-
1
-
-
33750303565
-
Hot-spot mimicry of a cytokine receptor by a small molecule
-
Thanos CD, DeLano WL, Wells JA (2006) Hot-spot mimicry of a cytokine receptor by a small molecule. Proc Nat Acad Sci 103:15422-15427.
-
(2006)
Proc Nat Acad Sci
, vol.103
, pp. 15422-15427
-
-
Thanos, C.D.1
Delano, W.L.2
Wells, J.A.3
-
4
-
-
0028916599
-
A hot spot of binding energy in a hormone-receptor interface
-
Clackson T, Wells J (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267:383-386.
-
(1995)
Science
, vol.267
, pp. 383-386
-
-
Clackson, T.1
Wells, J.2
-
5
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280:1-9.
-
(1998)
J Mol Biol
, vol.280
, pp. 1-9
-
-
Bogan, A.A.1
Thorn, K.S.2
-
6
-
-
0037195144
-
A simple physical model for binding energy hot spots in protein-protein complexes
-
Kortemme T, Baker D (2002) A simple physical model for binding energy hot spots in protein-protein complexes. Proc Nat Acad Sci 99:14116-14121.
-
(2002)
Proc Nat Acad Sci
, vol.99
, pp. 14116-14121
-
-
Kortemme, T.1
Baker, D.2
-
7
-
-
33847650393
-
Computational alanine scanning mutagenesis-an improved methodological approach
-
Moreira J, Fernandez-Recio IS, Ramos MJ (2007) Computational alanine scanning mutagenesis-an improved methodological approach. Nat J Comput Chem 28: 644-654.
-
(2007)
Nat J Comput Chem
, vol.28
, pp. 644-654
-
-
Moreira, J.1
Fernandez-Recio, I.S.2
Ramos, M.J.3
-
8
-
-
55649090573
-
Identification of hot-spot residues in protein-protein interactions by computational docking
-
Grosdidier S, Fernandez-Recio J (2008) Identification of hot-spot residues in protein-protein interactions by computational docking. BMC Bioinformatics 9:447-460.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 447-460
-
-
Grosdidier, S.1
Fernandez-Recio, J.2
-
9
-
-
77954304081
-
Drugscore PPI webserver: Fast and accurate in silico alanine scanning for scoring protein-protein interactions
-
Krger DM, Gohlke H (2010) Drugscore PPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions. Nucl Acids Res 38(Suppl 2):W480-W486.
-
(2010)
Nucl Acids Res
, vol.38
, Issue.SUPPL. 2
-
-
Krger, D.M.1
Gohlke, H.2
-
10
-
-
79953060278
-
Context-based identification of protein-protein interfaces and hot-spot residues
-
Geppert T, Hoy B, Wessler S, Schneider G (2011) Context-based identification of protein-protein interfaces and hot-spot residues. Chem Biol 18:344-353.
-
(2011)
Chem Biol
, vol.18
, pp. 344-353
-
-
Geppert, T.1
Hoy, B.2
Wessler, S.3
Schneider, G.4
-
11
-
-
0037609791
-
Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
-
Ma B, Elkayam T, Wolfson H, Nussinov R (2003) Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci 100:5772-5777.
-
(2003)
Proc Natl Acad Sci
, vol.100
, pp. 5772-5777
-
-
Ma, B.1
Elkayam, T.2
Wolfson, H.3
Nussinov, R.4
-
12
-
-
0034213559
-
Conservation of polar residues as hot-spots at protein interfaces
-
Hu Z, Ma B, Wolfson H, Nussinov R (2000) Conservation of polar residues as hot-spots at protein interfaces. Proteins 39:331-342.
-
(2000)
Proteins
, vol.39
, pp. 331-342
-
-
Hu, Z.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
13
-
-
38549092067
-
Hot-Sprint: Database of computational hot spots in protein interfaces
-
Guney E, Tuncbag N, Keskin O, Gursoy A (2008) Hot-Sprint: database of computational hot spots in protein interfaces. Nucleic Acids Res 36(Suppl 1):D662-D666.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.SUPPL. 1
-
-
Guney, E.1
Tuncbag, N.2
Keskin, O.3
Gursoy, A.4
-
14
-
-
66349094681
-
Identification of computational hot spots in protein interfaces: Combining solvent accessibility and inter-residue potentials improves the accuracy
-
Tuncbag N, Gursoy A, Keskin O (2009) Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics 25:1513-1520.
-
(2009)
Bioinformatics
, vol.25
, pp. 1513-1520
-
-
Tuncbag, N.1
Gursoy, A.2
Keskin, O.3
-
16
-
-
34548764386
-
An automated decision-tree approach to predicting protein interaction hot spots
-
Darnell SJ, Page D, Mitchell C (2007) An automated decision-tree approach to predicting protein interaction hot spots. Proteins: Struct Funct Bioinformatics 68: 813-823.
-
(2007)
Proteins: Struct Funct Bioinformatics
, vol.68
, pp. 813-823
-
-
Darnell, S.J.1
Page, D.2
Mitchell, C.3
-
17
-
-
3242879771
-
Computational alanine scanning of protein-protein interfaces
-
Kortemme D, Kim T, Baker D (2004) Computational alanine scanning of protein-protein interfaces. Sci STKE 219: pl2.
-
(2004)
Sci STKE
, vol.219
-
-
Kortemme, D.1
Kim, T.2
Baker, D.3
-
18
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois J, Nielsen R, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320:369-387.
-
(2002)
J Mol Biol
, vol.320
, pp. 369-387
-
-
Guerois, J.1
Nielsen, R.2
Serrano, L.3
-
19
-
-
70749125843
-
Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods
-
Lise S, Archambeau C, Pontil M, Jones D (2009) Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. BMC Bioinformatics 10:365.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 365
-
-
Lise, S.1
Archambeau, C.2
Pontil, M.3
Jones, D.4
-
20
-
-
34547573955
-
Protein-protein interaction hotspots carved into sequences
-
Ofran Y, Rost B (2007) Protein-protein interaction hotspots carved into sequences, PLoS Comput Biol 3:e119.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Ofran, Y.1
Rost, B.2
-
21
-
-
0035066602
-
A database of alanine mutations and their effects on the free energy of binding in protein interactions
-
Thorn KS, Bogan AA (2001) A database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 17: 284-285.
-
(2001)
Bioinformatics
, vol.17
, pp. 284-285
-
-
Thorn, K.S.1
Bogan, A.A.2
-
22
-
-
0042594456
-
The binding interface database (bid): A compilation of amino acid hot spots in protein interfaces
-
Fischer TB, Arunachalam KV, Bailey D, Mangual V, Bakhru S, Russo R, Huang D, Paczkowski M, Lalchandani V, Ramachandra C, Ellison B, Galer S, Shapley J, Fuentes E, Tsai J (2003) The binding interface database (bid): a compilation of amino acid hot spots in protein interfaces. Bioinformatics 19:1453-1454.
-
(2003)
Bioinformatics
, vol.19
, pp. 1453-1454
-
-
Fischer, T.B.1
Arunachalam, K.V.2
Bailey, D.3
Mangual, V.4
Bakhru, S.5
Russo, R.6
Huang, D.7
Paczkowski, M.8
Lalchandani, V.9
Ramachandra, C.10
Ellison, B.11
Galer, S.12
Shapley, J.13
Fuentes, E.14
Tsai, J.15
-
23
-
-
33846662784
-
ISIS: Interaction sites identified from sequence
-
Ofran Y, Rost B (2007) ISIS: interaction sites identified from sequence. Bioinformatics 23:e13-e16.
-
(2007)
Bioinformatics
, vol.23
-
-
Ofran, Y.1
Rost, B.2
-
24
-
-
0031036744
-
Human cellular retinoic acid binding proteins: Quantitative analysis of the ligand binding properties of the wild-type and sitedirected mutants
-
Wang L, Li Y, Yan H (1997) Human cellular retinoic acid binding proteins: quantitative analysis of the ligand binding properties of the wild-type and sitedirected mutants. J Biol Chem 272:1541-1547.
-
(1997)
J Biol Chem
, vol.272
, pp. 1541-1547
-
-
Wang, L.1
Li, Y.2
Yan, H.3
-
25
-
-
77649228104
-
The overlap of small molecule and protein binding sites within families of protein structures
-
Davis FP, Sali A (2010) The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comput Biol 6:e1000668.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Davis, F.P.1
Sali, A.2
-
26
-
-
84865494461
-
Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces
-
Zerbe BS, Hall DR, Vajda S, Whitty A, Kozakov D (2012) Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces. J Chem Inform Model 52:2236-2244.
-
(2012)
J Chem Inform Model
, vol.52
, pp. 2236-2244
-
-
Zerbe, B.S.1
Hall, D.R.2
Vajda, S.3
Whitty, A.4
Kozakov, D.5
-
28
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.D.1
Bashford, D.2
Bellott3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-Mccarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
29
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004), Development and testing of a general amber force field. J Comp Chem 25:1157-1173.
-
(2004)
J Comp Chem
, vol.25
, pp. 1157-1173
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
30
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
31
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748.
-
(1997)
J Mol Biol
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
32
-
-
0026813925
-
The computer program LUDI: A new method for the de novo design of enzyme inhibitors
-
Bohm HJ (1991) The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J Comput-Aided Mol Des 6:61-78.
-
(1991)
J Comput-Aided Mol des
, vol.6
, pp. 61-78
-
-
Bohm, H.J.1
-
34
-
-
84863296319
-
Algorithmic challenges in structure-based drug design and NMR structural biology
-
Wang L, Zou S, Wang Y (2012) Algorithmic challenges in structure-based drug design and NMR structural biology. Front Electr Electron Eng 7:69-84.
-
(2012)
Front Electr Electron Eng
, vol.7
, pp. 69-84
-
-
Wang, L.1
Zou, S.2
Wang, Y.3
-
35
-
-
0031370977
-
Ligsite: Automatic and efficient detection of potential small molecule-binding sites in proteins
-
Hendlich M, Rippmann F, Barnickel G (1997) Ligsite: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model 15:359-363.
-
(1997)
J Mol Graph Model
, vol.15
, pp. 359-363
-
-
Hendlich, M.1
Rippmann, F.2
Barnickel, G.3
-
36
-
-
1542390499
-
Identification of protein-protein interaction sites from docking energy landscapes
-
Fernandez-Recio J, Totrov M, Abagyan R (2004) Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 335:843-865.
-
(2004)
J Mol Biol
, vol.335
, pp. 843-865
-
-
Fernandez-Recio, J.1
Totrov, M.2
Abagyan, R.3
-
37
-
-
33845352894
-
Solution structure of mouse Cripto CFC domain and its inactive variant Trp107Ala
-
Calvanese L, Saporito A, Marasco D, D'Auria G, Minchiotti G, Pedone C, Paolillo L, Falcigno L, Ruvo M (2006) Solution structure of mouse Cripto CFC domain and its inactive variant Trp107Ala. J Med Chem 49: 7054-7062.
-
(2006)
J Med Chem
, vol.49
, pp. 7054-7062
-
-
Calvanese, L.1
Saporito, A.2
Marasco, D.3
D'auria, G.4
Minchiotti, G.5
Pedone, C.6
Paolillo, L.7
Falcigno, L.8
Ruvo, M.9
-
38
-
-
0038642113
-
Cripto forms a complex with activin and type ii activin receptors and can block activin signalling
-
Gray PC, Harrison CA, Vale W (2003) Cripto forms a complex with activin and type ii activin receptors and can block activin signalling. Proc Nat Acad Sci 100: 5193-5198.
-
(2003)
Proc Nat Acad Sci
, vol.100
, pp. 5193-5198
-
-
Gray, P.C.1
Harrison, C.A.2
Vale, W.3
-
39
-
-
41949137589
-
Cripto is a noncompetitive activin antagonist that forms analogous signaling complexes with activin and nodal
-
Kelber JA, Shani G, Booker EC, Vale WW, Gray PC (2008) Cripto is a noncompetitive activin antagonist that forms analogous signaling complexes with activin and nodal. J Biol Chem 283:4490-4500.
-
(2008)
J Biol Chem
, vol.283
, pp. 4490-4500
-
-
Kelber, J.A.1
Shani, G.2
Booker, E.C.3
Vale, W.W.4
Gray, P.C.5
-
40
-
-
79959471528
-
Alantolactone inhibits cell proliferation by interrupting the interaction between cripto-1 and activin receptor type ii a in activin signaling pathway
-
Shi Y, Bao YL, Wu Y, Yu CL, Huang YX, Sun Y, Zheng LH, Li YX (2011) Alantolactone inhibits cell proliferation by interrupting the interaction between cripto-1 and activin receptor type ii a in activin signaling pathway. J Biomol Screen 16:525-535.
-
(2011)
J Biomol Screen
, vol.16
, pp. 525-535
-
-
Shi, Y.1
Bao, Y.L.2
Wu, Y.3
Yu, C.L.4
Huang, Y.X.5
Sun, Y.6
Zheng, L.H.7
Li, Y.X.8
-
41
-
-
0037061646
-
Inhibition of protein-protein association by small molecules: Approaches and progress
-
Toogood PL (2001) Inhibition of protein-protein association by small molecules: approaches and progress. J Med Chem 45:1543-1558.
-
(2001)
J Med Chem
, vol.45
, pp. 1543-1558
-
-
Toogood, P.L.1
|