-
1
-
-
84876732154
-
Strategies for the discovery and engineering of enzymes for biocatalysis
-
Davids,T., Schmidt,M., Bottcher,D. and Bornscheuer,U.T. (2013) Strategies for the discovery and engineering of enzymes for biocatalysis. Curr. Opin. Chem. Biol., 17, 215-220.
-
(2013)
Curr. Opin. Chem. Biol.
, vol.17
, pp. 215-220
-
-
Davids, T.1
Schmidt, M.2
Bottcher, D.3
Bornscheuer, U.T.4
-
2
-
-
0030957783
-
Structure of carbamoyl phosphate synthetase: A journey of 96 A from substrate to product
-
Thoden,J.B., Holden,H.M., Wesenberg,G., Raushel,F.M. and Rayment,I. (1997) Structure of carbamoyl phosphate synthetase: a journey of 96 A from substrate to product. Biochemistry, 36, 6305-6316.
-
(1997)
Biochemistry
, vol.36
, pp. 6305-6316
-
-
Thoden, J.B.1
Holden, H.M.2
Wesenberg, G.3
Raushel, F.M.4
Rayment, I.5
-
3
-
-
84961644292
-
Substrate channelling as an approach to cascade reactions
-
Wheeldon,I., Minteer,S.D., Banta,S., Barton,S.C., Atanassov,P. and Sigman,M. (2016) Substrate channelling as an approach to cascade reactions. Nat. Chem., 8, 299-309.
-
(2016)
Nat. Chem.
, vol.8
, pp. 299-309
-
-
Wheeldon, I.1
Minteer, S.D.2
Banta, S.3
Barton, S.C.4
Atanassov, P.5
Sigman, M.6
-
4
-
-
84895795810
-
Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site
-
Singh,H., Arentson,B.W., Becker,D.F. and Tanner,J.J. (2014) Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site. Proc. Natl. Acad. Sci. U.S.A., 111, 3389-3394.
-
(2014)
Proc. Natl. Acad. Sci. U.S.A.
, vol.111
, pp. 3389-3394
-
-
Singh, H.1
Arentson, B.W.2
Becker, D.F.3
Tanner, J.J.4
-
5
-
-
62049085169
-
Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride
-
Guskov,A., Kern,J., Gabdulkhakov,A., Broser,M., Zouni,A. and Saenger,W. (2009) Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride. Nat. Struct. Mol. Biol., 16, 334-342.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 334-342
-
-
Guskov, A.1
Kern, J.2
Gabdulkhakov, A.3
Broser, M.4
Zouni, A.5
Saenger, W.6
-
6
-
-
33745628037
-
The geometry of the ribosomal polypeptide exit tunnel
-
Voss,N.R., Gerstein,M., Steitz,T.A. and Moore,P.B. (2006) The geometry of the ribosomal polypeptide exit tunnel. J. Mol. Biol., 360, 893-906.
-
(2006)
J. Mol. Biol.
, vol.360
, pp. 893-906
-
-
Voss, N.R.1
Gerstein, M.2
Steitz, T.A.3
Moore, P.B.4
-
7
-
-
0034637161
-
The structural basis of ribosome activity in peptide bond synthesis
-
Nissen,P. (2000) The structural basis of ribosome activity in peptide bond synthesis. Science, 289, 920-930.
-
(2000)
Science
, vol.289
, pp. 920-930
-
-
Nissen, P.1
-
8
-
-
84923867540
-
Anatomy of enzyme channels
-
Pravda,L., Berka,K., Svobodova Varekova,R., Sehnal,D., Banas,P., Laskowski,R.A., Koca,J. and Otyepka,M. (2014) Anatomy of enzyme channels. BMC Bioinformatics, 15, 379.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 379
-
-
Pravda, L.1
Berka, K.2
Varekova, S.R.3
Sehnal, D.4
Banas, P.5
Laskowski, R.A.6
Koca, J.7
Otyepka, M.8
-
9
-
-
84976485270
-
-
Cellular gatekeepers
-
Cellular gatekeepers (2016) Nat. Struct. Mol. Biol., 23, 463-463.
-
(2016)
Nat Struct. Mol. Biol.
, vol.23
, pp. 463
-
-
-
10
-
-
84868515149
-
Structural insights into the mechanisms of Mg2+ uptake, transport, and gating by CorA
-
Guskov,A., Nordin,N., Reynaud,A., Engman,H., Lundback,A.-K., Jong,A.J.O., Cornvik,T., Phua,T. and Eshaghi,S. (2012) Structural insights into the mechanisms of Mg2+ uptake, transport, and gating by CorA. Proc. Natl. Acad. Sci. U.S.A., 109, 18459-18464.
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 18459-18464
-
-
Guskov, A.1
Nordin, N.2
Reynaud, A.3
Engman, H.4
Lundback, A.-K.5
Jong, A.J.O.6
Cornvik, T.7
Phua, T.8
Eshaghi, S.9
-
11
-
-
34250336942
-
Ion transport across transmembrane pores
-
Leontiadou,H.,Mark,A.E. and Marrink,S.-J. (2007) Ion transport across transmembrane pores. Biophys. J., 92, 4209-4215.
-
(2007)
Biophys. J.
, vol.92
, pp. 4209-4215
-
-
Leontiadou, H.1
Mark, A.E.2
Marrink, S.-J.3
-
12
-
-
0035498860
-
Energetics of ion conduction through the K+ channel
-
Berneche,S. and Roux,B. (2001) Energetics of ion conduction through the K+ channel. Nature, 414, 73.
-
(2001)
Nature
, vol.414
, pp. 73
-
-
Berneche, S.1
Roux, B.2
-
13
-
-
85021640979
-
Crystal structure of the potassium-importing KdpFABC membrane complex
-
Huang,C.-S., Pedersen,B.P. and Stokes,D.L. (2017) Crystal structure of the potassium-importing KdpFABC membrane complex. Nature, 546, 681-685.
-
(2017)
Nature
, vol.546
, pp. 681-685
-
-
Huang, C.-S.1
Pedersen, B.P.2
Stokes, D.L.3
-
14
-
-
66549124907
-
The structures of quadruplex nucleic acids and their drug complexes
-
Neidle,S. (2009) The structures of quadruplex nucleic acids and their drug complexes. Curr. Opin. Struct. Biol., 19, 239-250.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 239-250
-
-
Neidle, S.1
-
15
-
-
70349330482
-
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate
-
Pavlova,M., Klvana,M., Prokop,Z., Chaloupkova,R., Banas,P., Otyepka,M.,Wade,R.C., Tsuda,M., Nagata,Y. and Damborsky,J. (2009) Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nat. Chem. Biol., 5, 727-733.
-
(2009)
Nat. Chem. Biol.
, vol.5
, pp. 727-733
-
-
Pavlova, M.1
Klvana, M.2
Prokop, Z.3
Chaloupkova, R.4
Banas, P.5
Otyepka, M.6
Wade, R.C.7
Tsuda, M.8
Nagata, Y.9
Damborsky, J.10
-
16
-
-
84921302202
-
Access channels to the buried active site control substrate specificity in CYP1A P450 enzymes
-
Urban,P., Truan,G. and Pompon,D. (2015) Access channels to the buried active site control substrate specificity in CYP1A P450 enzymes. Biochim. Biophys. Acta-Gen. Subj., 1850, 696-707.
-
(2015)
Biochim. Biophys. Acta-Gen. Subj.
, vol.1850
, pp. 696-707
-
-
Urban, P.1
Truan, G.2
Pompon, D.3
-
17
-
-
85032621140
-
Evolution of P450 monooxygenases toward formation of transient channels and exclusion of nonproductive gases
-
Ebert,M.C.C.J.C., D urr,S.L., A. Houle,A., Lamoureux,G. and Pelletier,J.N. (2016) Evolution of P450 monooxygenases toward formation of transient channels and exclusion of nonproductive gases. ACS Catal., 6, 7426-7437.
-
(2016)
ACS Catal.
, vol.6
, pp. 7426-7437
-
-
Ebert, M.C.C.J.C.1
Urr, S.L.D.2
Houle, A.A.3
Lamoureux, G.4
Pelletier, J.N.5
-
18
-
-
84857532829
-
Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations
-
Hendrychova,T., Berka,K., Navratilova,V., Anzenbacher,P. and Otyepka,M. (2012) Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations. Curr. Drug Metab., 13, 177-189.
-
(2012)
Curr. Drug Metab.
, vol.13
, pp. 177-189
-
-
Hendrychova, T.1
Berka, K.2
Navratilova, V.3
Anzenbacher, P.4
Otyepka, M.5
-
19
-
-
4344598766
-
Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction
-
Misura,K.M.S., Morozov,A. V. and Baker,D. (2004) Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. J. Mol. Biol., 342, 651-664.
-
(2004)
J. Mol. Biol.
, vol.342
, pp. 651-664
-
-
Misura, K.M.S.1
Morozov, A.V.2
Baker, D.3
-
20
-
-
85040943493
-
Detection of channels
-
. In: Koca,J, Svobodova,Varekova R, Pravda,L, Berka,K, Geidl,S, Sehnal,D and Otyepka,M (eds). Springer, Cham
-
Pravda,L., Berka,K., Sehnal,D., Otyepka,M., Svobodova Varekova,R. and Koca,J. (2016) Detection of Channels. In: Koca,J, Svobodova,Varekova R, Pravda,L, Berka,K, Geidl,S, Sehnal,D and Otyepka,M (eds). Structural Bioinformatics Tools for Drug Design. Springer, Cham, pp. 59-69.
-
(2016)
Structural Bioinformatics Tools for Drug Design
, pp. 59-69
-
-
Pravda, L.1
Berka, K.2
Sehnal, D.3
Otyepka, M.4
Svobodova Varekova, R.5
Koca, J.6
-
21
-
-
85020111651
-
Geometric detection algorithms for cavities on protein surfaces in molecular graphics: A survey
-
Simoes,T., Lopes,D., Dias,S., Fernandes,F., Pereira,J., Jorge,J., Bajaj,C. and Gomes,A. (2017) Geometric detection algorithms for cavities on protein surfaces in molecular graphics: a survey. Comput. Graph. Forum, doi:10.1111/cgf.13158.
-
(2017)
Comput. Graph. Forum
-
-
Simoes, T.1
Lopes, D.2
Dias, S.3
Fernandes, F.4
Pereira, J.5
Jorge, J.6
Bajaj, C.7
Gomes, A.8
-
22
-
-
0030404988
-
HOLE: A program for the analysis of the pore dimensions of ion channel structural models
-
Smart,O.S., Neduvelil,J.G., Wang,X., Wallace,B.A. and Sansom,M.S.P. (1996) HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph., 14, 354-360.
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 354-360
-
-
Smart, O.S.1
Neduvelil, J.G.2
Wang, X.3
Wallace, B.A.4
Sansom, M.S.P.5
-
23
-
-
33847142225
-
CAVER: A new tool to explore routes from protein clefts, pockets and cavities
-
Petrek,M., Otyepka,M., Banas,P., Kosinova,P., Koca,J. and Damborsky,J. (2006) CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics, 7, 316.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 316
-
-
Petrek, M.1
Otyepka, M.2
Banas, P.3
Kosinova, P.4
Koca, J.5
Damborsky, J.6
-
24
-
-
84868156224
-
CAVER 3.0: A tool for the analysis of transport pathways in dynamic protein structures
-
Chovancova,E., Pavelka,A., Benes,P., Strnad,O., Brezovsky,J., Kozlikova,B., Gora,A., Sustr,V., Klvana,M., Medek,P. et al. (2012) CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comput. Biol., 8, e1002708.
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002708
-
-
Chovancova, E.1
Pavelka, A.2
Benes, P.3
Strnad, O.4
Brezovsky, J.5
Kozlikova, B.6
Gora, A.7
Sustr, V.8
Klvana, M.9
Medek, P.10
-
25
-
-
35748972048
-
MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels
-
Petrek,M., Kosinova,P., Koca,J. and Otyepka,M. (2007) MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure, 15, 1357-1363.
-
(2007)
Structure
, vol.15
, pp. 1357-1363
-
-
Petrek, M.1
Kosinova, P.2
Koca, J.3
Otyepka, M.4
-
26
-
-
84884364871
-
MOLE 2.0: Advanced approach for analysis of biomacromolecular channels
-
Sehnal,D., Svobodova Varekova,R., Berka,K., Pravda,L., Navratilova,V., Banas,P., Ionescu,C.-M., Otyepka,M. and Koca,J. (2013) MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminform., 5, 39.
-
(2013)
J. Cheminform.
, vol.5
, pp. 39
-
-
Sehnal, D.1
Varekova, S.R.2
Berka, K.3
Pravda, L.4
Navratilova, V.5
Banas, P.6
Ionescu, C.-M.7
Otyepka, M.8
Koca, J.9
-
27
-
-
84864486886
-
MOLEonline 2.0: Interactive web-based analysis of biomacromolecular channels
-
Berka,K., Hanak,O., Sehnal,D., Banas,P., Navratilova,V., Jaiswal,D., Ionescu,C.-M., Svobodova Varekova,R., Koca,J. and Otyepka,M. (2012) MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res, 40, W222-W227.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. W222-W227
-
-
Berka, K.1
Hanak, O.2
Sehnal, D.3
Banas, P.4
Navratilova, V.5
Jaiswal, D.6
Ionescu, C.-M.7
Varekova, S.R.8
Koca, J.9
Otyepka, M.10
-
28
-
-
84978955214
-
Visual analysis of biomolecular cavities: State of the art
-
Krone,M., Kozlikova,B., Lindow,N., Baaden,M., Baum,D., Parulek,J., Hege,H.-C. and Viola,I. (2016) Visual analysis of biomolecular cavities: state of the art. Comput. Graph. Forum, 35, 527-551.
-
(2016)
Comput. Graph. Forum
, vol.35
, pp. 527-551
-
-
Krone, M.1
Kozlikova, B.2
Lindow, N.3
Baaden, M.4
Baum, D.5
Parulek, J.6
Hege, H.-C.7
Viola, I.8
-
29
-
-
85016147592
-
TransportDB 2.0: A database for exploring membrane transporters in sequenced genomes from all domains of life
-
Elbourne,L.D.H., Tetu,S.G., Hassan,K.A. and Paulsen,I.T. (2017) TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. Nucleic Acids Res., 45, D320-D324.
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D320-D324
-
-
Elbourne, L.D.H.1
Tetu, S.G.2
Hassan, K.A.3
Paulsen, I.T.4
-
30
-
-
84976904417
-
The transporter classification database (tcdb): Recent advances
-
Saier,M.H., Reddy,V.S., Tsu,B. V., Ahmed,M.S., Li,C. and Moreno-Hagelsieb,G. (2016) The Transporter Classification Database (TCDB): recent advances. Nucleic Acids Res., 44, D372-D379.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D372-D379
-
-
Saier, M.H.1
Reddy, V.S.2
Tsu, B.V.3
Ahmed, M.S.4
Li, C.5
Moreno-Hagelsieb, G.6
-
31
-
-
84861060898
-
OPM database and PPM web server: Resources for positioning of proteins in membranes
-
Lomize,M.A., Pogozheva,I.D., Joo,H., Mosberg,H.I. and Lomize,A.L. (2012) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res., 40, D370-D376.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D370-D376
-
-
Lomize, M.A.1
Pogozheva, I.D.2
Joo, H.3
Mosberg, H.I.4
Lomize, A.L.5
-
32
-
-
84874677954
-
Pdbtm: Protein data bank of transmembrane proteins after 8 years
-
Kozma,D., Simon,I. and Tusnady,G.E. (2013) PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Res., 41, D524-D529.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D524-D529
-
-
Kozma, D.1
Simon, I.2
Tusnady, G.E.3
-
33
-
-
85015861762
-
ABCMdb reloaded: Updates on mutations in ATP binding cassette proteins
-
Tordai,H., Jakab,K., Gyimesi,G., Andras,K., Brozik,A., Sarkadi,B. and Hegedus,T. (2017) ABCMdb reloaded: updates on mutations in ATP binding cassette proteins. Database, 2017, doi:10.1093/database/bax023.
-
(2017)
Database
, vol.2017
-
-
Tordai, H.1
Jakab, K.2
Gyimesi, G.3
Andras, K.4
Brozik, A.5
Sarkadi, B.6
Hegedus, T.7
-
34
-
-
79952512096
-
GATMD: Aminobutyric acid transporter mutagenesis database
-
Anderson,C.M., Kidd,P.D. and Eskandari,S. (2010) GATMD: aminobutyric acid transporter mutagenesis database. Database, 2010, baq028.
-
(2010)
Database
, vol.2010
, pp. baq028
-
-
Anderson, C.M.1
Kidd, P.D.2
Eskandari, S.3
-
35
-
-
78651307693
-
VKCDB: Voltage-gated K+ channel database updated and upgraded
-
Gallin,W.J. and Boutet,P.A. (2011) VKCDB: voltage-gated K+ channel database updated and upgraded. Nucleic Acids Res., 39, D362-D366.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D362-D366
-
-
Gallin, W.J.1
Boutet, P.A.2
-
36
-
-
84994056664
-
Channelpedia: An integrative and interactive database for ion channels
-
Ranjan,R., Khazen,G., Gambazzi,L., Ramaswamy,S., Hill,S.L., Schurmann,F. and Markram,H. (2011) Channelpedia: an integrative and interactive database for ion channels. Front. Neuroinform., 5, 36.
-
(2011)
Front. Neuroinform.
, vol.5
, pp. 36
-
-
Ranjan, R.1
Khazen, G.2
Gambazzi, L.3
Ramaswamy, S.4
Hill, S.L.5
Schurmann, F.6
Markram, H.7
-
37
-
-
84891772177
-
SuperPain-A resource on pain-relieving compounds targeting ion channels
-
Gohlke,B.O., Preissner,R. and Preissner,S. (2014) SuperPain-A resource on pain-relieving compounds targeting ion channels. Nucleic Acids Res., 42, D1107-D1112.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D1107-D1112
-
-
Gohlke, B.O.1
Preissner, R.2
Preissner, S.3
-
38
-
-
84891820493
-
PDBsum additions
-
de Beer,T.A.P., Berka,K., Thornton,J.M. and Laskowski,R.A. (2014) PDBsum additions. Nucleic Acids Res., 42, D292-D296.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D292-D296
-
-
De Beer, T.A.P.1
Berka, K.2
Thornton, J.M.3
Laskowski, R.A.4
-
39
-
-
0345059376
-
Announcing the worldwide Protein Data Bank
-
Berman,H., Henrick,K. and Nakamura,H. (2003) Announcing the worldwide Protein Data Bank. Nat. Struct. Biol., 10, 980.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 980
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
-
40
-
-
84976877697
-
PDBe: Improved accessibility of macromolecular structure data from PDB and EMDB
-
Velankar,S., van Ginkel,G., Alhroub,Y., Battle,G.M., Berrisford,J.M., Conroy,M.J., Dana,J.M., Gore,S.P., Gutmanas,A., Haslam,P. et al. (2016) PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res., 44, D385-D395.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D385-D395
-
-
Velankar, S.1
Van Ginkel, G.2
Alhroub, Y.3
Battle, G.M.4
Berrisford, J.M.5
Conroy, M.J.6
Dana, J.M.7
Gore, S.P.8
Gutmanas, A.9
Haslam, P.10
-
41
-
-
85027700608
-
UniProt: The universal protein knowledgebase
-
Wasmuth,E.V. and Lima,C.D. (2016) UniProt: the universal protein knowledgebase. Nucleic Acids Res., 45, 1-12.
-
(2016)
Nucleic Acids Res.
, vol.45
, pp. 1-12
-
-
Wasmuth, E.V.1
Lima, C.D.2
-
42
-
-
84891800735
-
The Catalytic Site Atlas 2.0: Cataloging catalytic sites and residues identified in enzymes
-
Furnham,N., Holliday,G.L., De Beer,T.A.P., Jacobsen,J.O.B., Pearson,W.R. and Thornton,J.M. (2014) The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res., 42, 1-5.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 1-5
-
-
Furnham, N.1
Holliday, G.L.2
De Beer, T.A.P.3
Jacobsen, J.O.B.4
Pearson, W.R.5
Thornton, J.M.6
-
43
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte,J. and Doolittle,R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157, 105-132.
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
44
-
-
0014349825
-
The characterization of amino acid sequences in proteins by statistical methods
-
Zimmerman,J.M., Eliezer,N. and Simha,R. (1968) The characterization of amino acid sequences in proteins by statistical methods. J. Theor. Biol., 21, 170-201.
-
(1968)
J. Theor. Biol.
, vol.21
, pp. 170-201
-
-
Zimmerman, J.M.1
Eliezer, N.2
Simha, R.3
-
45
-
-
0026636312
-
Hydrophobicity and structural classes in proteins
-
Cid,H., Bunster,M., Canales,M. and Gazitua,F. (1992) Hydrophobicity and structural classes in proteins. Protein Eng. Des. Sel., 5, 373-375.
-
(1992)
Protein Eng. Des. Sel.
, vol.5
, pp. 373-375
-
-
Cid, H.1
Bunster, M.2
Canales, M.3
Gazitua, F.4
-
46
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones,D.T., Taylor,W.R. and Thornton,J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Bioinformatics, 8, 275-282.
-
(1992)
Bioinformatics
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
47
-
-
85023206532
-
The Proteins API: Accessing key integrated protein and genome information
-
Nightingale,A., Antunes,R., Alpi,E., Bursteinas,B., Gonzales,L., Liu,W., Luo,J., Qi,G., Turner,E. and Martin,M. (2017) The Proteins API: accessing key integrated protein and genome information. Nucleic Acids Res., 45, W539-W544.
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. W539-W544
-
-
Nightingale, A.1
Antunes, R.2
Alpi, E.3
Bursteinas, B.4
Gonzales, L.5
Liu, W.6
Luo, J.7
Qi, G.8
Turner, E.9
Martin, M.10
-
48
-
-
84876579771
-
SIFTS: Structure integration with function, taxonomy and sequences resource
-
Velankar,S., Dana,J.M., Jacobsen,J., van Ginkel,G., Gane,P.J., Luo,J., Oldfield,T.J., O'Donovan,C., Martin,M.-J. and Kleywegt,G.J. (2013) SIFTS: structure integration with function, taxonomy and sequences resource. Nucleic Acids Res., 41, D483-D489.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D483-D489
-
-
Velankar, S.1
Dana, J.M.2
Jacobsen, J.3
Van Ginkel, G.4
Gane, P.J.5
Luo, J.6
Oldfield, T.J.7
O'Donovan, C.8
Martin, M.-J.9
Kleywegt, G.J.10
-
49
-
-
33846380189
-
What common structural features and variations of mammalian P450s are known to date?
-
Otyepka,M., Skopalik,J., Anzenbacherova,E. and Anzenbacher,P. (2007) What common structural features and variations of mammalian P450s are known to date? Biochim. Biophys. Acta, 1770, 376-389.
-
(2007)
Biochim. Biophys. Acta
, vol.1770
, pp. 376-389
-
-
Otyepka, M.1
Skopalik, J.2
Anzenbacherova, E.3
Anzenbacher, P.4
-
50
-
-
3042587451
-
A survey of active site access channels in cytochromes P450
-
Wade,R.C., Winn,P.J., Schlichting,I and Sudarko (2004) A survey of active site access channels in cytochromes P450. J. Inorg. Biochem., 98, 1175-1182.
-
(2004)
J. Inorg. Biochem.
, vol.98
, pp. 1175-1182
-
-
Wade, R.C.1
Winn, P.J.2
Schlichting, I.3
Sudarko4
-
51
-
-
84964426734
-
Role of enzyme flexibility in ligand access and egress to active site: Bias-exchange metadynamics study of 1,3,7-trimethyluric acid in cytochrome P450 3A4
-
Paloncyova,M. Navratilova,V., Berka,K., Laio,A. and Otyepka,M. (2016) Role of enzyme flexibility in ligand access and egress to active site: bias-exchange metadynamics study of 1,3,7-trimethyluric acid in cytochrome P450 3A4. J. Chem. Theory Comput., 21 ,2101-2109.
-
(2016)
J. Chem. Theory Comput.
, vol.21
, pp. 2101-2109
-
-
Paloncyova, M.1
Navratilova, V.2
Berka, K.3
Laio, A.4
Otyepka, M.5
-
52
-
-
21844434930
-
Structure and chemistry of cytochrome P450
-
Denisov,I.G., Makris,T.M., Sligar,S.G. and Schlichting,I. (2005) Structure and chemistry of cytochrome P450. Chem. Rev., 105, 2253-2278.
-
(2005)
Chem. Rev.
, vol.105
, pp. 2253-2278
-
-
Denisov, I.G.1
Makris, T.M.2
Sligar, S.G.3
Schlichting, I.4
-
53
-
-
78649837413
-
Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations
-
Li,W., Shen,J., Liu,G., Tang,Y. and Hoshino,T. (2011) Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations. Proteins Struct. Funct. Bioinforma., 79, 271-281.
-
(2011)
Proteins Struct. Funct. Bioinforma.
, vol.79
, pp. 271-281
-
-
Li, W.1
Shen, J.2
Liu, G.3
Tang, Y.4
Hoshino, T.5
-
54
-
-
70349509736
-
Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: Involvement of phenylalanine residues in the gating mechanism
-
Fishelovitch,D., Shaik,S., Wolfson,H.J. and Nussinov,R. (2009) Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism. J. Phys. Chem. B, 113, 13018-13025.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 13018-13025
-
-
Fishelovitch, D.1
Shaik, S.2
Wolfson, H.J.3
Nussinov, R.4
-
55
-
-
84857569031
-
Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450?
-
Otyepka,M., Berka,K. and Anzenbacher,P. (2012) Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450? Curr. Drug Metab., 13, 130-142.
-
(2012)
Curr. Drug Metab.
, vol.13
, pp. 130-142
-
-
Otyepka, M.1
Berka, K.2
Anzenbacher, P.3
-
56
-
-
0036851805
-
Substrate routes to the buried active site may vary among cytochromes P450: Mutagenesis of the F-G region in P450 2B1
-
Scott,E.E., He,Y.Q. and Halpert,J.R. (2002) Substrate routes to the buried active site may vary among cytochromes P450: mutagenesis of the F-G region in P450 2B1. Chem. Res. Toxicol., 15, 1407-1413.
-
(2002)
Chem. Res. Toxicol.
, vol.15
, pp. 1407-1413
-
-
Scott, E.E.1
He, Y.Q.2
Halpert, J.R.3
-
57
-
-
77954606283
-
Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode
-
Porubsky,P.R., Battaile,K.P. and Scott,E.E. (2010) Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode. J. Biol. Chem., 285, 22282-22290.
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 22282-22290
-
-
Porubsky, P.R.1
Battaile, K.P.2
Scott, E.E.3
-
58
-
-
57749122048
-
Structures of human cytochrome P-450 2E1
-
Porubsky,P.R., Meneely,K.M. and Scott,E.E. (2008) Structures of human cytochrome P-450 2E1. J. Biol. Chem., 283, 33698-33707.
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 33698-33707
-
-
Porubsky, P.R.1
Meneely, K.M.2
Scott, E.E.3
-
59
-
-
33846339293
-
The ins and outs of cytochrome P450s
-
Cojocaru,V., Winn,P.J. and Wade,R.C. (2007) The ins and outs of cytochrome P450s. Biochim. Biophys. Acta, 1770, 390-401.
-
(2007)
Biochim. Biophys. Acta
, vol.1770
, pp. 390-401
-
-
Cojocaru, V.1
Winn, P.J.2
Wade, R.C.3
-
60
-
-
84961290964
-
Potentials of mean force and escape times of surfactants from micelles and hydrophobic surfaces using molecular dynamics simulations
-
Yuan,F., Wang,S. and Larson,R.G. (2015) Potentials of mean force and escape times of surfactants from micelles and hydrophobic surfaces using molecular dynamics simulations. Langmuir, 31, 1336-1343.
-
(2015)
Langmuir
, vol.31
, pp. 1336-1343
-
-
Yuan, F.1
Wang, S.2
Larson, R.G.3
-
61
-
-
4644256131
-
The channel architecture of aquaporin 0 at a 2.2-A resolution
-
Harries,W.E.C., Akhavan,D.,Miercke,L.J.W., Khademi,S. and Stroud,R.M. (2004) The channel architecture of aquaporin 0 at a 2.2-A resolution. Proc. Natl. Acad. Sci. U.S.A., 101, 14045-14050.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 14045-14050
-
-
Harries, W.E.C.1
Akhavan, D.2
Miercke, L.J.W.3
Khademi, S.4
Stroud, R.M.5
-
62
-
-
84936845938
-
MemProtMD: Automated insertion of membrane protein structures into explicit lipid membranes
-
Stansfeld,P.J., Goose,J.E., Caffrey,M., Carpenter,E.P., Parker,J.L., Newstead,S. and Sansom,M.S.P. (2015) MemProtMD: automated insertion of membrane protein structures into explicit lipid membranes. Structure, 23, 1350-1361.
-
(2015)
Structure
, vol.23
, pp. 1350-1361
-
-
Stansfeld, P.J.1
Goose, J.E.2
Caffrey, M.3
Carpenter, E.P.4
Parker, J.L.5
Newstead, S.6
Sansom, M.S.P.7
-
63
-
-
6344285930
-
Genetic variation in eleven phase i drug metabolism genes in an ethnically diverse population
-
Solus,J.F., Arietta,B.J., Harris,J.R., Sexton,D.P., Steward,J.Q., McMunn,C., Ihrie,P., Mehall,J.M., Edwards,T.L. and Dawson,E.P. (2004) Genetic variation in eleven phase I drug metabolism genes in an ethnically diverse population. Pharmacogenomics, 5, 895-931.
-
(2004)
Pharmacogenomics
, vol.5
, pp. 895-931
-
-
Solus, J.F.1
Arietta, B.J.2
Harris, J.R.3
Sexton, D.P.4
Steward, J.Q.5
McMunn, C.6
Ihrie, P.7
Mehall, J.M.8
Edwards, T.L.9
Dawson, E.P.10
-
64
-
-
5044245324
-
Phe120 contributes to the regiospecificity of cytochrome P450 2D6: Mutation leads to the formation of a novel dextromethorphan metabolite
-
Flanagan,J.U.,Marechal,J.-D., Ward,R., Kemp,C.A., McLaughlin,L.A., Sutcliffe,M.J., Roberts,G.C.K., Paine,M.J.I. and Wolf,C.R. (2004) Phe120 contributes to the regiospecificity of cytochrome P450 2D6: mutation leads to the formation of a novel dextromethorphan metabolite. Biochem. J., 380, 353-360.
-
(2004)
Biochem. J.
, vol.380
, pp. 353-360
-
-
Flanagan, J.U.1
Marechal, J.-D.2
Ward, R.3
Kemp, C.A.4
McLaughlin, L.A.5
Sutcliffe, M.J.6
Roberts, G.C.K.7
Paine, M.J.I.8
Wolf, C.R.9
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