitchell, J.C.; Demerdash, O.N.; Takeda-Shitaka, M.; Terashi, G.; et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J. Mol. Biol. 2011, 414, 289-302.
-
(2011)
J. Mol. Biol.
, vol.414
, pp. 289-302
-
-
Fleishman, S.J.1
Whitehead, T.A.2
Strauch, E.M.3
Corn, J.E.4
Qin, S.5
Zhou, H.X.6
Mitchell, J.C.7
Demerdash, O.N.8
Takeda-Shitaka, M.9
Terashi, G.10
-
149
-
-
84860388898
-
Integrating atom-based and residue-based scoring functions for protein-protein docking
-
Vreven, T.; Hwang, H.; Weng, Z. Integrating atom-based and residue-based scoring functions for protein-protein docking. Protein Sci. 2011, 20, 1576-1586.
-
(2011)
Protein Sci.
, vol.20
, pp. 1576-1586
-
-
Vreven, T.1
Hwang, H.2
Weng, Z.3
-
150
-
-
61449104961
-
Fragment-based identification of druggable "hot spots" of proteins using fourier domain correlation techniques
-
Brenke, R.; Kozakov, D.; Chuang, G.Y.; Beglov, D.; Hall, D.; Landon, M.R.; Mattos, C.; Vajda, S. Fragment-based identification of druggable "hot spots" of proteins using fourier domain correlation techniques. Bioinformatics 2009, 25, 621-627.
-
(2009)
Bioinformatics
, vol.25
, pp. 621-627
-
-
Brenke, R.1
Kozakov, D.2
Chuang, G.Y.3
Beglov, D.4
Hall, D.5
Landon, M.R.6
Mattos, C.7
Vajda, S.8
-
151
-
-
17144373303
-
Druggability indices for protein targets derived from nmr-based screening data
-
Hajduk, P.J.; Huth, J.R.; Fesik, S.W. Druggability indices for protein targets derived from nmr-based screening data. J. Med. Chem. 2005, 48, 2518-2525.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 2518-2525
-
-
Hajduk, P.J.1
Huth, J.R.2
Fesik, S.W.3
-
152
-
-
84863243858
-
Computational prediction of protein hot spot residues
-
Morrow, J.K.; Zhang, S. Computational prediction of protein hot spot residues. Curr. Pharm. Des. 2012, 18, 1255-1265.
-
(2012)
Curr. Pharm. Des.
, vol.18
, pp. 1255-1265
-
-
Morrow, J.K.1
Zhang, S.2
-
153
-
-
0037007068
-
Computational mapping identifies the binding sites of organic solvents on proteins
-
Dennis, S.; Kortvelyesi, T.; Vajda, S. Computational mapping identifies the binding sites of organic solvents on proteins. Proc. Natl. Acad. Sci. USA 2002, 99, 4290-4295.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 4290-4295
-
-
Dennis, S.1
Kortvelyesi, T.2
Vajda, S.3
-
154
-
-
84904803244
-
A web server for predicting protein-protein interaction hot spots by using structural neighborhood properties
-
Deng, L.; Zhang, Q.C.; Chen, Z.; Meng, Y.; Guan, J.; Zhou, S. PredHS: A web server for predicting protein-protein interaction hot spots by using structural neighborhood properties. Nucleic Acids Res. 2015, 42, W290-W295.
-
(2015)
Nucleic Acids Res.
, vol.42
, pp. W290-W295
-
-
Deng, L.1
Zhang, Q.C.2
Chen, Z.3
Meng, Y.4
Guan, J.5
Zhou, S.6
Pred, H.S.7
-
155
-
-
79952205470
-
Predictions of hot spot residues at protein-protein interfaces using support vector machines
-
Lise, S.; Buchan, D.; Pontil, M.; Jones, D.T. Predictions of hot spot residues at protein-protein interfaces using support vector machines. PLoS ONE 2011, 6, e16774.
-
(2011)
PLoS ONE
, vol.6
, pp. e16774
-
-
Lise, S.1
Buchan, D.2
Pontil, M.3
Jones, D.T.4
-
156
-
-
79953060278
-
Context-based identification of proteinprotein interfaces and "hot-spot" residues
-
Geppert, T.; Hoy, B.; Wessler, S.; Schneider, G. Context-based identification of proteinprotein interfaces and "hot-spot" residues. Chem. Biol. 2011, 18, 344-353.
-
(2011)
Chem. Biol.
, vol.18
, pp. 344-353
-
-
Geppert, T.1
Hoy, B.2
Wessler, S.3
Schneider, G.4
-
157
-
-
77954294794
-
Hotpoint: Hot spot prediction server for protein interfaces
-
Tuncbag, N.; Keksin, O.; Gursoy, A. Hotpoint: Hot spot prediction server for protein interfaces. Nucleic Acids Res. 2010, 38, W402-W406.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W402-W406
-
-
Tuncbag, N.1
Keksin, O.2
Gursoy, A.3
-
158
-
-
3242887695
-
Protein structure prediction and analysis using the Robetta server
-
Kim, D.E.; Chivian, D.; Baker, D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 2004, 32, W526-W531.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. W526-W531
-
-
Kim, D.E.1
Chivian, D.2
Baker, D.3
-
159
-
-
80051576392
-
KFC2: A knowledge-based hot spot prediction method based on interface solvation, atomic density and plasticity features
-
Zhu, X.; Mitchell, J.C. KFC2: A knowledge-based hot spot prediction method based on interface solvation, atomic density and plasticity features. Proteins 2011, 79, 2671-2683.
-
(2011)
Proteins
, vol.79
, pp. 2671-2683
-
-
Zhu, X.1
Mitchell, J.C.2
-
160
-
-
78049492156
-
Presaging Critical Residues in Protein interfaces-Web Server (PCRPi-W): A Web Server to Chart Hot Spots in Protein Interfaces
-
Mora, J.S.; Assi, S.A. Presaging Critical Residues in Protein interfaces-Web Server (PCRPi-W): A Web Server to Chart Hot Spots in Protein Interfaces. PLoS ONE 2010, 5, e12352.
-
(2010)
PLoS ONE
, vol.5
, pp. e12352
-
-
Mora, J.S.1
Assi, S.A.2
-
161
-
-
0037138380
-
Can we infer peptide recognition specificity mediated by sh3 domains?
-
Cesareni, G.; Panni, S.; Nardelli, G.; Castagnoli, L. Can we infer peptide recognition specificity mediated by sh3 domains? FEBS Lett. 2002, 513, 38-44.
-
(2002)
FEBS Lett.
, vol.513
, pp. 38-44
-
-
Cesareni, G.1
Panni, S.2
Nardelli, G.3
Castagnoli, L.4
-
162
-
-
79959981040
-
Rosetta flexpepdock web server-High resolution modeling of peptide-protein interactions
-
London, N.; Raveh, B.; Cohen, E.; Fathi, G.; Schueler-Furman, O. Rosetta flexpepdock web server-High resolution modeling of peptide-protein interactions. Nucleic Acids Res. 2011, 39, W249-W253.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W249-W253
-
-
London, N.1
Raveh, B.2
Cohen, E.3
Fathi, G.4
Schueler-Furman, O.5
-
163
-
-
0026794581
-
The three-dimensional structure of HLA-b27 at 2.1 Å resolution suggests a general mechanism for tight peptide binding to MHC
-
Madden, D.R.; Gorga, J.C.; Strominger, J.L.; Wiley, D.C. The three-dimensional structure of HLA-b27 at 2.1 Å resolution suggests a general mechanism for tight peptide binding to mhc. Cell 1992, 70, 1035-1048.
-
(1992)
Cell
, vol.70
, pp. 1035-1048
-
-
Madden, D.R.1
Gorga, J.C.2
Strominger, J.L.3
Wiley, D.C.4
-
164
-
-
15644379801
-
Recognition of unique carboxyl-terminal motifs by distinct pdz domains
-
Songyang, Z.; Fanning, A.S.; Fu, C.; Xu, J.; Marfatia, S.M.; Chishti, A.H.; Crompton, A.; Chan, A.C.; Anderson, J.M.; Cantley, L.C. Recognition of unique carboxyl-terminal motifs by distinct pdz domains. Science 1997, 275, 73-77.
-
(1997)
Science
, vol.275
, pp. 73-77
-
-
Songyang, Z.1
Fanning, A.S.2
Fu, C.3
Xu, J.4
Marfatia, S.M.5
Chishti, A.H.6
Crompton, A.7
Chan, A.C.8
Anderson, J.M.9
Cantley, L.C.10
-
165
-
-
0030424581
-
Structure and function of the ww domain
-
Sudol, M. Structure and function of the ww domain. Prog. Biophys. Mol. Biol. 1996, 65, 113-132.
-
(1996)
Prog. Biophys. Mol. Biol.
, vol.65
, pp. 113-132
-
-
Sudol, M.1
-
166
-
-
0037088751
-
Tech.Sight. Analyzing biomolecular interactions
-
Wilson, W.D. Tech.Sight. Analyzing biomolecular interactions. Science 2002, 295, 2103-2105.
-
(2002)
Science
, vol.295
, pp. 2103-2105
-
-
Wilson, W.D.1
-
167
-
-
0029836953
-
Discovering high-affinity ligands for proteins: Sar by nmr
-
Shuker, S.B.; Hajduk, P.J.; Meadows, R.P.; Fesik, S.W. Discovering high-affinity ligands for proteins: Sar by nmr. Science 1996, 274, 1531-1534.
-
(1996)
Science
, vol.274
, pp. 1531-1534
-
-
Shuker, S.B.1
Hajduk, P.J.2
Meadows, R.P.3
Fesik, S.W.4
-
168
-
-
33751204422
-
Fragment-based lead discovery: A chemical update
-
Erlanson, D.A. Fragment-based lead discovery: A chemical update. Curr. Opin. Biotechnol. 2006, 17, 643-652.
-
(2006)
Curr. Opin. Biotechnol.
, vol.17
, pp. 643-652
-
-
Erlanson, D.A.1
-
169
-
-
0036255761
-
Protein detection using proximity-dependent DNA ligation assays
-
Fredriksson, S.; Gullberg, M.; Jarvius, J.; Olsson, C.; Pietras, K.; Gustafsdottir, S.M.; Ostman, A.; Landegren, U. Protein detection using proximity-dependent DNA ligation assays. Nat. Biotechnol. 2002, 20, 473-477.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 473-477
-
-
Fredriksson, S.1
Gullberg, M.2
Jarvius, J.3
Olsson, C.4
Pietras, K.5
Gustafsdottir, S.M.6
Ostman, A.7
Landegren, U.8
-
170
-
-
66449121455
-
Lipid g protein-coupled receptor ligand identification using β-arrestin pathhunter assay
-
Yin, H.; Chu, A.; Li, W.; Wang, B.; Shelton, F.; Otero, F.; Nguyen, D.G.; Caldwell, J.S.; Chen, Y.A. Lipid g protein-coupled receptor ligand identification using β-arrestin pathhunter assay. J. Biol. Chem. 2009, 284, 12328-12338.
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 12328-12338
-
-
Yin, H.1
Chu, A.2
Li, W.3
Wang, B.4
Shelton, F.5
Otero, F.6
Nguyen, D.G.7
Caldwell, J.S.8
Chen, Y.A.9
-
171
-
-
53249098939
-
Detecting protein-protein interactions with cfp-yfp fret by acceptor photobleaching
-
Karpova, T.; McNally, J.G. Detecting protein-protein interactions with cfp-yfp fret by acceptor photobleaching. Curr. Protoc. Cytom. 2006, doi:10.1002/0471142956.cy1207s35.
-
(2006)
Curr. Protoc. Cytom.
-
-
Karpova, T.1
McNally, J.G.2
-
172
-
-
84908373179
-
Structure-guided design and optimization of small molecules targeting the protein-protein interaction between the von hippel-lindau (VHL) e3 ubiquitin ligase and the hypoxia inducible factor (HIF) α subunit with in vitro nanomolar affinities
-
Galdeano, C.; Gadd, M.S.; Soares, P.; Scaffidi, S.; Van Molle, I.; Birced, I.; Hewitt, S.; Dias, D.M.; Ciulli, A. Structure-guided design and optimization of small molecules targeting the protein-protein interaction between the von hippel-lindau (VHL) e3 ubiquitin ligase and the hypoxia inducible factor (HIF) α subunit with in vitro nanomolar affinities. J. Med. Chem. 2014, 57, 8657-8663.
-
(2014)
J. Med. Chem.
, vol.57
, pp. 8657-8663
-
-
Galdeano, C.1
Gadd, M.S.2
Soares, P.3
Scaffidi, S.4
Van Molle, I.5
Birced, I.6
Hewitt, S.7
Dias, D.M.8
Ciulli, A.9
-
173
-
-
84875221885
-
Small-molecule inhibition of the uPAR•uPA interaction: Synthesis, biochemical, cellular, in vivo pharmacokinetics and efficacy studies in breast cancer metastasis
-
Mani, T.; Wang, F.; Knabe, W.E.; Sinn, A.L.; Khanna, M.; Jo, I.; Sandusky, G.E.; Sledge, G.W., Jr.; Jones, D.R.; Khanna, R.; et al. Small-molecule inhibition of the uPAR•uPA interaction: Synthesis, biochemical, cellular, in vivo pharmacokinetics and efficacy studies in breast cancer metastasis. Bioorg. Med. Chem. 2013, 21, 2145-2155.
-
(2013)
Bioorg. Med. Chem.
, vol.21
, pp. 2145-2155
-
-
Mani, T.1
Wang, F.2
Knabe, W.E.3
Sinn, A.L.4
Khanna, M.5
Jo, I.6
Sandusky, G.E.7
Sledge, G.W.8
Jones, D.R.9
Khanna, R.10
-
174
-
-
84902440363
-
Identification of an ATG8-ATG3 protein-protein interaction inhibitor from the medicines for malaria venture malaria box active in blood and liver stage plasmodium falciparum parasites
-
Hain, A.U.; Bartee, D.; Sanders, N.G.; Miller, A.S.; Sullivan, D.J.; Levitskaya, J.; Meyers, C.F.; Bosch, J. Identification of an ATG8-ATG3 protein-protein interaction inhibitor from the medicines for malaria venture malaria box active in blood and liver stage plasmodium falciparum parasites. J. Med. Chem. 2014, 57, 4521-4531.
-
(2014)
J. Med. Chem.
, vol.57
, pp. 4521-4531
-
-
Hain, A.U.1
Bartee, D.2
Sanders, N.G.3
Miller, A.S.4
Sullivan, D.J.5
Levitskaya, J.6
Meyers, C.F.7
Bosch, J.8
-
175
-
-
84868506702
-
Structural characterization and inhibition of the plasmodium ATG8-ATG3 interaction
-
Hain, A.U.; Weltzer, R.R.; Hammond, H.; Jayabalasingham, B.; Dinglasan, R.R.; Graham, D.R.; Colquhoun, D.R.; Coppens, I.; Bosch, J. Structural characterization and inhibition of the plasmodium ATG8-ATG3 interaction. J. Struct. Biol. 2012, 180, 551-562.
-
(2012)
J. Struct. Biol.
, vol.180
, pp. 551-562
-
-
Hain, A.U.1
Weltzer, R.R.2
Hammond, H.3
Jayabalasingham, B.4
Dinglasan, R.R.5
Graham, D.R.6
Colquhoun, D.R.7
Coppens, I.8
Bosch, J.9
-
176
-
-
84903973479
-
Comparison of weak affinity chromatography and surface plasmon resonance in determining affinity of small molecules
-
Duong-Thi, M.D.; Bergstrom, G.; Mandenius, C.F.; Bergstrom, M.; Fex, T.; Ohlson, S. Comparison of weak affinity chromatography and surface plasmon resonance in determining affinity of small molecules. Anal. Biochem. 2014, 461, 57-59.
-
(2014)
Anal. Biochem.
, vol.461
, pp. 57-59
-
-
Duong-Thi, M.D.1
Bergstrom, G.2
Mandenius, C.F.3
Bergstrom, M.4
Fex, T.5
Ohlson, S.6
-
177
-
-
70349932423
-
Autodock4 and autodocktools4: Automated docking with selective receptor flexibility
-
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.
-
(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
-
178
-
-
0035025191
-
Dock 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
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.
-
(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
-
179
-
-
36749077465
-
Automatic prediction of protein interactions with large scale motion
-
Schneidman-Duhovny, D.; Nussinov, R.; Wolfson, H.J. Automatic prediction of protein interactions with large scale motion. Proteins 2007, 69, 764-773.
-
(2007)
Proteins
, vol.69
, pp. 764-773
-
-
Schneidman-Duhovny, D.1
Nussinov, R.2
Wolfson, H.J.3
-
180
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner, R.A.; Banks, J.L.; Murphy, R.B.; Halgren, T.A.; Klicic, J.J.; Mainz, D.T.; Repasky, M.P.; Knoll, E.H.; Shelley, M.; Perry, J.K.; et al. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47, 1739-1749.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.P.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
-
181
-
-
67650097331
-
Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy
-
Cross, J.B.; Thompson, D.C.; Rai, B.K.; Baber, J.C.; Fan, K.Y.; Hu, Y.; Humblet, C. Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy. J. Chem. Inf. Model. 2009, 49, 1455-1474.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1455-1474
-
-
Cross, J.B.1
Thompson, D.C.2
Rai, B.K.3
Baber, J.C.4
Fan, K.Y.5
Hu, Y.6
Humblet, C.7
-
182
-
-
59149107045
-
α-Helix mimetics as inhibitors of protein-protein interactions
-
Saraogi, I.; Hamilton, A.D. α-Helix mimetics as inhibitors of protein-protein interactions. Biochem. Soc. Trans. 2008, 36, 1414-1417.
-
(2008)
Biochem. Soc. Trans.
, vol.36
, pp. 1414-1417
-
-
Saraogi, I.1
Hamilton, A.D.2
-
183
-
-
0034801374
-
Toward proteomimetics: Terphenyl derivatives as structural and functional mimics of extended regions of an α-helix
-
Orner, B.P.; Ernst, J.T.; Hamilton, A.D. Toward proteomimetics: Terphenyl derivatives as structural and functional mimics of extended regions of an α-helix. J. Am. Chem. Soc. 2001, 123, 5382-5383.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 5382-5383
-
-
Orner, B.P.1
Ernst, J.T.2
Hamilton, A.D.3
-
184
-
-
65549118222
-
Synthetic inhibitors of extended helix-protein interactions based on a biphenyl 4,4?-dicarboxamide scaffold
-
Rodriguez, J.M.; Nevola, L.; Ross, N.T.; Lee, G.I.; Hamilton, A.D. Synthetic inhibitors of extended helix-protein interactions based on a biphenyl 4,4?-dicarboxamide scaffold. Chembiochem 2009, 10, 829-833.
-
(2009)
Chembiochem
, vol.10
, pp. 829-833
-
-
Rodriguez, J.M.1
Nevola, L.2
Ross, N.T.3
Lee, G.I.4
Hamilton, A.D.5
-
185
-
-
0032982070
-
Two new β-strand mimics
-
Tsai, J.H.; Waldman, A.S.; Nowick, J.S. Two new β-strand mimics. Bioorg. Med. Chem. 1999, 7, 29-38.
-
(1999)
Bioorg. Med. Chem.
, vol.7
, pp. 29-38
-
-
Tsai, J.H.1
Waldman, A.S.2
Nowick, J.S.3
-
186
-
-
4544342753
-
Using a β-hairpin to mimic an α-helix: Cyclic peptidomimetic inhibitors of the p53-hdm2 protein-protein interaction
-
Fasan, R.; Dias, R.L.; Moehle, K.; Zerbe, O.; Vrijbloed, J.W.; Obrecht, D.; Robinson, J.A. Using a β-hairpin to mimic an α-helix: Cyclic peptidomimetic inhibitors of the p53-hdm2 protein-protein interaction. Angew. Chem. 2004, 43, 2109-2112.
-
(2004)
Angew. Chem.
, vol.43
, pp. 2109-2112
-
-
Fasan, R.1
Dias, R.L.2
Moehle, K.3
Zerbe, O.4
Vrijbloed, J.W.5
Obrecht, D.6
Robinson, J.A.7
-
187
-
-
70350304181
-
The β-D-glucose scaffold as a β-turn mimetic
-
Hirschmann, R.F.; Nicolaou, K.C.; Angeles, A.R.; Chen, J.S.; Smith, A.B., 3rd. The β-D-glucose scaffold as a β-turn mimetic. Acc. Chem. Res. 2009, 42, 1511-1520.
-
(2009)
Acc. Chem. Res.
, vol.42
, pp. 1511-1520
-
-
Hirschmann, R.F.1
Nicolaou, K.C.2
Angeles, A.R.3
Chen, J.S.4
Smith, A.B.5
-
188
-
-
16244401304
-
Recognition of proline-rich motifs by protein-protein-interaction domains
-
Ball, L.J.; Kuhne, R.; Schneider-Mergener, J.; Oschkinat, H. Recognition of proline-rich motifs by protein-protein-interaction domains. Angew. Chem. 2005, 44, 2852-2869.
-
(2005)
Angew. Chem.
, vol.44
, pp. 2852-2869
-
-
Ball, L.J.1
Kuhne, R.2
Schneider-Mergener, J.3
Oschkinat, H.4
-
189
-
-
84870952757
-
Multicomponent Synthesis of Diverse 1,4-Benzodiazepine Scaffolds
-
Huang, Y.; Khoury, K.; Chanas, T.; Dömling, A. Multicomponent Synthesis of Diverse 1,4-Benzodiazepine Scaffolds. Org. Lett. 2012, 14, 5916-5919.
-
(2012)
Org. Lett.
, vol.14
, pp. 5916-5919
-
-
Huang, Y.1
Khoury, K.2
Chanas, T.3
Dömling, A.4
-
190
-
-
79960524750
-
Minimalist and universal peptidomimetics
-
Ko, E.; Liu, J.; Burgess, K. Minimalist and universal peptidomimetics. Chem. Soc. Rev. 2011, 40, 4411-4421.
-
(2011)
Chem. Soc. Rev.
, vol.40
, pp. 4411-4421
-
-
Ko, E.1
Liu, J.2
Burgess, K.3
-
191
-
-
84860538154
-
Structural biology and drug discovery for protein-protein interactions
-
Jubb, H.; Higueruelo, A.P.; Winter, A.; Blundell, T.L. Structural biology and drug discovery for protein-protein interactions. Trends Pharmacol. Sci. 2012, 33, 241-248.
-
(2012)
Trends Pharmacol. Sci.
, vol.33
, pp. 241-248
-
-
Jubb, H.1
Higueruelo, A.P.2
Winter, A.3
Blundell, T.L.4
-
192
-
-
20444486559
-
An inhibitor of bcl-2 family proteins induces regression of solid tumours
-
Oltersdorf, T.; Elmore, S.W.; Shoemaker, A.R.; Armstrong, R.C.; Augeri, D.J.; Belli, B.A.; Bruncko, M.; Deckwerth, T.L.; Dinges, J.; Hajduk, P.J.; et al. An inhibitor of bcl-2 family proteins induces regression of solid tumours. Nature 2005, 435, 677-681.
-
(2005)
Nature
, vol.435
, pp. 677-681
-
-
Oltersdorf, T.1
Elmore, S.W.2
Shoemaker, A.R.3
Armstrong, R.C.4
Augeri, D.J.5
Belli, B.A.6
Bruncko, M.7
Deckwerth, T.L.8
Dinges, J.9
Hajduk, P.J.10
-
193
-
-
84876779164
-
Recent applications of isotopic labeling for protein nmr in drug discovery
-
Hiroaki, H. Recent applications of isotopic labeling for protein nmr in drug discovery. Expert Opin. Drug Discov. 2013, 8, 523-536.
-
(2013)
Expert Opin. Drug Discov.
, vol.8
, pp. 523-536
-
-
Hiroaki, H.1
-
194
-
-
35048895357
-
Targeting protein-protein interactions: Lessons from P53/MDM2
-
Murray, J.K.; Gellman, S.H. Targeting protein-protein interactions: Lessons from P53/MDM2. Biopolymers 2007, 88, 657-686.
-
(2007)
Biopolymers
, vol.88
, pp. 657-686
-
-
Murray, J.K.1
Gellman, S.H.2
-
195
-
-
79958143460
-
Modulators of protein-protein interactions: Novel approaches in targeting protein kinases and other pharmaceutically relevant biomolecules
-
Rechfeld, F.; Gruber, P.; Hofmann, J.; Kirchmair, J. Modulators of protein-protein interactions: Novel approaches in targeting protein kinases and other pharmaceutically relevant biomolecules. Curr. Top. Med. Chem. 2011, 11, 1305-1319.
-
(2011)
Curr. Top. Med. Chem.
, vol.11
, pp. 1305-1319
-
-
Rechfeld, F.1
Gruber, P.2
Hofmann, J.3
Kirchmair, J.4
-
196
-
-
84896737016
-
Characterization and structure of the vaccinia virus nf-kappab antagonist a46
-
Fedosyuk, S.; Grishkovskaya, I.; de Almeida Ribeiro, E., Jr.; Skern, T. Characterization and structure of the vaccinia virus nf-kappab antagonist a46. J. Biol. Chem. 2014, 289, 3749-3762.
-
(2014)
J. Biol. Chem.
, vol.289
, pp. 3749-3762
-
-
Fedosyuk, S.1
Grishkovskaya, I.2
De Almeida Ribeiro, E.3
Skern, T.4
-
197
-
-
84887496644
-
Structural basis and targeting of the interaction between fibroblast growth factor-inducible 14 and tumor necrosis factor-like weak inducer of apoptosis
-
Dhruv, H.; Loftus, J.C.; Narang, P.; Petit, J.L.; Fameree, M.; Burton, J.; Tchegho, G.; Chow, D.; Yin, H.; Al-Abed, Y.; et al. Structural basis and targeting of the interaction between fibroblast growth factor-inducible 14 and tumor necrosis factor-like weak inducer of apoptosis. J. Biol. Chem. 2013, 288, 32261-32276.
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 32261-32276
-
-
Dhruv, H.1
Loftus, J.C.2
Narang, P.3
Petit, J.L.4
Fameree, M.5
Burton, J.6
Tchegho, G.7
Chow, D.8
Yin, H.9
Al-Abed, Y.10
-
198
-
-
84886549484
-
Novel toll-like receptor 4 (TLR4) antagonists identified by structure- and ligand-based virtual screening
-
Svajger, U.; Brus, B.; Turk, S.; Sova, M.; Hodnik, V.; Anderluh, G.; Gobec, S. Novel toll-like receptor 4 (TLR4) antagonists identified by structure- and ligand-based virtual screening. Eur. J. Med. Chem. 2013, 70, 393-399.
-
(2013)
Eur. J. Med. Chem.
, vol.70
, pp. 393-399
-
-
Svajger, U.1
Brus, B.2
Turk, S.3
Sova, M.4
Hodnik, V.5
Anderluh, G.6
Gobec, S.7
-
199
-
-
79955798852
-
Exploring nmr ensembles of calcium binding proteins: Perspectives to design inhibitors of protein-protein interactions
-
Isvoran, A.; Badel, A.; Craescu, C.T.; Miron, S.; Miteva, M.A. Exploring nmr ensembles of calcium binding proteins: Perspectives to design inhibitors of protein-protein interactions. BMC Struct. Biol. 2011, 11, doi:10.1186/1472-6807-11-24.
-
(2011)
BMC Struct. Biol.
, vol.11
-
-
Isvoran, A.1
Badel, A.2
Craescu, C.T.3
Miron, S.4
Miteva, M.A.5
-
200
-
-
84908246685
-
Combining ligand- and structure-based approaches for the discovery of new inhibitors of the EPHA2-ephrin-A1 interaction
-
Pala, D.; Castelli, R.; Incerti, M.; Russo, S.; Tognolini, M.; Giorgio, C.; Hassan-Mohamed, I.; Zanotti, I.; Vacondio, F.; Rivara, S.; et al. Combining ligand- and structure-based approaches for the discovery of new inhibitors of the EPHA2-ephrin-A1 interaction. J. Chem. Inf. Model. 2014, 54, 2621-2626.
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 2621-2626
-
-
Pala, D.1
Castelli, R.2
Incerti, M.3
Russo, S.4
Tognolini, M.5
Giorgio, C.6
Hassan-Mohamed, I.7
Zanotti, I.8
Vacondio, F.9
Rivara, S.10
-
201
-
-
59249104006
-
Rhoptry neck protein RON2 forms a complex with microneme protein ama1 in plasmodium falciparum merozoites
-
Cao, J.; Kaneko, O.; Thongkukiatkul, A.; Tachibana, M.; Otsuki, H.; Gao, Q.; Tsuboi, T.; Torii, M. Rhoptry neck protein RON2 forms a complex with microneme protein ama1 in plasmodium falciparum merozoites. Parasitol. Int. 2009, 58, 29-35.
-
(2009)
Parasitol. Int.
, vol.58
, pp. 29-35
-
-
Cao, J.1
Kaneko, O.2
Thongkukiatkul, A.3
Tachibana, M.4
Otsuki, H.5
Gao, Q.6
Tsuboi, T.7
Torii, M.8
-
202
-
-
80051964398
-
Binding of plasmodium merozoite proteins ron2 and ama1 triggers commitment to invasion
-
Srinivasan, P.; Beatty, W.L.; Diouf, A.; Herrera, R.; Ambroggio, X.; Moch, J.K.; Tyler, J.S.; Narum, D.L.; Pierce, S.K.; Boothroyd, J.C.; et al. Binding of plasmodium merozoite proteins ron2 and ama1 triggers commitment to invasion. Proc. Natl. Acad. Sci. USA 2011, 108, 13275-13280.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 13275-13280
-
-
Srinivasan, P.1
Beatty, W.L.2
Diouf, A.3
Herrera, R.4
Ambroggio, X.5
Moch, J.K.6
Tyler, J.S.7
Narum, D.L.8
Pierce, S.K.9
Boothroyd, J.C.10
-
203
-
-
84893305943
-
Design, synthesis and evaluation of N6-substituted 2-aminoadenosine-5[prime or minute]-N-methylcarboxamides as A3 adenosine receptor agonists
-
Devine, S.M.; May, L.T.; Scammells, P.J. Design, synthesis and evaluation of N6-substituted 2-aminoadenosine-5[prime or minute]-N-methylcarboxamides as A3 adenosine receptor agonists. MedChemComm 2014, 5, 192-196.
-
(2014)
MedChemComm
, vol.5
, pp. 192-196
-
-
Devine, S.M.1
May, L.T.2
Scammells, P.J.3
-
204
-
-
84930872420
-
Computational and biophysical approaches to protein-protein interaction inhibition of plasmodium falciparum ama1/ron2 complex
-
Pihan, E.; Delgadillo, R.F.; Tonkin, M.L.; Pugniere, M.; Lebrun, M.; Boulanger, M.J.; Douguet, D. Computational and biophysical approaches to protein-protein interaction inhibition of plasmodium falciparum ama1/ron2 complex. J. Comput. Aided Mol. Des. 2015, 29, 525-539.
-
(2015)
J. Comput. Aided Mol. Des.
, vol.29
, pp. 525-539
-
-
Pihan, E.1
Delgadillo, R.F.2
Tonkin, M.L.3
Pugniere, M.4
Lebrun, M.5
Boulanger, M.J.6
Douguet, D.7
-
205
-
-
62449330667
-
Empirical scoring functions for advanced protein-ligand docking with plants
-
Korb, O.; Stutzle, T.; Exner, T.E. Empirical scoring functions for advanced protein-ligand docking with plants. J. Chem. Inf. Model. 2009, 49, 84-96.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 84-96
-
-
Korb, O.1
Stutzle, T.2
Exner, T.E.3
-
206
-
-
84858609719
-
Identification of a small molecule that modulates platelet glycoprotein ib-von willebrand factor interaction
-
Broos, K.; Trekels, M.; Jose, R.A.; Demeulemeester, J.; Vandenbulcke, A.; Vandeputte, N.; Venken, T.; Egle, B.; De Borggraeve, W.M.; Deckmyn, H.; et al. Identification of a small molecule that modulates platelet glycoprotein ib-von willebrand factor interaction. J. Biol. Chem. 2012, 287, 9461-9472.
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 9461-9472
-
-
Broos, K.1
Trekels, M.2
Jose, R.A.3
Demeulemeester, J.4
Vandenbulcke, A.5
Vandeputte, N.6
Venken, T.7
Egle, B.8
De Borggraeve, W.M.9
Deckmyn, H.10
-
207
-
-
54949095069
-
The humanized anti-glycoprotein ib monoclonal antibody h6B4-Fab is a potent and safe antithrombotic in a high shear arterial thrombosis model in baboons
-
Fontayne, A.; Meiring, M.; Lamprecht, S.; Roodt, J.; Demarsin, E.; Barbeaux, P.; Deckmyn, H. The humanized anti-glycoprotein ib monoclonal antibody h6B4-Fab is a potent and safe antithrombotic in a high shear arterial thrombosis model in baboons. Thromb. Haemost. 2008, 100, 670-677.
-
(2008)
Thromb. Haemost.
, vol.100
, pp. 670-677
-
-
Fontayne, A.1
Meiring, M.2
Lamprecht, S.3
Roodt, J.4
Demarsin, E.5
Barbeaux, P.6
Deckmyn, H.7
-
208
-
-
79960058122
-
Antithrombotic drug candidate alx-0081 shows superior preclinical efficacy and safety compared with currently marketed antiplatelet drugs
-
Ulrichts, H.; Silence, K.; Schoolmeester, A.; de Jaegere, P.; Rossenu, S.; Roodt, J.; Priem, S.; Lauwereys, M.; Casteels, P.; Van Bockstaele, F.; et al. Antithrombotic drug candidate alx-0081 shows superior preclinical efficacy and safety compared with currently marketed antiplatelet drugs. Blood 2011, 118, 757-765.
-
(2011)
Blood
, vol.118
, pp. 757-765
-
-
Ulrichts, H.1
Silence, K.2
Schoolmeester, A.3
De Jaegere, P.4
Rossenu, S.5
Roodt, J.6
Priem, S.7
Lauwereys, M.8
Casteels, P.9
Van Bockstaele, F.10
-
209
-
-
2542480051
-
Crystal structure of the wild-type von willebrand factor A1-glycoprotein Ibα complex reveals conformation differences with a complex bearing von willebrand disease mutations
-
Dumas, J.J.; Kumar, R.; McDonagh, T.; Sullivan, F.; Stahl, M.L.; Somers, W.S.; Mosyak, L. Crystal structure of the wild-type von willebrand factor A1-glycoprotein Ibα complex reveals conformation differences with a complex bearing von willebrand disease mutations. J. Biol. Chem. 2004, 279, 23327-23334.
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 23327-23334
-
-
Dumas, J.J.1
Kumar, R.2
McDonagh, T.3
Sullivan, F.4
Stahl, M.L.5
Somers, W.S.6
Mosyak, L.7
-
210
-
-
0342424187
-
Fast prediction and visualization of protein binding pockets with pass
-
Brady, G.P., Jr.; Stouten, P.F. Fast prediction and visualization of protein binding pockets with pass. J. Comput. Aided Mol. Des. 2000, 14, 383-401.
-
(2000)
J. Comput. Aided Mol. Des.
, vol.14
, pp. 383-401
-
-
Brady, G.P.1
Stouten, P.F.2
-
211
-
-
34248232474
-
Hotpatch: A statistical approach to finding biologically relevant features on protein surfaces
-
Pettit, F.K.; Bare, E.; Tsai, A.; Bowie, J.U. Hotpatch: A statistical approach to finding biologically relevant features on protein surfaces. J. Mol. Biol. 2007, 369, 863-879.
-
(2007)
J. Mol. Biol.
, vol.369
, pp. 863-879
-
-
Pettit, F.K.1
Bare, E.2
Tsai, A.3
Bowie, J.U.4
-
212
-
-
84875463042
-
Molecular mechanisms of t cell co-stimulation and co-inhibition
-
Chen, L.; Flies, D.B. Molecular mechanisms of t cell co-stimulation and co-inhibition. Nat. Rev. Immunol. 2013, 13, 227-242.
-
(2013)
Nat. Rev. Immunol.
, vol.13
, pp. 227-242
-
-
Chen, L.1
Flies, D.B.2
-
213
-
-
0037340388
-
The nature of molecular recognition by t cells
-
Davis, S.J.; Ikemizu, S.; Evans, E.J.; Fugger, L.; Bakker, T.R.; van der Merwe, P.A. The nature of molecular recognition by t cells. Nat. Immunol. 2003, 4, 217-224.
-
(2003)
Nat. Immunol.
, vol.4
, pp. 217-224
-
-
Davis, S.J.1
Ikemizu, S.2
Evans, E.J.3
Fugger, L.4
Bakker, T.R.5
Van Der Merwe, P.A.6
-
214
-
-
52949129859
-
Cell adhesion molecules: Structure, function, drug design, and biomaterials
-
Satyanarayanajois, S.D. Cell adhesion molecules: Structure, function, drug design, and biomaterials. Curr. Pharm. Des. 2008, 14, 2126-2127.
-
(2008)
Curr. Pharm. Des.
, vol.14
, pp. 2126-2127
-
-
Satyanarayanajois, S.D.1
-
215
-
-
70649086092
-
Genetic variants at CD28, prdm1 and CD2/CD58 are associated with rheumatoid arthritis risk
-
Raychaudhuri, S.; Thomson, B.P.; Remmers, E.F.; Eyre, S.; Hinks, A.; Guiducci, C.; Catanese, J.J.; Xie, G.; Stahl, E.A.; Chen, R.; et al. Genetic variants at CD28, prdm1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nat. Genet. 2009, 41, 1313-1318.
-
(2009)
Nat. Genet.
, vol.41
, pp. 1313-1318
-
-
Raychaudhuri, S.1
Thomson, B.P.2
Remmers, E.F.3
Eyre, S.4
Hinks, A.5
Guiducci, C.6
Catanese, J.J.7
Xie, G.8
Stahl, E.A.9
Chen, R.10
-
216
-
-
0035965140
-
Molecular dissection of the CD2-CD58 counter-receptor interface identifies CD2 Tyr86 and CD58 Lys34 residues as the functional "hot spot"
-
Kim, M.; Sun, Z.Y.; Byron, O.; Campbell, G.; Wagner, G.; Wang, J.; Reinherz, E.L. Molecular dissection of the CD2-CD58 counter-receptor interface identifies CD2 Tyr86 and CD58 Lys34 residues as the functional "hot spot". J. Mol. Biol. 2001, 312, 711-720.
-
(2001)
J. Mol. Biol.
, vol.312
, pp. 711-720
-
-
Kim, M.1
Sun, Z.Y.2
Byron, O.3
Campbell, G.4
Wagner, G.5
Wang, J.6
Reinherz, E.L.7
-
217
-
-
0033037036
-
Structure of a heterophilic adhesion complex between the human CD2 and CD58 (LFA-3) counterreceptors
-
Wang, J.H.; Smolyar, A.; Tan, K.; Liu, J.H.; Kim, M.; Sun, Z.Y.; Wagner, G.; Reinherz, E.L. Structure of a heterophilic adhesion complex between the human CD2 and CD58 (LFA-3) counterreceptors. Cell 1999, 97, 791-803.
-
(1999)
Cell
, vol.97
, pp. 791-803
-
-
Wang, J.H.1
Smolyar, A.2
Tan, K.3
Liu, J.H.4
Kim, M.5
Sun, Z.Y.6
Wagner, G.7
Reinherz, E.L.8
-
218
-
-
61449206310
-
Design of β-hairpin peptides for modulation of cell adhesion by β-turn constraint
-
Giddu, S.; Subramanian, V.; Yoon, H.S.; Satyanarayanajois, S.D. Design of β-hairpin peptides for modulation of cell adhesion by β-turn constraint. J. Med. Chem. 2009, 52, 726-736.
-
(2009)
J. Med. Chem.
, vol.52
, pp. 726-736
-
-
Giddu, S.1
Subramanian, V.2
Yoon, H.S.3
Satyanarayanajois, S.D.4
-
219
-
-
84879524742
-
Immunosuppression by co-stimulatory molecules: Inhibition of CD2-CD48/CD58 interaction by peptides from CD2 to suppress progression of collagen-induced arthritis in mice
-
Gokhale, A.; Kanthala, S.; Latendresse, J.; Taneja, V.; Satyanarayanajois, S. Immunosuppression by co-stimulatory molecules: Inhibition of CD2-CD48/CD58 interaction by peptides from CD2 to suppress progression of collagen-induced arthritis in mice. Chem. Biol. Drug Des. 2013, 82, 106-118.
-
(2013)
Chem. Biol. Drug Des.
, vol.82
, pp. 106-118
-
-
Gokhale, A.1
Kanthala, S.2
Latendresse, J.3
Taneja, V.4
Satyanarayanajois, S.5
-
220
-
-
79961226789
-
Conformationally constrained peptides from CD2 to modulate protein-protein interactions between CD2 and CD58
-
Gokhale, A.; Weldeghiorghis, T.K.; Taneja, V.; Satyanarayanajois, S.D. Conformationally constrained peptides from CD2 to modulate protein-protein interactions between CD2 and CD58. J. Med. Chem. 2011, 54, 5307-5319.
-
(2011)
J. Med. Chem.
, vol.54
, pp. 5307-5319
-
-
Gokhale, A.1
Weldeghiorghis, T.K.2
Taneja, V.3
Satyanarayanajois, S.D.4
-
221
-
-
77955257453
-
A peptide from the β-strand region of CD2 protein that inhibits cell adhesion and suppresses arthritis in a mouse model
-
Satyanarayanajois, S.D.; Buyuktimkin, B.; Gokhale, A.; Ronald, S.; Siahaan, T.J.; Latendresse, J.R. A peptide from the β-strand region of CD2 protein that inhibits cell adhesion and suppresses arthritis in a mouse model. Chem. Biol. Drug Des. 2010, 76, 234-244.
-
(2010)
Chem. Biol. Drug Des.
, vol.76
, pp. 234-244
-
-
Satyanarayanajois, S.D.1
Buyuktimkin, B.2
Gokhale, A.3
Ronald, S.4
Siahaan, T.J.5
Latendresse, J.R.6
-
222
-
-
48249158391
-
Structure-based view of epidermal growth factor receptor regulation
-
Ferguson, K.M. Structure-based view of epidermal growth factor receptor regulation. Annu. Rev. Biophys. 2008, 37, 353-373.
-
(2008)
Annu. Rev. Biophys.
, vol.37
, pp. 353-373
-
-
Ferguson, K.M.1
-
223
-
-
34248198978
-
Her2 therapy. Her2 (ERBB2): Functional diversity from structurally conserved building blocks
-
Landgraf, R. Her2 therapy. Her2 (ERBB2): Functional diversity from structurally conserved building blocks. Breast Cancer Res. BCR 2007, 9, 202.
-
(2007)
Breast Cancer Res. BCR
, vol.9
, pp. 202
-
-
Landgraf, R.1
-
224
-
-
0242694519
-
Her-2-targeted therapy: Lessons learned and future directions
-
Nahta, R.; Esteva, F.J. Her-2-targeted therapy: Lessons learned and future directions. Clin. Cancer Res. 2003, 9, 5078-5084.
-
(2003)
Clin. Cancer Res.
, vol.9
, pp. 5078-5084
-
-
Nahta, R.1
Esteva, F.J.2
-
225
-
-
33846278358
-
Her2 inhibition: From discovery to clinical practice
-
Chang, J.C. Her2 inhibition: From discovery to clinical practice. Clin. Cancer Res. 2007, 13, 1-3.
-
(2007)
Clin. Cancer Res.
, vol.13
, pp. 1-3
-
-
Chang, J.C.1
-
226
-
-
84865651620
-
Inhibition of protein-protein interaction of HER2-EGFR and HER2-HER3 by a rationally designed peptidomimetic
-
Banappagari, S.; Corti, M.; Pincus, S.; Satyanarayanajois, S. Inhibition of protein-protein interaction of HER2-EGFR and HER2-HER3 by a rationally designed peptidomimetic. J. Biomol. Struct. Dyn. 2012, 30, 594-606.
-
(2012)
J. Biomol. Struct. Dyn.
, vol.30
, pp. 594-606
-
-
Banappagari, S.1
Corti, M.2
Pincus, S.3
Satyanarayanajois, S.4
-
227
-
-
84884224841
-
Design, synthesis and characterization of peptidomimetic conjugate of bodipy targeting HER2 protein extracellular domain
-
Banappagari, S.; McCall, A.; Fontenot, K.; Vicente, M.G.; Gujar, A.; Satyanarayanajois, S. Design, synthesis and characterization of peptidomimetic conjugate of bodipy targeting HER2 protein extracellular domain. Eur. J. Med. Chem. 2013, 65, 60-69.
-
(2013)
Eur. J. Med. Chem.
, vol.65
, pp. 60-69
-
-
Banappagari, S.1
McCall, A.2
Fontenot, K.3
Vicente, M.G.4
Gujar, A.5
Satyanarayanajois, S.6
-
228
-
-
78649865434
-
A conformationally constrained peptidomimetic binds to the extracellular region of HER2 protein
-
Banappagari, S.; Ronald, S.; Satyanarayanajois, S.D. A conformationally constrained peptidomimetic binds to the extracellular region of HER2 protein. J. Biomol. Struct. Dyn. 2010, 28, 289-308.
-
(2010)
J. Biomol. Struct. Dyn.
, vol.28
, pp. 289-308
-
-
Banappagari, S.1
Ronald, S.2
Satyanarayanajois, S.D.3
-
229
-
-
79961147772
-
Structure-activity relationship of conformationally constrained peptidomimetics for antiproliferative activity in HER2-overexpressing breast cancer cell lines
-
Banappagari, S.; Ronald, S.; Satyanarayanajois, S.D. Structure-activity relationship of conformationally constrained peptidomimetics for antiproliferative activity in HER2-overexpressing breast cancer cell lines. MedChemComm 2011, 2, 752-759.
-
(2011)
MedChemComm
, vol.2
, pp. 752-759
-
-
Banappagari, S.1
Ronald, S.2
Satyanarayanajois, S.D.3
-
230
-
-
84929379646
-
Novel peptidomimetics for inhibition of HER2:HER3 heterodimerization in HER2-positive breast cancer
-
Kanthala, S.; Banappagari, S.; Gokhale, A.; Liu, Y.Y.; Xin, G.; Zhao, Y.; Jois, S. Novel peptidomimetics for inhibition of HER2:HER3 heterodimerization in HER2-positive breast cancer. Chem. Biol. Drug Des. 2014, 85, 702-714.
-
(2014)
Chem. Biol. Drug Des.
, vol.85
, pp. 702-714
-
-
Kanthala, S.1
Banappagari, S.2
Gokhale, A.3
Liu, Y.Y.4
Xin, G.5
Zhao, Y.6
Jois, S.7
-
231
-
-
84897052943
-
Structure-activity relationships of peptidomimetics that inhibit ppi of HER2-HER3
-
Kanthala, S.; Gauthier, T.; Satyanarayanajois, S. Structure-activity relationships of peptidomimetics that inhibit ppi of HER2-HER3. Biopolymers 2014, 101, 693-702.
-
(2014)
Biopolymers
, vol.101
, pp. 693-702
-
-
Kanthala, S.1
Gauthier, T.2
Satyanarayanajois, S.3
-
232
-
-
68949204378
-
Design, synthesis, and docking studies of peptidomimetics based on HER2-herceptin binding site with potential antiproliferative activity against breast cancer cell lines
-
Satyanarayanajois, S.; Villalba, S.; Jianchao, L.; Lin, G.M. Design, synthesis, and docking studies of peptidomimetics based on HER2-herceptin binding site with potential antiproliferative activity against breast cancer cell lines. Chem. Biol. Drug Des. 2009, 74, 246-257.
-
(2009)
Chem. Biol. Drug Des.
, vol.74
, pp. 246-257
-
-
Satyanarayanajois, S.1
Villalba, S.2
Jianchao, L.3
Lin, G.M.4
-
233
-
-
77956181220
-
Structure of the complex between HER2 and an antibody paratope formed by side chains from tryptophan and serine
-
Fisher, R.D.; Ultsch, M.; Lingel, A.; Schaefer, G.; Shao, L.; Birtalan, S.; Sidhu, S.S.; Eigenbrot, C. Structure of the complex between HER2 and an antibody paratope formed by side chains from tryptophan and serine. J. Mol. Biol. 2010, 402, 217-229.
-
(2010)
J. Mol. Biol.
, vol.402
, pp. 217-229
-
-
Fisher, R.D.1
Ultsch, M.2
Lingel, A.3
Schaefer, G.4
Shao, L.5
Birtalan, S.6
Sidhu, S.S.7
Eigenbrot, C.8
-
234
-
-
73349090936
-
Discovery of small molecule inhibitors of protein-protein interactions using combined ligand and target score normalization
-
Casey, F.P.; Pihan, E.; Shields, D.C. Discovery of small molecule inhibitors of protein-protein interactions using combined ligand and target score normalization. J. Chem. Inf. Model. 2009, 49, 2708-2717.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2708-2717
-
-
Casey, F.P.1
Pihan, E.2
Shields, D.C.3
-
235
-
-
37649000332
-
Protein protein interaction inhibition (2P2I) combining high throughput and virtual screening: Application to the HIV-1 nef protein
-
Betzi, S.; Restouin, A.; Opi, S.; Arold, S.T.; Parrot, I.; Guerlesquin, F.; Morelli, X.; Collette, Y. Protein protein interaction inhibition (2P2I) combining high throughput and virtual screening: Application to the HIV-1 nef protein. Proc. Natl. Acad. Sci. USA 2007, 104, 19256-19261.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 19256-19261
-
-
Betzi, S.1
Restouin, A.2
Opi, S.3
Arold, S.T.4
Parrot, I.5
Guerlesquin, F.6
Morelli, X.7
Collette, Y.8
-
236
-
-
77955356550
-
Design of potent inhibitors of human rad51 recombinase based on brc motifs of brca2 protein: Modeling and experimental validation of a chimera peptide
-
Nomme, J.; Renodon-Corniere, A.; Asanomi, Y.; Sakaguchi, K.; Stasiak, A.Z.; Stasiak, A.; Norden, B.; Tran, V.; Takahashi, M. Design of potent inhibitors of human rad51 recombinase based on brc motifs of brca2 protein: Modeling and experimental validation of a chimera peptide. J. Med. Chem. 2010, 53, 5782-5791.
-
(2010)
J. Med. Chem.
, vol.53
, pp. 5782-5791
-
-
Nomme, J.1
Renodon-Corniere, A.2
Asanomi, Y.3
Sakaguchi, K.4
Stasiak, A.Z.5
Stasiak, A.6
Norden, B.7
Tran, V.8
Takahashi, M.9
-
237
-
-
22144454687
-
Strategies for targeting protein-protein interactions with synthetic agents
-
Yin, H.; Hamilton, A.D. Strategies for targeting protein-protein interactions with synthetic agents. Angew. Chem. 2005, 44, 4130-4163.
-
(2005)
Angew. Chem.
, vol.44
, pp. 4130-4163
-
-
Yin, H.1
Hamilton, A.D.2
-
238
-
-
69549124720
-
Stabilizers of the max homodimer identified in virtual ligand screening inhibit myc function
-
Jiang, H.; Bower, K.E.; Beuscher, A.E.; Zhou, B.; Bobkov, A.A.; Olson, A.J.; Vogt, P.K. Stabilizers of the max homodimer identified in virtual ligand screening inhibit myc function. Mol. Pharmacol. 2009, 76, 491-502.
-
(2009)
Mol. Pharmacol.
, vol.76
, pp. 491-502
-
-
Jiang, H.1
Bower, K.E.2
Beuscher, A.E.3
Zhou, B.4
Bobkov, A.A.5
Olson, A.J.6
Vogt, P.K.7
-
239
-
-
0037462459
-
X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors
-
Nair, S.K.; Burley, S.K. X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors. Cell 2003, 112, 193-205.
-
(2003)
Cell
, vol.112
, pp. 193-205
-
-
Nair, S.K.1
Burley, S.K.2
-
240
-
-
33645377497
-
Structure-based development of target-specific compound libraries
-
Orry, A.J.; Abagyan, R.A.; Cavasotto, C.N. Structure-based development of target-specific compound libraries. Drug Discov. Today 2006, 11, 261-266.
-
(2006)
Drug Discov. Today
, vol.11
, pp. 261-266
-
-
Orry, A.J.1
Abagyan, R.A.2
Cavasotto, C.N.3
|