-
1
-
-
50249114683
-
An improved relaxed complex scheme for receptor flexibility in computer-Aided drug design
-
Amaro RE, Baron R, and McCammon JA (2008) An improved relaxed complex scheme for receptor flexibility in computer-Aided drug design. J Comput Aided Mol Des 22:693-705.
-
(2008)
J Comput Aided Mol Des
, vol.22
, pp. 693-705
-
-
Amaro, R.E.1
Baron, R.2
McCammon, J.A.3
-
2
-
-
77953321799
-
Downregulation of xpf-ercc1 enhances cisplatin efficacy in cancer cells
-
Arora S, Kothandapani A, Tillison K, Kalman-Maltese V, and Patrick SM (2010) Downregulation of XPF-ERCC1 enhances cisplatin efficacy in cancer cells. DNA Repair (Amst) 9:745-753.
-
(2010)
DNA Repair (Amst)
, Issue.9
, pp. 745-753
-
-
Arora, S.1
Kothandapani, A.2
Tillison, K.3
Kalman-Maltese, V.4
Patrick, S.M.5
-
3
-
-
58149168589
-
Non-peptidic small molecule inhibitors against bcl-2 for cancer therapy
-
Azmi AS and Mohammad RM (2009) Non-peptidic small molecule inhibitors against Bcl-2 for cancer therapy. J Cell Physiol 218:13-21.
-
(2009)
J Cell Physiol
, vol.218
, pp. 13-21
-
-
Azmi, A.S.1
Mohammad, R.M.2
-
4
-
-
74649083070
-
Ensemble-based virtual screening reveals dual-inhibitors for the p53-mdm2mdmx interactions
-
Barakat K, Mane J, Friesen D, and Tuszynski J (2010) Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions. J Mol Graph Model 28:555-568
-
(2010)
J Mol Graph Model
, vol.28
, pp. 555-568
-
-
Barakat, K.1
Mane, J.2
Friesen, D.3
Tuszynski, J.4
-
5
-
-
79751538280
-
Relaxed complex scheme suggests novel inhibitors for the lyase activity of dna polymerase beta
-
Barakat K and Tuszynski J (2011) Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta. J Mol Graph Model 29:702-716.
-
(2011)
J Mol Graph Model
, vol.29
, pp. 702-716
-
-
Barakat, K.1
Tuszynski, J.2
-
6
-
-
84871265063
-
Virtual screening and biological evaluation of inhibitors targeting the xpa-ercc1 interaction
-
Barakat KH, Jordheim LP, Perez-Pineiro R, Wishart D, Dumontet C, and Tuszynski JA (2012) Virtual screening and biological evaluation of inhibitors targeting the XPA-ERCC1 interaction. PLoS ONE 7:e51329.
-
(2012)
PLoS ONE
, vol.7
-
-
Barakat, K.H.1
Jordheim, L.P.2
Perez-Pineiro, R.3
Wishart, D.4
Dumontet, C.5
Tuszynski, J.A.6
-
7
-
-
70349303452
-
Characterization of an inhibitory dynamic pharmacophore for the ercc1-xpa interaction using a combined molecular dynamics and virtual screening approach
-
Barakat KH, Torin Huzil J, Luchko T, Jordheim L, Dumontet C, and Tuszynski J (2009) Characterization of an inhibitory dynamic pharmacophore for the ERCC1-XPA interaction using a combined molecular dynamics and virtual screening approach. J Mol Graph Model 28:113-130.
-
(2009)
J Mol Graph Model
, vol.28
, pp. 113-130
-
-
Barakat, K.H.1
Torin Huzil, J.2
Luchko, T.3
Jordheim, L.4
Dumontet, C.5
Tuszynski, J.6
-
8
-
-
23444454552
-
The amber biomolecular simulation programs
-
Case DA, Cheatham T, Darden T, Gohlke H, Luo R, Merz KM Jr., Onufriev A, Simmerling C, Wang B, and Woods R (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668-1688
-
(2005)
J Comput Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.10
-
9
-
-
0021118703
-
Quantitative analysis of dose-effect relationships: The combined effects of multiple drugs or enzyme inhibitors
-
Chou TC and Talalay P (1984) Quantitative analysis of dose-effect relationships: the combined effects of multiple drugs or enzyme inhibitors. Adv Enzyme Regul 22: 27-55.
-
(1984)
Adv Enzyme Regul
, vol.22
, pp. 27-55
-
-
Chou, T.C.1
Talalay, P.2
-
10
-
-
77957836576
-
Dual function of myd88 in ras signaling and inflammation, leading to mouse and human cell transformation
-
Coste I, Le Corf K, Kfoury A, Hmitou I, Druillennec S, Hainaut P, Eychene A, Lebecque S, and Renno T (2010) Dual function of MyD88 in RAS signaling and inflammation, leading to mouse and human cell transformation. J Clin Invest 120:3663-3667.
-
(2010)
J Clin Invest
, vol.120
, pp. 3663-3667
-
-
Coste, I.1
Le Corf, K.2
Kfoury, A.3
Hmitou, I.4
Druillennec, S.5
Hainaut, P.6
Eychene, A.7
Lebecque, S.8
Renno, T.9
-
11
-
-
0026722362
-
Activity of aphidicolin glycinate alone or in combination with cisplatin in a murine ovarian tumor resistant to cisplatin
-
Damia G, Tagliabue G, Zucchetti M, Davoli E, Sessa C, Cavalli F, and D'Incalci M (1992) Activity of aphidicolin glycinate alone or in combination with cisplatin in a murine ovarian tumor resistant to cisplatin. Cancer Chemother Pharmacol 30: 459-464.
-
(1992)
Cancer Chemother Pharmacol
, vol.30
, pp. 459-464
-
-
Damia, G.1
Tagliabue, G.2
Zucchetti, M.3
Davoli, E.4
Sessa, C.5
Cavalli, F.6
D'Incalci, M.7
-
12
-
-
34547559704
-
Pdb2pqr: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
(Web Server issue):W522-5
-
Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, and Baker NA (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 (Web Server issue):W522-5.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Dolinsky, T.J.1
Czodrowski, P.2
Li, H.3
Nielsen, J.E.4
Jensen, J.H.5
Klebe, G.6
Baker, N.A.7
-
13
-
-
0034087890
-
Biosensor analysis of the interaction between immobilized human serum albumin and drug compounds for prediction of human serum albumin binding levels
-
Frostell-Karlsson A, Remaeus A, Roos H, Andersson K, Borg P, Hämäläinen M, and Karlsson R (2000) Biosensor analysis of the interaction between immobilized human serum albumin and drug compounds for prediction of human serum albumin binding levels. J Med Chem 43:1986-1992.
-
(2000)
J Med Chem
, vol.43
, pp. 1986-1992
-
-
Frostell-Karlsson, A.1
Remaeus, A.2
Roos, H.3
Andersson, K.4
Borg, P.5
Hämäläinen, M.6
Karlsson, R.7
-
14
-
-
84859771379
-
Molecular mechanisms of cisplatin resistance
-
Galluzzi L, Senovilla L, Vitale I, Michels J, Martins I, Kepp O, Castedo M, and Kroemer G (2012) Molecular mechanisms of cisplatin resistance. Oncogene 31: 1869-1883.
-
(2012)
Oncogene
, vol.31
, pp. 1869-1883
-
-
Galluzzi, L.1
Senovilla, L.2
Vitale, I.3
Michels, J.4
Martins, I.5
Kepp, O.6
Castedo, M.7
Kroemer, G.8
-
15
-
-
49149147973
-
Iterative partial equalization of orbital electronegativity: A rapid access to atomic charges
-
Gasteiger J and Marsili M (1980) Iterative partial equalization of orbital electronegativity: a rapid access to atomic charges. Tetrahedron 36:3219-3228
-
(1980)
Tetrahedron
, vol.36
, pp. 3219-3228
-
-
Gasteiger, J.1
Marsili, M.2
-
16
-
-
77956661470
-
Regulation of excision repair cross-complementation group 1 by snail contributes to cisplatin resistance in head and neck cancer
-
Hsu DS, Lan HY, Huang CH, Tai SK, Chang SY, Tsai TL, Chang CC, Tzeng CH, Wu KJ, and Kao JY et al. (2010) Regulation of excision repair cross-complementation group 1 by Snail contributes to cisplatin resistance in head and neck cancer. Clin Cancer Res 16:4561-4571.
-
(2010)
Clin Cancer Res
, vol.16
, pp. 4561-4571
-
-
Hsu, D.S.1
Lan, H.Y.2
Huang, C.H.3
Tai, S.K.4
Chang, S.Y.5
Tsai, T.L.6
Chang, C.C.7
Tzeng, C.H.8
Wu, K.J.9
Kao, J.Y.10
-
17
-
-
80054107639
-
Excision repair crosscomplementation group 1 (ercc1) status and lung cancer outcomes: A metaanalysis of published studies and recommendations
-
Hubner RA, Riley RD, Billingham LJ, and Popat S (2011) Excision repair crosscomplementation group 1 (ERCC1) status and lung cancer outcomes: a metaanalysis of published studies and recommendations. PLoS ONE 6:e25164.
-
(2011)
PLoS ONE
, vol.6
-
-
Hubner, R.A.1
Riley, R.D.2
Billingham, L.J.3
Popat, S.4
-
18
-
-
2542422438
-
Structure, recognition, and processing of cisplatin-dna adducts
-
Jamieson ER and Lippard SJ (1999) Structure, Recognition, and Processing of Cisplatin-DNA Adducts. Chem Rev 99:2467-2498
-
(1999)
Chem Rev
, vol.99
, pp. 2467-2498
-
-
Jamieson, E.R.1
Lippard, S.J.2
-
19
-
-
23844466231
-
Increased expression of the large subunit of ribonucleotide reductase is involved in resistance to gemcitabine in human mammary adenocarcinoma cells
-
Jordheim LP, Guittet O, Lepoivre M, Galmarini CM, and Dumontet C (2005) Increased expression of the large subunit of ribonucleotide reductase is involved in resistance to gemcitabine in human mammary adenocarcinoma cells. Mol Cancer Ther 4:1268-1276.
-
(2005)
Mol Cancer Ther
, vol.4
, pp. 1268-1276
-
-
Jordheim, L.P.1
Guittet, O.2
Lepoivre, M.3
Galmarini, C.M.4
Dumontet, C.5
-
20
-
-
0042415783
-
Namd2: Greater scalability for parallel molecular dynamics
-
Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, and Schulten K (1999) NAMD2: Greater Scalability for Parallel Molecular Dynamics. J Comput Phys 151:283-312.
-
(1999)
J Comput Phys
, vol.151
, pp. 283-312
-
-
Kale, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
21
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, and Wang W et al. (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889-897.
-
(2000)
Acc Chem Res
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
-
22
-
-
20444377245
-
Validation and use of the mm-pbsa approach for drug discovery
-
Kuhn B, Gerber P, Schulz-Gasch T, and Stahl M (2005) Validation and use of the MM-PBSA approach for drug discovery. J Med Chem 48:4040-4048
-
(2005)
J Med Chem
, vol.48
, pp. 4040-4048
-
-
Kuhn, B.1
Gerber, P.2
Schulz-Gasch, T.3
Stahl, M.4
-
23
-
-
84879121058
-
Principles of fluorescence spectroscopy, second ed. Kluwer academic/plenum, new york. Lin jh, perryman al, schames jr, and mccammon ja (2002) computational drug design accommodating receptor flexibility: The relaxed complex scheme
-
Lakowicz JR(1999) Principles of fluorescence spectroscopy, Second ed. Kluwer Academic/Plenum, New York. Lin JH, Perryman AL, Schames JR, and McCammon JA (2002) Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc 124:5632-5633.
-
(1999)
J Am Chem Soc
, vol.124
, pp. 5632-5633
-
-
Lakowicz, J.R.1
-
24
-
-
0035436539
-
Repair of dna interstrand crosslinks: Molecular mechanisms and clinical relevance
-
McHugh PJ, Spanswick VJ, and Hartley JA (2001) Repair of DNA interstrand crosslinks: molecular mechanisms and clinical relevance. Lancet Oncol 2:483-490.
-
(2001)
Lancet Oncol
, vol.2
, pp. 483-490
-
-
McHugh, P.J.1
Spanswick, V.J.2
Hartley, J.A.3
-
25
-
-
84869005179
-
Dna repair endonuclease ercc1-xpf as a novel therapeutic target to overcome chemoresistance in cancer therapy
-
McNeil EM and Melton DW (2012) DNA repair endonuclease ERCC1-XPF as a novel therapeutic target to overcome chemoresistance in cancer therapy. Nucleic Acids Res 40:9990-10004.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 9990-10004
-
-
McNeil, E.M.1
Melton, D.W.2
-
26
-
-
11644261806
-
Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function
-
Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, and Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639-1662.
-
(1998)
J Comput Chem
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
27
-
-
2942709644
-
The structure-specific endonuclease ercc1-xpf is required to resolve dna interstrand cross-link-induced double-strand breaks
-
Niedernhofer LJ, Odijk H, Budzowska M, van Drunen E, Maas A, Theil AF, de Wit J, Jaspers NG, Beverloo HB, and Hoeijmakers JH et al. (2004) The structure-specific endonuclease Ercc1-Xpf is required to resolve DNA interstrand cross-link-induced double-strand breaks. Mol Cell Biol 24:5776-5787.
-
(2004)
Mol Cell Biol
, vol.24
, pp. 5776-5787
-
-
Niedernhofer, L.J.1
Odijk, H.2
Budzowska, M.3
Van Drunen, E.4
Maas, A.5
Theil, A.F.6
De Wit, J.7
Jaspers, N.G.8
Beverloo, H.B.9
Hoeijmakers, J.H.10
-
28
-
-
62349131315
-
Dna repair in mammalian cells : Nucleotide excision repair: Variations on versatility
-
Nouspikel T (2009) DNA repair in mammalian cells : Nucleotide excision repair: variations on versatility. Cell Mol Life Sci 66:994-1009.
-
(2009)
Cell Mol Life Sci
, vol.66
, pp. 994-1009
-
-
Nouspikel, T.1
-
29
-
-
0027958095
-
Antitumor activity and biochemical effects of aphidicolin glycinate (nsc 303812) alone and in combination with cisplatin in vivo
-
O'Dwyer PJ, Moyer JD, Suffness M, Harrison SD, Jr., Cysyk R, Hamilton TC, and Plowman J (1994) Antitumor activity and biochemical effects of aphidicolin glycinate (NSC 303812) alone and in combination with cisplatin in vivo. Cancer Res 54:724-729.
-
(1994)
Cancer Res
, vol.54
, pp. 724-729
-
-
O'Dwyer, P.J.1
Moyer, J.D.2
Suffness, M.3
Harrison, S.D.4
Jr. Cysyk, R.5
Hamilton, T.C.6
Plowman, J.7
-
30
-
-
66249084554
-
Kinetics of h2ax phosphorylation after exposure to cisplatin
-
Olive PL and Banáth JP (2009) Kinetics of H2AX phosphorylation after exposure to cisplatin. Cytometry B Clin Cytom 76:79-90.
-
(2009)
Cytometry B Clin Cytom
, vol.76
, pp. 79-90
-
-
Olive, P.L.1
Banáth, J.P.2
-
31
-
-
27344436659
-
Scalable molecular dynamics with namd
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, and Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781-1802.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
32
-
-
77955889858
-
Multiple roles of ercc1-xpf in mammalian interstrand crosslink repair
-
Rahn JJ, Adair GM, and Nairn RS (2010) Multiple roles of ERCC1-XPF in mammalian interstrand crosslink repair. Environ Mol Mutagen 51:567-581.
-
(2010)
Environ Mol Mutagen
, vol.51
, pp. 567-581
-
-
Rahn, J.J.1
Adair, G.M.2
Nairn, R.S.3
-
33
-
-
55949092708
-
High sensitivity of brca1-deficient mammary tumors to the parp inhibitor azd2281 alone and in combination with platinum drugs
-
Rottenberg S, Jaspers JE, Kersbergen A, van der Burg E, Nygren AO, Zander SA, Derksen PW, de Bruin M, Zevenhoven J, and Lau A et al. (2008) High sensitivity of BRCA1-deficient mammary tumors to the PARP inhibitor AZD2281 alone and in combination with platinum drugs. Proc Natl Acad Sci USA 105: 17079-17084.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 17079-17084
-
-
Rottenberg, S.1
Jaspers, J.E.2
Kersbergen, A.3
Van Der Burg, E.4
Nygren, A.O.5
Zander, S.A.6
Derksen, P.W.7
De Bruin, M.8
Zevenhoven, J.9
Lau, A.10
-
34
-
-
53049108040
-
Targeting the mdm2-p53 interaction for cancer therapy
-
Shangary S and Wang S (2008) Targeting the MDM2-p53 interaction for cancer therapy. Clin Cancer Res 14:5318-5324.
-
(2008)
Clin Cancer Res
, vol.14
, pp. 5318-5324
-
-
Shangary, S.1
Wang, S.2
-
35
-
-
36649006642
-
Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms
-
Shao J, Tanner SW, Thompson N, and Cheatham TE, 3rd (2007) Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms. J Chem Theory Comput 3:2312-2334.
-
(2007)
J Chem Theory Comput
, vol.3
, pp. 2312-2334
-
-
Shao, J.1
Tanner, S.W.2
Thompson, N.3
Cheatham III, T.E.4
-
36
-
-
28844480409
-
The structure of the human ercc1/xpf interaction domains reveals a complementary role for the two proteins in nucleotide excision repair
-
Tripsianes K, Folkers G, Ab E, Das D, Odijk H, Jaspers NG, Hoeijmakers JH, Kaptein R, and Boelens R (2005) The structure of the human ERCC1/XPF interaction domains reveals a complementary role for the two proteins in nucleotide excision repair. Structure 13:1849-1858
-
(2005)
Structure
, vol.13
, pp. 1849-1858
-
-
Tripsianes, K.1
Folkers, G.2
Ab, E.3
Das, D.4
Odijk, H.5
Jaspers, N.G.6
Hoeijmakers, J.H.7
Kaptein, R.8
Boelens, R.9
-
37
-
-
36249002305
-
Structural basis for the recruitment of ercc1-xpf to nucleotide excision repair complexes by xpa
-
Tsodikov OV, Ivanov D, Orelli B, Staresincic L, Shoshani I, Oberman R, Schärer OD, Wagner G, and Ellenberger T (2007) Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA. EMBO J 26: 4768-4776.
-
(2007)
EMBO J
, vol.26
, pp. 4768-4776
-
-
Tsodikov, O.V.1
Ivanov, D.2
Orelli, B.3
Staresincic, L.4
Shoshani, I.5
Oberman, R.6
Schärer, O.D.7
Wagner, G.8
Ellenberger, T.9
-
38
-
-
84879094682
-
Cisplatin sensitivity of testis tumour cells is due to deficiency in interstrand-crosslink repair and low ERCC1-XPF expression. Mol Cancer 9: 248van de Weert M and Stell L (2011) Fluorescence quenching and ligand binding: A critical discussion of a popular methodology
-
Usanova S, Piée-Staffa A, Sied U, Thomale J, Schneider A, Kaina B, and Köberle B (2010) Cisplatin sensitivity of testis tumour cells is due to deficiency in interstrand-crosslink repair and low ERCC1-XPF expression. Mol Cancer 9: 248van de Weert M and Stell L (2011) Fluorescence quenching and ligand binding: A critical discussion of a popular methodology. J Mol Struct 998:144-150.
-
(2010)
J Mol Struct
, vol.998
, pp. 144-150
-
-
Usanova, S.1
Piée-Staffa, A.2
Sied, U.3
Thomale, J.4
Schneider, A.5
Kaina, B.6
Köberle, B.7
-
39
-
-
77955876503
-
Mammalian nucleotide excision repair proteins and interstrand crosslink repair
-
Wood RD (2010) Mammalian nucleotide excision repair proteins and interstrand crosslink repair. Environ Mol Mutagen 51:520-526.
-
(2010)
Environ Mol Mutagen
, vol.51
, pp. 520-526
-
-
Wood, R.D.1
-
40
-
-
3142773418
-
Oncogenic h-ras up-regulates expression of ercc1 to protect cells from platinumbased anticancer agents
-
Youn CK, Kim MH, Cho HJ, Kim HB, Chang IY, Chung MH, and You HJ (2004) Oncogenic H-Ras up-regulates expression of ERCC1 to protect cells from platinumbased anticancer agents. Cancer Res 64:4849-4857.
-
(2004)
Cancer Res
, vol.64
, pp. 4849-4857
-
-
Youn, C.K.1
Kim, M.H.2
Cho, H.J.3
Kim, H.B.4
Chang, I.Y.5
Chung, M.H.6
You, H.J.7
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