-
1
-
-
79953251130
-
Adhesive water networks facilitate binding of protein interfaces
-
10.1038/ncomms1258 10.1038/ncomms1258
-
Ahmad M, Gu W, Geyer T, Helms V (2011) Adhesive water networks facilitate binding of protein interfaces. Nat Commun 2:261. doi: 10.1038/ncomms1258
-
(2011)
Nat Commun
, vol.2
, pp. 261
-
-
Ahmad, M.1
Gu, W.2
Geyer, T.3
Helms, V.4
-
2
-
-
33644550021
-
Structural systems biology: Modelling protein interactions
-
10.1038/nrm1859 10.1038/nrm1859
-
Aloy P, Russell RB (2006) Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 7:188-197. doi: 10.1038/nrm1859
-
(2006)
Nat Rev Mol Cell Biol
, vol.7
, pp. 188-197
-
-
Aloy, P.1
Russell, R.B.2
-
3
-
-
0035812694
-
Protein structure prediction and structural genomics
-
10.1126/science.1065659
-
Baker D, Sali A (2001) Protein structure prediction and structural genomics. Sci Signal 294:93-96. doi: 10.1126/science.1065659
-
(2001)
Sci Signal
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
4
-
-
38849196324
-
Water as an active constituent in cell biology
-
10.1021/cr068037a 10.1021/cr068037a
-
Ball P (2008) Water as an active constituent in cell biology. Chem Rev 108:74-108. doi: 10.1021/cr068037a
-
(2008)
Chem Rev
, vol.108
, pp. 74-108
-
-
Ball, P.1
-
5
-
-
33846036096
-
The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
-
10.1093/nar/gkl971 10.1093/nar/gkl971
-
Berman H, Henrick K, Nakamura H, Markley JL (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35:D301-D303. doi: 10.1093/nar/gkl971
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
Markley, J.L.4
-
6
-
-
37049014272
-
Version 1.2 of the crystallography and NMR system
-
10.1038/nprot.2007.406 10.1038/nprot.2007.406
-
Brunger AT (2007) Version 1.2 of the crystallography and NMR system. Nat Protoc 2:2728-2733. doi: 10.1038/nprot.2007.406
-
(2007)
Nat Protoc
, vol.2
, pp. 2728-2733
-
-
Brunger, A.T.1
-
7
-
-
53149105939
-
Structural insight into the mechanisms of Wnt signaling antagonism by Dkk
-
10.1074/jbc.M802375200 10.1074/jbc.M802375200
-
Chen L, Wang K, Shao Y et al (2008) Structural insight into the mechanisms of Wnt signaling antagonism by Dkk. J Biol Chem 283:23364-23370. doi: 10.1074/jbc.M802375200
-
(2008)
J Biol Chem
, vol.283
, pp. 23364-23370
-
-
Chen, L.1
Wang, K.2
Shao, Y.3
-
8
-
-
80755172250
-
Exploring translocation of proteins on DNA by NMR
-
10.1007/s10858-011-9555-8 10.1007/s10858-011-9555-8
-
Clore GM (2011) Exploring translocation of proteins on DNA by NMR. J Biomol NMR 51:209-219. doi: 10.1007/s10858-011-9555-8
-
(2011)
J Biomol NMR
, vol.51
, pp. 209-219
-
-
Clore, G.M.1
-
9
-
-
0037464588
-
A vision for the future of genomics research
-
10.1038/nature01626 2003Natur.422.835C 10.1038/nature01626
-
Collins FS, Green ED, Guttmacher AE, Guyer MS (2003) A vision for the future of genomics research. Nature 422:835-847. doi: 10.1038/nature01626
-
(2003)
Nature
, vol.422
, pp. 835-847
-
-
Collins, F.S.1
Green, E.D.2
Guttmacher, A.E.3
Guyer, M.S.4
-
10
-
-
38449097802
-
From protein-protein complexes to interactomics.
-
Bertrand E, Faupel M (eds)
-
Collura V, Boissy G (2007) From protein-protein complexes to interactomics. In: Bertrand E, Faupel M (eds) Subcellular biochemistry, vol 43. pp 135-183
-
(2007)
Subcellular Biochemistry
, vol.43
, pp. 135-183
-
-
Collura, V.1
Boissy, G.2
-
11
-
-
27744567556
-
Interactome: Gateway into systems biology
-
doi: 10.1093/hmg/ddi335
-
Cusick ME, Klitgord N, Vidal M, Hill DE (2005) Interactome: gateway into systems biology. Hum Mol Genet 14(Spec No. 2):R171-R181. doi: 10.1093/hmg/ddi335
-
(2005)
Hum Mol Genet
, vol.14
, Issue.SPEC NO. 2
-
-
Cusick, M.E.1
Klitgord, N.2
Vidal, M.3
Hill, D.E.4
-
12
-
-
36748998784
-
HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets
-
10.1002/prot.21723 10.1002/prot.21723
-
de Vries SJ, van Dijk ADJ, Krzeminski M et al (2007) HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins Struct Funct Bioinform 69:726-733. doi: 10.1002/prot.21723
-
(2007)
Proteins Struct Funct Bioinform
, vol.69
, pp. 726-733
-
-
De Vries, S.J.1
Van Dijk, A.D.J.2
Krzeminski, M.3
-
13
-
-
0037442962
-
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
-
10.1021/ja026939x 10.1021/ja026939x
-
Dominguez C, Boelens R, Bonvin AMJJ (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731-1737. doi: 10.1021/ja026939x
-
(2003)
J Am Chem Soc
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.3
-
14
-
-
0028228418
-
The entropic cost of bound water in crystals and biomolecules
-
10.1126/science.264.5159.670 1994Sci.264.670D 10.1126/science.264.5159. 670
-
Dunitz JD (1994) The entropic cost of bound water in crystals and biomolecules. Science 264:670. doi: 10.1126/science.264.5159.670
-
(1994)
Science
, vol.264
, pp. 670
-
-
Dunitz, J.D.1
-
15
-
-
36749089518
-
Gene regulation in the postgenomic era: Technology takes the wheel
-
10.1016/j.molcel.2007.11.022 10.1016/j.molcel.2007.11.022
-
Dunn RK, Kingston RE (2007) Gene regulation in the postgenomic era: technology takes the wheel. Mol Cell 28:708-714. doi: 10.1016/j.molcel.2007.11. 022
-
(2007)
Mol Cell
, vol.28
, pp. 708-714
-
-
Dunn, R.K.1
Kingston, R.E.2
-
16
-
-
1542390499
-
Identification of protein-protein interaction sites from docking energy landscapes
-
10.1016/j.jmb.2003.10.069
-
Fernández-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
-
-
Fernández-Recio, J.1
Totrov, M.2
Abagyan, R.3
-
17
-
-
0036286321
-
Simulations of nucleic acids and their complexes
-
10.1021/ar010023y
-
Giudice E, Lavery R (2002) Simulations of nucleic acids and their complexes. Acc Chem Res 35:350-357
-
(2002)
Acc Chem Res
, vol.35
, pp. 350-357
-
-
Giudice, E.1
Lavery, R.2
-
18
-
-
0032555574
-
Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts
-
10.1074/jbc.273.34.21721 10.1074/jbc.273.34.21721
-
Horton NC (1998) Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts. J Biol Chem 273:21721-21729. doi: 10.1074/jbc.273.34.21721
-
(1998)
J Biol Chem
, vol.273
, pp. 21721-21729
-
-
Horton, N.C.1
-
19
-
-
50249094315
-
Exploiting ordered waters in molecular docking
-
10.1021/jm8006239 10.1021/jm8006239
-
Huang N, Shoichet BK (2008) Exploiting ordered waters in molecular docking. J Med Chem 51:4862-4865. doi: 10.1021/jm8006239
-
(2008)
J Med Chem
, vol.51
, pp. 4862-4865
-
-
Huang, N.1
Shoichet, B.K.2
-
20
-
-
0003742069
-
-
Department of Biochemistry and Molecular Biology, University College London
-
Hubbard SJ, Thornton JM (1993) NACCESS computer program. Department of Biochemistry and Molecular Biology, University College London
-
(1993)
NACCESS Computer Program
-
-
Hubbard, S.J.1
Thornton, J.M.2
-
21
-
-
0028955215
-
Hydration of nucleic acid fragments: Comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes
-
10.1016/S0006-3495(95)80381-4 10.1016/S0006-3495(95)80381-4
-
Hummer G, García AE, Soumpasis DM (1995) Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes. Biophys J 68:1639-1652. doi: 10.1016/S0006-3495(95)80381-4
-
(1995)
Biophys J
, vol.68
, pp. 1639-1652
-
-
Hummer, G.1
García, A.E.2
Soumpasis, D.M.3
-
22
-
-
0033572790
-
Wet and dry interfaces: The role of solvent in protein-protein and protein-DNA recognition
-
10.1016/S0969-2126(00)88333-1
-
Janin J (1999) Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition. Structure 7:R277-R279
-
(1999)
Structure
, vol.7
-
-
Janin, J.1
-
23
-
-
3042596869
-
The role of water in protein-DNA recognition
-
10.1146/annurev.biophys.33.110502.140414 10.1146/annurev.biophys.33. 110502.140414
-
Jayaram B, Jain T (2004) The role of water in protein-DNA recognition. Annu Rev Biophys Biomol Struct 33:343-361. doi: 10.1146/annurev.biophys.33. 110502.140414
-
(2004)
Annu Rev Biophys Biomol Struct
, vol.33
, pp. 343-361
-
-
Jayaram, B.1
Jain, T.2
-
24
-
-
0033574510
-
Protein-DNA interactions: A structural analysis
-
10.1006/jmbi.1999.2659 10.1006/jmbi.1999.2659
-
Jones S, van Heyningen P, Berman HM, Thornton JM (1999) Protein-DNA interactions: a structural analysis. J Mol Biol 287:877-896. doi: 10.1006/jmbi.1999.2659
-
(1999)
J Mol Biol
, vol.287
, pp. 877-896
-
-
Jones, S.1
Van Heyningen, P.2
Berman, H.M.3
Thornton, J.M.4
-
25
-
-
84860284066
-
PDB-REDO: Constructive validation, more than just looking for errors
-
10.1107/S0907444911054515 10.1107/S0907444911054515
-
Joosten RP, Joosten K, Murshudov GN, Perrakis A (2012) PDB-REDO: constructive validation, more than just looking for errors. Acta Crystallogr D Biol Crystallogr 68:484-496. doi: 10.1107/S0907444911054515
-
(2012)
Acta Crystallogr D Biol Crystallogr
, vol.68
, pp. 484-496
-
-
Joosten, R.P.1
Joosten, K.2
Murshudov, G.N.3
Perrakis, A.4
-
26
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
10.1063/1.445869 1983JChPh.79.926J 10.1063/1.445869
-
Jorgensen WL, Chandrasekhar J, Madura JD (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935. doi: 10.1063/1.445869
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
-
27
-
-
3142657230
-
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes
-
10.1126/science.1097064 2004Sci.305.386K 10.1126/science.1097064
-
Kalodimos CG, Biris N, Bonvin AMJJ et al (2004) Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305:386-389. doi: 10.1126/science.1097064
-
(2004)
Science
, vol.305
, pp. 386-389
-
-
Kalodimos, C.G.1
Biris, N.2
Bonvin, A.3
-
28
-
-
84855932280
-
Explicit treatment of water molecules in data-driven protein-protein docking: The solvated HADDOCKing approach
-
10.1007/978-1-61779-465-0-22 10.1007/978-1-61779-465-0-22
-
Kastritis PL, van Dijk ADJ, Bonvin AMJJ (2012a) Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach. Methods Mol Biol 819:355-374. doi: 10.1007/978-1-61779-465-0-22
-
(2012)
Methods Mol Biol
, vol.819
, pp. 355-374
-
-
Kastritis, P.L.1
Van Dijk, A.D.J.2
Bonvin, A.3
-
30
-
-
77957948556
-
Blind predictions of protein interfaces by docking calculations in CAPRI
-
10.1002/prot.22850 10.1002/prot.22850
-
Lensink MF, Wodak SJ (2010a) Blind predictions of protein interfaces by docking calculations in CAPRI. Proteins Struct Funct Bioinform 78:3085-3095. doi: 10.1002/prot.22850
-
(2010)
Proteins Struct Funct Bioinform
, vol.78
, pp. 3085-3095
-
-
Lensink, M.F.1
Wodak, S.J.2
-
31
-
-
77957934896
-
Docking and scoring protein interactions: CAPRI 2009
-
10.1002/prot.22818 10.1002/prot.22818
-
Lensink MF, Wodak SJ (2010b) Docking and scoring protein interactions: CAPRI 2009. Proteins Struct Funct Bioinform 78:3073-3084. doi: 10.1002/prot.22818
-
(2010)
Proteins Struct Funct Bioinform
, vol.78
, pp. 3073-3084
-
-
Lensink, M.F.1
Wodak, S.J.2
-
32
-
-
33846424559
-
Water at biomolecular binding interfaces
-
10.1039/b612449f 10.1039/b612449f
-
Li Z, Lazaridis T (2007) Water at biomolecular binding interfaces. Phys Chem Chem Phys 9:573-581. doi: 10.1039/b612449f
-
(2007)
Phys Chem Chem Phys
, vol.9
, pp. 573-581
-
-
Li, Z.1
Lazaridis, T.2
-
33
-
-
84865283412
-
Atomistic modeling of protein-DNA interaction specificity: Progress and applications
-
10.1016/j.sbi.2012.06.002 10.1016/j.sbi.2012.06.002
-
Liu LA, Bradley P (2012) Atomistic modeling of protein-DNA interaction specificity: progress and applications. Curr Opin Struct Biol 22:397-405. doi: 10.1016/j.sbi.2012.06.002
-
(2012)
Curr Opin Struct Biol
, vol.22
, pp. 397-405
-
-
Liu, L.A.1
Bradley, P.2
-
34
-
-
77950876974
-
Fast determination of the optimal rotational matrix for macromolecular superpositions
-
doi: 10.1002/jcc.21439
-
Liu P, Agrafiotis DK, Theobald DL (2010) Fast determination of the optimal rotational matrix for macromolecular superpositions. J Comput Chem 1561-1563. doi: 10.1002/jcc.21439
-
(2010)
J Comput Chem
, pp. 1561-1563
-
-
Liu, P.1
Agrafiotis, D.K.2
Theobald, D.L.3
-
35
-
-
0031574026
-
NUCPLOT: A program to generate schematic diagrams of protein-nucleic acid interactions
-
10.1093/nar/29.13.2860 10.1093/nar/25.24.4940
-
Luscombe NM, Laskowski RA, Thornton JM (1997) NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Res 25:4940-4945. doi: 10.1093/nar/29.13.2860
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 4940-4945
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
36
-
-
0033647653
-
An overview of the structures of protein-DNA complexes
-
10.1186/gb-2000-1-1-reviews001 10.1186/gb-2000-1-1-reviews001
-
Luscombe NM, Austin SE, Berman HM, Thornton JM (2000) An overview of the structures of protein-DNA complexes. Genome Biol 1:1-10. doi: 10.1186/gb-2000-1-1-reviews001
-
(2000)
Genome Biol
, vol.1
, pp. 1-10
-
-
Luscombe, N.M.1
Austin, S.E.2
Berman, H.M.3
Thornton, J.M.4
-
37
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
-
10.1093/nar/29.13.2860
-
Luscombe NM, Laskowski RA, Thornton JM (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res 29:2860-2874
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
38
-
-
0036286851
-
Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment
-
10.1021/ar0100273
-
Makarov V, Pettitt BM, Feig M (2002) Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc Chem Res 35:376-384
-
(2002)
Acc Chem Res
, vol.35
, pp. 376-384
-
-
Makarov, V.1
Pettitt, B.M.2
Feig, M.3
-
39
-
-
47549102750
-
Energy-based prediction of amino acid-nucleotide base recognition
-
10.1002/jcc.20954 10.1002/jcc.20954
-
Marabotti A, Spyrakis F, Facchiano A et al (2008) Energy-based prediction of amino acid-nucleotide base recognition. J Comput Chem 29:1955-1969. doi: 10.1002/jcc.20954
-
(2008)
J Comput Chem
, vol.29
, pp. 1955-1969
-
-
Marabotti, A.1
Spyrakis, F.2
Facchiano, A.3
-
40
-
-
84862209611
-
Next challenges in protein-protein docking: From proteome to interactome and beyond
-
doi: 10.1002/wcms.91
-
Melquiond AS, Karaca E, Kastritis PL, Bonvin AM (2011) Next challenges in protein-protein docking: from proteome to interactome and beyond. WIREs Comput Mol Sci 642-651. doi: 10.1002/wcms.91
-
(2011)
WIREs Comput Mol Sci
, pp. 642-651
-
-
Melquiond, A.S.1
Karaca, E.2
Kastritis, P.L.3
Bonvin, A.M.4
-
41
-
-
32344449937
-
Docking of aminoglycosides to hydrated and flexible RNA
-
10.1021/jm0508437 10.1021/jm0508437
-
Moitessier N, Westhof E, Hanessian S (2006) Docking of aminoglycosides to hydrated and flexible RNA. J Med Chem 49:1023-1033. doi: 10.1021/jm0508437
-
(2006)
J Med Chem
, vol.49
, pp. 1023-1033
-
-
Moitessier, N.1
Westhof, E.2
Hanessian, S.3
-
42
-
-
0033573827
-
Structural features of protein-nucleic acid recognition sites
-
10.1021/bi982362d 10.1021/bi982362d
-
Nadassy K, Wodak SJ, Janin J (1999) Structural features of protein-nucleic acid recognition sites. Biochemistry 38:1999-2017. doi: 10.1021/bi982362d
-
(1999)
Biochemistry
, vol.38
, pp. 1999-2017
-
-
Nadassy, K.1
Wodak, S.J.2
Janin, J.3
-
43
-
-
21044449889
-
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
-
10.1002/prot.20408 10.1002/prot.20408
-
Nederveen AJ, Doreleijers JF, Vranken W et al (2005) RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins Struct Funct Bioinform 59:662-672. doi: 10.1002/prot.20408
-
(2005)
Proteins Struct Funct Bioinform
, vol.59
, pp. 662-672
-
-
Nederveen, A.J.1
Doreleijers, J.F.2
Vranken, W.3
-
44
-
-
0024294634
-
Crystal structure of trp repressor/operator complex at atomic resolution
-
10.1038/335321a0 1988Natur.335.321O 10.1038/335321a0
-
Otwinowski Z, Schevitz RW, Zhang RG et al (1988) Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335:321-329. doi: 10.1038/335321a0
-
(1988)
Nature
, vol.335
, pp. 321-329
-
-
Otwinowski, Z.1
Schevitz, R.W.2
Zhang, R.G.3
-
45
-
-
84879905777
-
Crystallization of protein-DNA complexes
-
10.1002/9780470015902.a0002720.pub2
-
Pakotiprapha D, Jeruzalmi D (2009) Crystallization of protein-DNA complexes. Encycl Life Sci (ELS). doi: 10.1002/9780470015902.a0002720.pub2
-
(2009)
Encycl Life Sci (ELS)
-
-
Pakotiprapha, D.1
Jeruzalmi, D.2
-
46
-
-
0034659815
-
Proteomics to study genes and genomes
-
10.1038/35015709 10.1038/35015709
-
Pandey A, Mann M (2000) Proteomics to study genes and genomes. Nature 405:837-846. doi: 10.1038/35015709
-
(2000)
Nature
, vol.405
, pp. 837-846
-
-
Pandey, A.1
Mann, M.2
-
47
-
-
84860477162
-
Frontiers in molecular dynamics simulations of DNA
-
10.1021/ar2001217 10.1021/ar2001217
-
Pérez A, Luque FJ, Orozco M (2012) Frontiers in molecular dynamics simulations of DNA. Acc Chem Res 45:196-205. doi: 10.1021/ar2001217
-
(2012)
Acc Chem Res
, vol.45
, pp. 196-205
-
-
Pérez, A.1
Luque, F.J.2
Orozco, M.3
-
48
-
-
0035976713
-
Do water molecules mediate protein-DNA recognition?
-
10.1006/jmbi.2001.5154 10.1006/jmbi.2001.5154
-
Reddy CK, Das A, Jayaram B (2001) Do water molecules mediate protein-DNA recognition? J Mol Biol 314:619-632. doi: 10.1006/jmbi.2001.5154
-
(2001)
J Mol Biol
, vol.314
, pp. 619-632
-
-
Reddy, C.K.1
Das, A.2
Jayaram, B.3
-
49
-
-
79551475673
-
Proteogenomics
-
10.1002/pmic.201000615 10.1002/pmic.201000615
-
Renuse S, Chaerkady R, Pandey A (2011) Proteogenomics. Proteomics 11:620-630. doi: 10.1002/pmic.201000615
-
(2011)
Proteomics
, vol.11
, pp. 620-630
-
-
Renuse, S.1
Chaerkady, R.2
Pandey, A.3
-
50
-
-
4444278858
-
Predicting interactions of winged-helix transcription factors with DNA
-
10.1002/prot.20193 10.1002/prot.20193
-
Roberts VA, Case DA, Tsui V (2004) Predicting interactions of winged-helix transcription factors with DNA. Proteins Struct Funct Bioinform 57:172-187. doi: 10.1002/prot.20193
-
(2004)
Proteins Struct Funct Bioinform
, vol.57
, pp. 172-187
-
-
Roberts, V.A.1
Case, D.A.2
Tsui, V.3
-
51
-
-
84862179897
-
Clustering biomolecular complexes by residue contacts similarity
-
10.1002/prot.24078
-
Rodrigues JPGLM, Trellet M, Schmitz C et al (2012) Clustering biomolecular complexes by residue contacts similarity. Proteins Struct Funct Bioinform 80:1810-1817. doi: 10.1002/prot.24078
-
(2012)
Proteins Struct Funct Bioinform
, vol.80
, pp. 1810-1817
-
-
Rodrigues, J.1
Trellet, M.2
Schmitz, C.3
-
52
-
-
79953761333
-
Search and sampling in structural bioinformatics
-
J. Gu E. Bourne (eds) Wiley Hoboken
-
Samish I (2009) Search and sampling in structural bioinformatics. In: Gu J, Bourne PE (eds) Structural bioinformatics. Wiley, Hoboken, pp 207-235
-
(2009)
Structural Bioinformatics
, pp. 207-235
-
-
Samish, I.1
-
53
-
-
0026896780
-
Hydration of DNA bases: Analysis of crystallographic data
-
10.1002/bip.360320703 10.1002/bip.360320703
-
Schneider B, Cohen D, Berman HM (1992) Hydration of DNA bases: analysis of crystallographic data. Biopolymers 32:725-750. doi: 10.1002/bip.360320703
-
(1992)
Biopolymers
, vol.32
, pp. 725-750
-
-
Schneider, B.1
Cohen, D.2
Berman, H.M.3
-
54
-
-
0031047683
-
The role of water in protein-DNA interactions
-
10.1016/S0959-440X(97)80016-4
-
Schwabe JW (1997) The role of water in protein-DNA interactions. Curr Opin Struct Biol 7:126-134
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 126-134
-
-
Schwabe, J.W.1
-
55
-
-
0028315988
-
Determinants of repressor/operator recognition from the structure of the trp operator binding site
-
10.1038/368469a0 1994Natur.368.469S 10.1038/368469a0
-
Shakked Z, Guzikevich-Guerstein G, Frolow F et al (1994) Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature 368:469-473. doi: 10.1038/368469a0
-
(1994)
Nature
, vol.368
, pp. 469-473
-
-
Shakked, Z.1
Guzikevich-Guerstein, G.2
Frolow, F.3
-
56
-
-
0029910813
-
Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences
-
1996PNAS.9312272S 10.1073/pnas.93.22.12272
-
Sidorova NY, Rau DC (1996) Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences. Proc Natl Acad Sci USA 93:12272-12277
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 12272-12277
-
-
Sidorova, N.Y.1
Rau, D.C.2
-
57
-
-
33846894984
-
Energetics of the protein-DNA-water interaction
-
10.1186/1472-6807-7-4 10.1186/1472-6807-7-4
-
Spyrakis F, Cozzini P, Bertoli C et al (2007) Energetics of the protein-DNA-water interaction. BMC Struct Biol 7:4. doi: 10.1186/1472-6807-7-4
-
(2007)
BMC Struct Biol
, vol.7
, pp. 4
-
-
Spyrakis, F.1
Cozzini, P.2
Bertoli, C.3
-
58
-
-
29844457403
-
Rapid calculation of RMSDs using a quaternion-based characteristic polynomial
-
10.1107/S0108767305015266 2005AcCrA.61.478T 10.1107/S0108767305015266
-
Theobald DL (2005) Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallogr A Found Crystallogr 61:478-480. doi: 10.1107/S0108767305015266
-
(2005)
Acta Crystallogr A Found Crystallogr
, vol.61
, pp. 478-480
-
-
Theobald, D.L.1
-
59
-
-
33750014560
-
Solvated docking: Introducing water into the modelling of biomolecular complexes
-
10.1093/bioinformatics/btl395 10.1093/bioinformatics/btl395
-
van Dijk ADJ, Bonvin AMJJ (2006) Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinformatics 22:2340-2347. doi: 10.1093/bioinformatics/btl395
-
(2006)
Bioinformatics
, vol.22
, pp. 2340-2347
-
-
Van Dijk, A.D.J.1
Bonvin, A.2
-
60
-
-
49249118038
-
A protein-DNA docking benchmark
-
10.1093/nar/gkn386 10.1093/nar/gkn386
-
van Dijk M, Bonvin AMJJ (2008) A protein-DNA docking benchmark. Nucleic Acids Res 36:e88. doi: 10.1093/nar/gkn386
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 88
-
-
Van Dijk, M.1
Bonvin, A.2
-
61
-
-
67849110013
-
3D-DART: A DNA structure modelling server
-
10.1093/nar/gkp287 10.1093/nar/gkp287
-
van Dijk M, Bonvin AMJJ (2009) 3D-DART: a DNA structure modelling server. Nucleic Acids Res 37:W235-W239. doi: 10.1093/nar/gkp287
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Van Dijk, M.1
Bonvin, A.2
-
62
-
-
77957242417
-
Pushing the limits of what is achievable in protein-DNA docking: Benchmarking HADDOCK's performance
-
10.1093/nar/gkq222 10.1093/nar/gkq222
-
van Dijk M, Bonvin AMJJ (2010) Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance. Nucleic Acids Res 38:5634-5647. doi: 10.1093/nar/gkq222
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 5634-5647
-
-
Van Dijk, M.1
Bonvin, A.2
-
63
-
-
12544256528
-
Data-driven docking for the study of biomolecular complexes
-
10.1111/j.1742-4658.2004.04473.x 10.1111/j.1742-4658.2004.04473.x
-
van Dijk ADJ, Boelens R, Bonvin AMJJ (2005) Data-driven docking for the study of biomolecular complexes. FEBS J 272:293-312. doi: 10.1111/j.1742-4658. 2004.04473.x
-
(2005)
FEBS J
, vol.272
, pp. 293-312
-
-
Van Dijk, A.D.J.1
Boelens, R.2
Bonvin, A.3
-
64
-
-
33746285812
-
Information-driven protein-DNA docking using HADDOCK: It is a matter of flexibility
-
10.1093/nar/gkl412 10.1093/nar/gkl412
-
van Dijk M, van Dijk ADJ, Hsu V et al (2006) Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Res 34:3317-3325. doi: 10.1093/nar/gkl412
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3317-3325
-
-
Van Dijk, M.1
Van Dijk, A.D.J.2
Hsu, V.3
-
65
-
-
4644229880
-
NMR studies of protein-nucleic acid interactions
-
10.1385/1-59259-809-9:289
-
Varani G, Chen Y, Leeper TC (2004) NMR studies of protein-nucleic acid interactions. Methods Mol Biol 278:289-312. doi: 10.1385/1-59259-809-9:289
-
(2004)
Methods Mol Biol
, vol.278
, pp. 289-312
-
-
Varani, G.1
Chen, Y.2
Leeper, T.C.3
-
66
-
-
77956593725
-
Modeling the hydration layer around proteins: HyPred
-
10.1016/j.bpj.2010.06.027 10.1016/j.bpj.2010.06.027
-
Virtanen JJ, Makowski L, Sosnick TR, Freed KF (2010) Modeling the hydration layer around proteins: HyPred. Biophys J 99:1611-1619. doi: 10.1016/j.bpj.2010.06.027
-
(2010)
Biophys J
, vol.99
, pp. 1611-1619
-
-
Virtanen, J.J.1
Makowski, L.2
Sosnick, T.R.3
Freed, K.F.4
-
67
-
-
79953685152
-
The impact of next-generation sequencing on genomics
-
10.1016/j.jgg.2011.02.003 10.1016/j.jgg.2011.02.003
-
Zhang J, Chiodini R, Badr A, Zhang G (2011) The impact of next-generation sequencing on genomics. J Genet Genomics 38:95-109. doi: 10.1016/j.jgg.2011.02. 003
-
(2011)
J Genet Genomics
, vol.38
, pp. 95-109
-
-
Zhang, J.1
Chiodini, R.2
Badr, A.3
Zhang, G.4
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