-
1
-
-
78349281122
-
Solventinduced lid opening in lipases: A molecular dynamics study
-
10.1002/pro.493
-
Rehm S, Trodler P, Pleiss J (2010) Solventinduced lid opening in lipases: a molecular dynamics study. Protein Sci 19:2122-2130. doi:10.1002/pro.493
-
(2010)
Protein Sci.
, vol.19
, pp. 2122-2130
-
-
Rehm, S.1
Trodler, P.2
Pleiss, J.3
-
2
-
-
0031042532
-
Computational studies of the activation of lipases and the effect of a hydrophobic environment
-
Peters GH, Toxvaerd S, Olsen OH et al (1997) Computational studies of the activation of lipases and the effect of a hydrophobic environment. Protein Eng 10(2):137-147. doi: 10.1093/protein/10.2.137 (Pubitemid 27113276)
-
(1997)
Protein Engineering
, vol.10
, Issue.2
, pp. 137-147
-
-
Peters, G.H.1
Toxvaerd, S.2
Olsen, O.H.3
Svendsen, A.4
-
3
-
-
10944226987
-
Structure and dynamics of Candida rugosa lipase: The role of organic solvent
-
DOI 10.1007/s00894-004-0203-z
-
Tejo BA, Salleh AB, Pleiss J (2004) Structure and dynamics of Candida rugosa lipase: the role of organic solvent. J Mol Model 10:358-366. doi: 10.1007/s00894-004-0203-z (Pubitemid 40012064)
-
(2004)
Journal of Molecular Modeling
, vol.10
, Issue.5-6
, pp. 358-366
-
-
Tejo, B.A.1
Salleh, A.B.2
Pleiss, J.3
-
4
-
-
34548429987
-
Activation of Candida rugosa lipase at alkane-aqueous interfaces: A molecular dynamics study
-
DOI 10.1016/j.febslet.2007.08.002, PII S0014579307008678
-
James JJ, Lakshmi BS, Gautam P (2007) Activation of Candida rugosa lipase at alkaneaqueous interfaces: a molecular dynamics study. FEBS Lett 581:4377-4383. doi: 10.1016/j. febslet.2007.08.002 (Pubitemid 47368194)
-
(2007)
FEBS Letters
, vol.581
, Issue.23
, pp. 4377-4383
-
-
James, J.J.1
Lakshmi, B.S.2
Seshasayee, A.S.N.3
Gautam, P.4
-
5
-
-
70349333394
-
Insights into lid movements of Burkholderia cepacia lipase inferred from molecular dynamics simulations
-
10.1002/prot.22462
-
Barbe S, Lafaquière V, Guieysse D et al (2009) Insights into lid movements of Burkholderia cepacia lipase inferred from molecular dynamics simulations. Proteins 77:509-523. doi: 10.1002/prot.22462
-
(2009)
Proteins
, vol.77
, pp. 509-523
-
-
Barbe, S.1
Lafaquière, V.2
Guieysse, D.3
-
6
-
-
67649548462
-
Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase
-
10.1186/1472-6807-9-38
-
Trodler P, Schmid RD, Pleiss J (2009) Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase. BMC Struct Biol 9(38):1-13. doi: 10.1186/1472-6807-9-38
-
(2009)
BMC Struct. Biol.
, vol.9
, Issue.38
, pp. 1-13
-
-
Trodler, P.1
Schmid, R.D.2
Pleiss, J.3
-
7
-
-
40449100818
-
Modeling structure and flexibility of Candida antarctica lipase B in organic solvents
-
DOI 10.1186/1472-6807-8-9
-
Trodler P, Pleiss J (2008) Modeling structure and fl exibility of Candida antarctica lipase B in organic solvents. BMC Struct Biol 8(9):1-10. doi: 10.1186/1472-6807-8-9 (Pubitemid 351343782)
-
(2008)
BMC Structural Biology
, vol.8
, pp. 9
-
-
Trodler, P.1
Pleiss, J.2
-
8
-
-
2242458567
-
Interfacial orientation of Thermomyces lanuginosa lipase on phospholipid vesicles investigated by electron spin resonance relaxation spectroscopy
-
DOI 10.1021/bi020158r
-
Hedin EMK, Høyrup P, Patkar SA et al (2002) Interfacial orientation of Thermomyces lanuginosa lipase on phospholipid vesicles investigated by electron spin resonance relaxation spectroscopy. Biochemistry 41:14185-14196. doi: 10.1021/ bi020158r (Pubitemid 35403337)
-
(2002)
Biochemistry
, vol.41
, Issue.48
, pp. 14185-14196
-
-
Hedin, E.M.K.1
Hoyrup, P.2
Patkar, S.A.3
Vind, J.4
Svendsen, A.5
Fransson, L.6
Hult, K.7
-
9
-
-
68949083196
-
Study of Thermomyces lanuginosa lipase in the presence of tributyrylglycerol and water
-
10.1016/ j.bpj. 2009. 03.040
-
Santini S, Crowet JM, Thomas A et al (2009) Study of Thermomyces lanuginosa lipase in the presence of tributyrylglycerol and water. Biophys J 96:4814-4825. doi: 10.1016/ j.bpj.2009.03.040
-
(2009)
Biophys. J.
, vol.96
, pp. 4814-4825
-
-
Santini, S.1
Crowet, J.M.2
Thomas, A.3
-
10
-
-
0036286862
-
Orientation and conformation of a lipase at an interface studied by molecular dynamics simulations
-
Jensen M, Jensen TR, Kjaer K et al (2002) Orientation and conformation of a lipase at an interface studied by molecular dynamics simulations. Biophys J 83(1):98-111. doi: 10.1016/ S0006-3495(02)75152-7 (Pubitemid 34694723)
-
(2002)
Biophysical Journal
, vol.83
, Issue.1
, pp. 98-111
-
-
Jensen, M.O.1
Jensen, T.R.2
Kjaer, K.3
Bjornholm, T.4
Mouritsen, O.G.5
Peters, G.H.6
-
11
-
-
84859950817
-
Lipase B from 529 Candida antarctica binds to a hydrophobic 530 substrate-water interface via three hydropho- 531 bic anchor regions surrounding the active site 532 entrance
-
submitted 53
-
Gruber CC, Pleiss J (2011) Lipase B from 529 Candida antarctica binds to a hydrophobic 530 substrate-water interface via three hydropho- 531 bic anchor regions surrounding the active site 532 entrance. J Mol Catal B-Enzym 2012, submitted 53
-
(2011)
J. Mol. Catal. B-Enzym. 2012
-
-
Gruber, C.C.1
Pleiss, J.2
-
12
-
-
46249092554
-
GROMACS 4: Algorithms for highly effi cient, load-balanced, and scalable molecular simulation
-
10.1021/ct700301q
-
Hess B, Kutzner C, van der Spoel D (2008) GROMACS 4: algorithms for highly effi cient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435-447. doi: 10.1021/ct700301q
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
-
13
-
-
0029417196
-
Crystallographic and molecular-modeling studies of lipase B from Candida antarctica reveal a stereospecifi city pocket for secondary alcohols
-
10.1021/ bi00051a035
-
Uppenberg J, Ohrner N, Norin M et al (1995) Crystallographic and molecular-modeling studies of lipase B from Candida antarctica reveal a stereospecifi city pocket for secondary alcohols. Biochemistry 34:16838-16851. doi: 10.1021/ bi00051a035
-
(1995)
Biochemistry
, vol.34
, pp. 16838-16851
-
-
Uppenberg, J.1
Ohrner, N.2
Norin, M.3
-
14
-
-
0028773288
-
The sequence, crystal structure determination and refi nement of two crystal forms of lipase B from Candida antarctica
-
10.1016/S0969- 2126(00) 00031-9
-
Uppenberg J, Hansen MT, Patkar S et al (1994) The sequence, crystal structure determination and refi nement of two crystal forms of lipase B from Candida antarctica . Structure 2-5:453-454. doi: 10.1016/S0969- 2126(00)00031-9
-
(1994)
Structure
, vol.2-5
, pp. 453-454
-
-
Uppenberg, J.1
Hansen, M.T.2
Patkar, S.3
-
15
-
-
0036327837
-
Lipases from Candida antarctica : Unique biocatalysts from a unique origin
-
10.1021/op0200165
-
Kirk O, Christensen MW (2002) Lipases from Candida antarctica : unique biocatalysts from a unique origin. Org Proc Res Dev 6(4):446-451. doi: 10.1021/op0200165
-
(2002)
Org. Proc. Res. Dev.
, vol.6
, Issue.4
, pp. 446-451
-
-
Kirk, O.1
Christensen, M.W.2
-
16
-
-
23444454552
-
The Amber biomolecular simulation programs
-
DOI 10.1002/jcc.20290
-
Case DA, Cheatham TE 3rd, Darden T et al (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668-1688. doi: 10.1002/jcc.2029 (Pubitemid 43076180)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.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.J.10
-
17
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
10.1002/jcc.21287
-
Brooks BR, Brooks CL 3rd, Mackerell AD Jr et al (2009) CHARMM: the biomolecular simulation program. J Comp Chem 30:1545-1615. doi: 10.1002/jcc.21287
-
(2009)
J. Comp. Chem.
, vol.30
, pp. 1545-1615
-
-
Brooks, B.R.1
Brooks III, C.L.2
Mackerell Jr., A.D.3
-
18
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
DOI 10.1002/jcc.20289
-
Phillips JC, Braun R, Wang W et al (2005) Scalable molecular dynamics with NAMD. J Comp Chem 26:1781-1802. doi: 10.1002/jcc.20289 (Pubitemid 43078511)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, 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
-
19
-
-
0037093644
-
Increasing the precision of comparative models with YASARA NOVA - A self-parameterizing force field
-
DOI 10.1002/prot.10104
-
Krieger E, Koraimann G, Vriend G (2002) Increasing the precision of comparative models with yasara nova - a self-parameterizing force fi eld. Proteins 47:393-402. doi: 10.1002/prot.10104 (Pubitemid 34438688)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.47
, Issue.3
, pp. 393-402
-
-
Krieger, E.1
Koraimann, G.2
Vriend, G.3
-
21
-
-
79951476387
-
PROPKA3: Consistent treatment of internal and surface residues in empirical pKa predictions
-
10.1021/ct100578z
-
Olsson MHM, Søndergaard CR, Rostkowski M et al (2011) PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J Chem Theory Comput 7(2):525-537. doi: 10.1021/ct100578z
-
(2011)
J. Chem. Theory Comput.
, vol.7
, Issue.2
, pp. 525-537
-
-
Olsson, M.H.M.1
Søndergaard, C.R.2
Rostkowski, M.3
-
22
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
DOI 10.1021/jp003919d
-
Kaminski GA, Friesner R (2001) Evaluation and reparametrization of the OPLS-AA force fi eld for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105:6474-6487. doi: 10.1021/ jp003919d (Pubitemid 35339015)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.28
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
23
-
-
10844247921
-
A modified TIP3P water potential for simulation with Ewald summation
-
DOI 10.1063/1.1808117
-
Price DJ, Brooks CL (2004) A modifi ed TIP3P water potential for simulation with Ewald summation. J Chem Phys 121(20):10096-10103. doi: 10.1063/1.1808117 (Pubitemid 40001663)
-
(2004)
Journal of Chemical Physics
, vol.121
, Issue.20
, pp. 10096-10103
-
-
Price, D.J.1
Brooks III, C.L.2
-
25
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
-
Berger O, Edholm O, Jähnig F (1997) Molecular dynamics simulations of a fl uid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J 72:2002-2013. doi: 10.1016/S0006-3495(97)78845-3 (Pubitemid 27184429)
-
(1997)
Biophysical Journal
, vol.72
, Issue.5
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jahnig, F.3
-
26
-
-
33745630723
-
Membrane protein simulations with a united-atom lipid and all-atom protein model: Lipid-protein interactions, side chain transfer free energies and model proteins
-
DOI 10.1088/0953-8984/18/28/S07, PII S0953898406150286, S07
-
Tieleman PD, MacCallum JL, Ash WL et al (2006) Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins. J Phys Condens Matter 18:1221-1234. doi: 10.1088/0953-8984/18/28/S07 (Pubitemid 43982969)
-
(2006)
Journal of Physics Condensed Matter
, vol.18
, Issue.28
-
-
Tieleman, D.P.1
MacCallum, J.L.2
Ash, W.L.3
Kandt, C.4
Xu, Z.5
Monticelli, L.6
-
28
-
-
0028539745
-
Density and viscosity of low-molecular weight triglycerides and their mixtures
-
10.1007/BF02540548
-
Eiteman MA, Goodrun JW (1994) Density and viscosity of low-molecular weight triglycerides and their mixtures. J Am Oil Chem Soc 11:1261-1265. doi: 10.1007/BF02540548
-
(1994)
J. Am. Oil. Chem. Soc.
, vol.11
, pp. 1261-1265
-
-
Eiteman, M.A.1
Goodrun, J.W.2
-
29
-
-
35748972048
-
MOLE: A voronoi diagram-based explorer of molecular channels, pores, and tunnels
-
DOI 10.1016/j.str.2007.10.007, PII S0969212607003759
-
Petrek M, Kosinová P, Koca J et al (2007) MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure 15:1357-1363. doi: 10.1016/j. str.2007.10.007 (Pubitemid 350051932)
-
(2007)
Structure
, vol.15
, Issue.11
, pp. 1357-1363
-
-
Petrek, M.1
Kosinova, P.2
Koca, J.3
Otyepka, M.4
-
30
-
-
33847142225
-
CAVER: A new tool to explore routes from protein clefts, pockets and cavities
-
10.1186/1471- 2105- 7-316
-
Petrek M, Otyepka M, Banás P et al (2006) CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 7(316):1-9. doi: 10.1186/1471- 2105-7-316
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.316
, pp. 1-9
-
-
Petrek, M.1
Otyepka, M.2
Banás, P.3
-
31
-
-
79251524910
-
Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities
-
10.1002/jcc.21645
-
Gruber CC, Pleiss J (2011) Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities. J Comput Chem 32(4):600-606. doi: 10.1002/jcc.21645
-
(2011)
J. Comput. Chem.
, vol.32
, Issue.4
, pp. 600-606
-
-
Gruber, C.C.1
Pleiss, J.2
|