-
1
-
-
56049114390
-
Mitochondrial fatty acid oxidation defects - Remaining challenges
-
Gregersen, N., Andresen, B. S., Pedersen, C. B., Olsen, R. K. J., Corydon, T. J., and Bross, P. (2008) Mitochondrial fatty acid oxidation defects-remaining challenges J. Inherited Metab. Dis. 31, 643-657 10.1007/s10545-008-0990-y
-
(2008)
J. Inherited Metab. Dis.
, vol.31
, pp. 643-657
-
-
Gregersen, N.1
Andresen, B.S.2
Pedersen, C.B.3
Olsen, R.K.J.4
Corydon, T.J.5
Bross, P.6
-
2
-
-
0027304244
-
Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate
-
Kim, J. J., Wang, M., and Paschke, R. (1993) Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate Proc. Natl. Acad. Sci. U. S. A. 90, 7523-7527 10.1073/pnas.90.16.7523
-
(1993)
Proc. Natl. Acad. Sci. U. S. A.
, vol.90
, pp. 7523-7527
-
-
Kim, J.J.1
Wang, M.2
Paschke, R.3
-
3
-
-
0842265784
-
Acyl-CoA dehydrogenases and acyl-CoA oxidases. Structural basis for mechanistic similarities and differences
-
Kim, J.-J. P. and Miura, R. (2004) Acyl-CoA dehydrogenases and acyl-CoA oxidases. Structural basis for mechanistic similarities and differences Eur. J. Biochem. 271, 483-493 10.1046/j.1432-1033.2003.03948.x
-
(2004)
Eur. J. Biochem.
, vol.271
, pp. 483-493
-
-
Kim, J.-J.P.1
Miura, R.2
-
4
-
-
12444298922
-
Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA
-
Satoh, A., Nakajima, Y., Miyahara, I., Hirotsu, K., Tanaka, T., Nishina, Y., Shiga, K., Tamaoki, H., Setoyama, C., and Miura, R. (2003) Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA J. Biochem. 134, 297-304 10.1093/jb/mvg143
-
(2003)
J. Biochem.
, vol.134
, pp. 297-304
-
-
Satoh, A.1
Nakajima, Y.2
Miyahara, I.3
Hirotsu, K.4
Tanaka, T.5
Nishina, Y.6
Shiga, K.7
Tamaoki, H.8
Setoyama, C.9
Miura, R.10
-
5
-
-
29344452147
-
Medium-chain acyl-CoA dehydrogenase deficiency: Genotype-biochemical phenotype correlations
-
Waddell, L., Wiley, V., Carpenter, K., Bennetts, B., Angel, L., Andresen, B. S., and Wilcken, B. (2006) Medium-chain acyl-CoA dehydrogenase deficiency: Genotype-biochemical phenotype correlations Mol. Genet. Metab. 87, 32-39 10.1016/j.ymgme.2005.09.020
-
(2006)
Mol. Genet. Metab.
, vol.87
, pp. 32-39
-
-
Waddell, L.1
Wiley, V.2
Carpenter, K.3
Bennetts, B.4
Angel, L.5
Andresen, B.S.6
Wilcken, B.7
-
6
-
-
77957593706
-
The clinical manifestation of MCAD deficiency: Challenges towards adulthood in the screened population
-
Schatz, U. A. and Ensenauer, R. (2010) The clinical manifestation of MCAD deficiency: challenges towards adulthood in the screened population J. Inherited Metab. Dis. 33, 513-520 10.1007/s10545-010-9115-5
-
(2010)
J. Inherited Metab. Dis.
, vol.33
, pp. 513-520
-
-
Schatz, U.A.1
Ensenauer, R.2
-
7
-
-
84899493496
-
Retrospective study of the medium-chain acyl-CoA dehydrogenase deficiency in Portugal
-
Ventura, F. V., Leandro, P., Luz, A., Rivera, I. A., Silva, M. F. B., Ramos, R., Rocha, H., Lopes, A., Fonseca, H., Gaspar, A., Diogo, L., Martins, E., Leão-Teles, E., Vilarinho, L., and Tavares de Almeida, I. (2014) Retrospective study of the medium-chain acyl-CoA dehydrogenase deficiency in Portugal Clin. Genet. 85, 555-561 10.1111/cge.12227
-
(2014)
Clin. Genet.
, vol.85
, pp. 555-561
-
-
Ventura, F.V.1
Leandro, P.2
Luz, A.3
Rivera, I.A.4
Silva, M.F.B.5
Ramos, R.6
Rocha, H.7
Lopes, A.8
Fonseca, H.9
Gaspar, A.10
Diogo, L.11
Martins, E.12
Leão-Teles, E.13
Vilarinho, L.14
Tavares De Almeida, I.15
-
8
-
-
84958618764
-
The Biochemistry and Physiology of Mitochondrial Fatty Acid β-Oxidation and Its Genetic Disorders
-
Houten, S. M., Violante, S., Ventura, F. V., and Wanders, R. J. A. (2016) The Biochemistry and Physiology of Mitochondrial Fatty Acid β-Oxidation and Its Genetic Disorders Annu. Rev. Physiol. 78, 23-44 10.1146/annurev-physiol-021115-105045
-
(2016)
Annu. Rev. Physiol.
, vol.78
, pp. 23-44
-
-
Houten, S.M.1
Violante, S.2
Ventura, F.V.3
Wanders, R.J.A.4
-
9
-
-
33745098087
-
Newborn screening for medium-chain acyl-CoA dehydrogenase deficiency: A global perspective
-
Rhead, W. J. (2006) Newborn screening for medium-chain acyl-CoA dehydrogenase deficiency: A global perspective J. Inherited Metab. Dis. 29, 370-377 10.1007/s10545-006-0292-1
-
(2006)
J. Inherited Metab. Dis.
, vol.29
, pp. 370-377
-
-
Rhead, W.J.1
-
10
-
-
84860915155
-
MCAD deficiency in Denmark
-
Andresen, B. S., Lund, A. M., Hougaard, D. M., Christensen, E., Gahrn, B., Christensen, M., Bross, P., Vested, A., Simonsen, H., Skogstrand, K., Olpin, S., Brandt, N. J., Skovby, F., Nørgaard-Pedersen, B., and Gregersen, N. (2012) MCAD deficiency in Denmark Mol. Genet. Metab. 106, 175-188 10.1016/j.ymgme.2012.03.018
-
(2012)
Mol. Genet. Metab.
, vol.106
, pp. 175-188
-
-
Andresen, B.S.1
Lund, A.M.2
Hougaard, D.M.3
Christensen, E.4
Gahrn, B.5
Christensen, M.6
Bross, P.7
Vested, A.8
Simonsen, H.9
Skogstrand, K.10
Olpin, S.11
Brandt, N.J.12
Skovby, F.13
Nørgaard-Pedersen, B.14
Gregersen, N.15
-
11
-
-
84945259193
-
Medium-Chain Acyl-Coenzyme A Dehydrogenase Deficiency
-
(Pagon, R. Bird, T. and Dolan, C. Eds.). University of Washington, Seattle
-
Matern, D. and Rinaldo, P. (2015) Medium-Chain Acyl-Coenzyme A Dehydrogenase Deficiency. In Gene Reviews (Pagon, R., Bird, T., and Dolan, C., Eds.). University of Washington, Seattle.
-
(2015)
Gene Reviews
-
-
Matern, D.1
Rinaldo, P.2
-
12
-
-
0028902952
-
Effects of two mutations detected in medium chain acyl-CoA dehydrogenase (MCAD)-deficient patients on folding, oligomer assembly, and stability of MCAD enzyme
-
Bross, P., Jespersen, C., Jensen, T. G., Andresen, B. S., Kristensen, M. J., Winter, V., Nandy, A., Kräutle, F., Ghisla, S., and Bolundi, L. (1995) Effects of two mutations detected in medium chain acyl-CoA dehydrogenase (MCAD)-deficient patients on folding, oligomer assembly, and stability of MCAD enzyme J. Biol. Chem. 270, 10284-10290 10.1074/jbc.270.17.10284
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 10284-10290
-
-
Bross, P.1
Jespersen, C.2
Jensen, T.G.3
Andresen, B.S.4
Kristensen, M.J.5
Winter, V.6
Nandy, A.7
Kräutle, F.8
Ghisla, S.9
Bolundi, L.10
-
13
-
-
0027369381
-
Co-overexpression of bacterial GroESL chaperonins partly overcomes non-productive folding and tetramer assembly of E. Coli-expressed human medium-chain acyl-CoA dehydrogenase (MCAD) carrying the prevalent disease-causing K304E mutation
-
Bross, P., Andersen, B. A., Winter, V., Kräutle, F., Jensen, T. G., Nandy, A., Kølvraa, S., Ghisla, S., Bolund, L., and Gregersen, N. (1993) Co-overexpression of bacterial GroESL chaperonins partly overcomes non-productive folding and tetramer assembly of E. coli-expressed human medium-chain acyl-CoA dehydrogenase (MCAD) carrying the prevalent disease-causing K304E mutation Biochim. Biophys. Acta, Mol. Basis Dis. 1182, 264-274 10.1016/0925-4439(93)90068-C
-
(1993)
Biochim. Biophys. Acta, Mol. Basis Dis.
, vol.1182
, pp. 264-274
-
-
Bross, P.1
Andersen, B.A.2
Winter, V.3
Kräutle, F.4
Jensen, T.G.5
Nandy, A.6
Kølvraa, S.7
Ghisla, S.8
Bolund, L.9
Gregersen, N.10
-
14
-
-
64649093848
-
Protein misfolding is the molecular mechanism underlying MCADD identified in newborn screening
-
Maier, E. M., Gersting, S. W., Kemter, K. F., Jank, J. M., Reindl, M., Messing, D. D., Truger, M. S., Sommerhoff, C. P., and Muntau, A. C. (2009) Protein misfolding is the molecular mechanism underlying MCADD identified in newborn screening Hum. Mol. Genet. 18, 1612-1623 10.1093/hmg/ddp079
-
(2009)
Hum. Mol. Genet.
, vol.18
, pp. 1612-1623
-
-
Maier, E.M.1
Gersting, S.W.2
Kemter, K.F.3
Jank, J.M.4
Reindl, M.5
Messing, D.D.6
Truger, M.S.7
Sommerhoff, C.P.8
Muntau, A.C.9
-
15
-
-
33646775349
-
The epidemiology of medium chain acyl-CoA dehydrogenase deficiency: An update
-
Grosse, S. D., Khoury, M. J., Greene, C. L., Crider, K. S., and Pollitt, R. J. (2006) The epidemiology of medium chain acyl-CoA dehydrogenase deficiency: an update Genet. Med. 8, 205-212 10.1097/01.gim.0000204472.25153.8d
-
(2006)
Genet. Med.
, vol.8
, pp. 205-212
-
-
Grosse, S.D.1
Khoury, M.J.2
Greene, C.L.3
Crider, K.S.4
Pollitt, R.J.5
-
16
-
-
0028284447
-
Characterization of Wild-Type Human Medium-Chain Acyl-CoA Dehydrogenase (MCAD) and Mutant Enzymes Present in MCAD-Deficient Patients by Two-Dimensional Gel Electrophoresis: Evidence for Posttranslational Modification of the Enzyme
-
Bross, P., Jensen, T. G., Andresen, B. S., Kjeldsen, M., Nandy, A., Kolvraa, S., Ghisla, S., Rasched, I., Bolund, L., and Gregersen, N. (1994) Characterization of Wild-Type Human Medium-Chain Acyl-CoA Dehydrogenase (MCAD) and Mutant Enzymes Present in MCAD-Deficient Patients by Two-Dimensional Gel Electrophoresis: Evidence for Posttranslational Modification of the Enzyme Biochem. Med. Metab. Biol. 52, 36-44 10.1006/bmmb.1994.1031
-
(1994)
Biochem. Med. Metab. Biol.
, vol.52
, pp. 36-44
-
-
Bross, P.1
Jensen, T.G.2
Andresen, B.S.3
Kjeldsen, M.4
Nandy, A.5
Kolvraa, S.6
Ghisla, S.7
Rasched, I.8
Bolund, L.9
Gregersen, N.10
-
17
-
-
84911995156
-
Functional studies of 18 heterologously expressed medium-chain acyl-CoA dehydrogenase (MCAD) variants
-
Koster, K.-L., Sturm, M., Herebian, D., Smits, S. H. J., and Spiekerkoetter, U. (2014) Functional studies of 18 heterologously expressed medium-chain acyl-CoA dehydrogenase (MCAD) variants J. Inherited Metab. Dis. 37, 917-928 10.1007/s10545-014-9732-5
-
(2014)
J. Inherited Metab. Dis.
, vol.37
, pp. 917-928
-
-
Koster, K.-L.1
Sturm, M.2
Herebian, D.3
Smits, S.H.J.4
Spiekerkoetter, U.5
-
18
-
-
8244246432
-
Biochemical Characterization of Purified, Human Recombinant Lys304Glu Medium-Chain Acyl-Coa Dehydrogenase Containing the Common Disease-Causing Mutation and Comparison with the Normal Enzyme
-
Kieweg, V., Krautle, F.-G., Nandy, A., Engst, S., Vock, P., Abdel-Ghany, A.-G., Bross, P., Gregersen, N., Rasched, I., Strauss, A., and Ghisla, S. (1997) Biochemical Characterization of Purified, Human Recombinant Lys304Glu Medium-Chain Acyl-Coa Dehydrogenase Containing the Common Disease-Causing Mutation and Comparison with the Normal Enzyme Eur. J. Biochem. 246, 548-556 10.1111/j.1432-1033.1997.00548.x
-
(1997)
Eur. J. Biochem.
, vol.246
, pp. 548-556
-
-
Kieweg, V.1
Krautle, F.-G.2
Nandy, A.3
Engst, S.4
Vock, P.5
Abdel-Ghany, A.-G.6
Bross, P.7
Gregersen, N.8
Rasched, I.9
Strauss, A.10
Ghisla, S.11
-
19
-
-
84899517298
-
The Domain-Specific and Temperature-Dependent Protein Misfolding Phenotype of Variant Medium-Chain acyl-CoA Dehydrogenase
-
Jank, J. M., Maier, E. M., Reiß, D. D., Haslbeck, M., Kemter, K. F., Truger, M. S., Sommerhoff, C. P., Ferdinandusse, S., Wanders, R. J., Gersting, S. W., and Muntau, A. C. (2014) The Domain-Specific and Temperature-Dependent Protein Misfolding Phenotype of Variant Medium-Chain acyl-CoA Dehydrogenase PLoS One 9, e93852 10.1371/journal.pone.0093852
-
(2014)
PLoS One
, vol.9
, pp. e93852
-
-
Jank, J.M.1
Maier, E.M.2
Reiß, D.D.3
Haslbeck, M.4
Kemter, K.F.5
Truger, M.S.6
Sommerhoff, C.P.7
Ferdinandusse, S.8
Wanders, R.J.9
Gersting, S.W.10
Muntau, A.C.11
-
20
-
-
84962748843
-
Insights into Medium-chain acyl-CoA dehydrogenase structure by Molecular Dynamics simulations
-
Bonito, C. A., Leandro, P., Ventura, F. V., and Guedes, R. C. (2016) Insights into Medium-chain acyl-CoA dehydrogenase structure by Molecular Dynamics simulations Chem. Biol. Drug Des. 88, 281-292 10.1111/cbdd.12755
-
(2016)
Chem. Biol. Drug Des.
, vol.88
, pp. 281-292
-
-
Bonito, C.A.1
Leandro, P.2
Ventura, F.V.3
Guedes, R.C.4
-
21
-
-
4444259930
-
Expression and purification of His-tagged rat mitochondrial medium-chain acyl-CoA dehydrogenase wild-type and Arg256 mutant proteins
-
Zeng, J. and Li, D. (2004) Expression and purification of His-tagged rat mitochondrial medium-chain acyl-CoA dehydrogenase wild-type and Arg256 mutant proteins Protein Expression Purif. 37, 472-478 10.1016/j.pep.2004.06.021
-
(2004)
Protein Expression Purif.
, vol.37
, pp. 472-478
-
-
Zeng, J.1
Li, D.2
-
22
-
-
0017184389
-
A Rapid and Sensitive Method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding
-
Bradford, M. (1976) A Rapid and Sensitive Method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding Anal. Biochem. 72, 248-254 10.1016/0003-2697(76)90527-3
-
(1976)
Anal. Biochem.
, vol.72
, pp. 248-254
-
-
Bradford, M.1
-
23
-
-
0006493479
-
Size exclusion chromatography and size exclusion HPLC of proteins
-
Tayyab, S., Qamar, S., and Islam, M. (1991) Size exclusion chromatography and size exclusion HPLC of proteins Biochem. Educ. 19, 149-152 10.1016/0307-4412(91)90060-L
-
(1991)
Biochem. Educ.
, vol.19
, pp. 149-152
-
-
Tayyab, S.1
Qamar, S.2
Islam, M.3
-
24
-
-
16344382388
-
Thermodynamic Stability of Carbonic Anhydrase: Measurements of Binding Affinity and Stoichiometry Using ThermoFluor
-
Matulis, D., Kranz, J. K., Salemme, F. R., and Todd, M. J. (2005) Thermodynamic Stability of Carbonic Anhydrase: Measurements of Binding Affinity and Stoichiometry Using ThermoFluor Biochemistry 44, 5258-5266 10.1021/bi048135v
-
(2005)
Biochemistry
, vol.44
, pp. 5258-5266
-
-
Matulis, D.1
Kranz, J.K.2
Salemme, F.R.3
Todd, M.J.4
-
25
-
-
37249005205
-
The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability
-
Niesen, F. H., Berglund, H., and Vedadi, M. (2007) The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability Nat. Protoc. 2, 2212-2221 10.1038/nprot.2007.321
-
(2007)
Nat. Protoc.
, vol.2
, pp. 2212-2221
-
-
Niesen, F.H.1
Berglund, H.2
Vedadi, M.3
-
26
-
-
67349110220
-
Study of kinetics of thermal aggregation of mitochondrial aspartate aminotransferase by dynamic light scattering: Protective effect of α-Crystallin
-
Golub, N. V., Markossian, K. a, Sholukh, M. V., Muranov, K. O., and Kurganov, B. I. (2009) Study of kinetics of thermal aggregation of mitochondrial aspartate aminotransferase by dynamic light scattering: protective effect of α-Crystallin Eur. Biophys. J. 38, 547-556 10.1007/s00249-009-0403-7
-
(2009)
Eur. Biophys. J.
, vol.38
, pp. 547-556
-
-
Golub, N.V.1
Markossian, K.A.2
Sholukh, M.V.3
Muranov, K.O.4
Kurganov, B.I.5
-
27
-
-
0029822206
-
Crystal Structures of the Wild Type and the Glu376Gly/Thr255Glu Mutant of Human Medium-Chain Acyl-CoA Dehydrogenase: Influence of the Location of the Catalytic Base on Substrate Specificity
-
Lee, H.-J. K., Wang, M., Paschke, R., Nandy, A., Ghisla, S., and Kim, J.-J. P. (1996) Crystal Structures of the Wild Type and the Glu376Gly/Thr255Glu Mutant of Human Medium-Chain Acyl-CoA Dehydrogenase: Influence of the Location of the Catalytic Base on Substrate Specificity Biochemistry 35, 12412-12420 10.1021/bi9607867
-
(1996)
Biochemistry
, vol.35
, pp. 12412-12420
-
-
Lee, H.-J.K.1
Wang, M.2
Paschke, R.3
Nandy, A.4
Ghisla, S.5
Kim, J.-J.P.6
-
28
-
-
84973646291
-
-
version 2014.09 Chemical Computing Group Inc. Montreal
-
Molecular Operating Environment (MOE), version 2014.09 (2016) Chemical Computing Group Inc., Montreal.
-
(2016)
Molecular Operating Environment (MOE)
-
-
-
29
-
-
0034206335
-
The GROMOS96 benchmarks for molecular simulation
-
Bonvin, A. M., Mark, A. E., and van Gunsteren, W. F. (2000) The GROMOS96 benchmarks for molecular simulation Comput. Phys. Commun. 128, 550-557 10.1016/S0010-4655(99)00540-8
-
(2000)
Comput. Phys. Commun.
, vol.128
, pp. 550-557
-
-
Bonvin, A.M.1
Mark, A.E.2
Van Gunsteren, W.F.3
-
30
-
-
0008819754
-
The GROMOS Biomolecular Simulation Program Package
-
Scott, W. R., Hünenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Krüger, P., and van Gunsteren, W. F. (1999) The GROMOS Biomolecular Simulation Program Package J. Phys. Chem. A 103, 3596-3607 10.1021/jp984217f
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 3596-3607
-
-
Scott, W.R.1
Hünenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Krüger, P.9
Van Gunsteren, W.F.10
-
31
-
-
4444282928
-
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
-
Oostenbrink, C., Villa, A., Mark, A. E., and van Gunsteren, W. F. (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem. 25, 1656-1676 10.1002/jcc.20090
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.E.3
Van Gunsteren, W.F.4
-
32
-
-
0029633168
-
GROMACS: A message-passing parallel molecular dynamics implementation
-
Berendsen, H. J., van der Spoel, D., and van Drunen, R. (1995) GROMACS: A message-passing parallel molecular dynamics implementation Comput. Phys. Commun. 91, 43-56 10.1016/0010-4655(95)00042-E
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 43-56
-
-
Berendsen, H.J.1
Van Der Spoel, D.2
Van Drunen, R.3
-
33
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl, E., Hess, B., and van der Spoel, D. (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Model. 7, 306-317 10.1007/s008940100045
-
(2001)
J. Mol. Model.
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
34
-
-
46249092554
-
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-
Hess, B., Kutzner, C., van der Spoel, D., and Lindahl, E. (2008) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 4, 435-447 10.1021/ct700301q
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
35
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., and Berendsen, H. J. (2005) GROMACS: fast, flexible, and free J. Comput. Chem. 26, 1701-1718 10.1002/jcc.20291
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.6
-
36
-
-
84961981789
-
An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0
-
Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., Oostenbrink, C., and Mark, A. E. (2011) An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0 J. Chem. Theory Comput. 7, 4026-4037 10.1021/ct200196m
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 4026-4037
-
-
Malde, A.K.1
Zuo, L.2
Breeze, M.3
Stroet, M.4
Poger, D.5
Nair, P.C.6
Oostenbrink, C.7
Mark, A.E.8
-
37
-
-
84899933010
-
Testing and validation of the Automated Topology Builder (ATB) version 2.0: Prediction of hydration free enthalpies
-
Koziara, K. B., Stroet, M., Malde, A. K., and Mark, A. E. (2014) Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies J. Comput.-Aided Mol. Des. 28, 221-233 10.1007/s10822-014-9713-7
-
(2014)
J. Comput.-Aided Mol. Des.
, vol.28
, pp. 221-233
-
-
Koziara, K.B.1
Stroet, M.2
Malde, A.K.3
Mark, A.E.4
-
38
-
-
7544226311
-
PRODRG: A tool for high-throughput crystallography of protein-ligand complexes
-
Schüttelkopf, A. W. and van Aalten, D. M. (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallogr., Sect. D: Biol. Crystallogr. 60, 1355-1363 10.1107/S0907444904011679
-
(2004)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.60
, pp. 1355-1363
-
-
Schüttelkopf, A.W.1
Van Aalten, D.M.2
-
39
-
-
0002775934
-
Interaction Models for Water in Relation to Protein Hydration
-
(Pullman, B. Ed.), Springer, Dordrecht, The Netherlands
-
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., and Hermans, J. (1981) Interaction Models for Water in Relation to Protein Hydration. In Intermolecular Forces (Pullman, B., Ed.) pp 331-342, Springer, Dordrecht, The Netherlands.
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
40
-
-
33846086933
-
Canonical sampling through velocity rescaling
-
Bussi, G., Donadio, D., and Parrinello, M. (2007) Canonical sampling through velocity rescaling J. Chem. Phys. 126, 014101 10.1063/1.2408420
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
41
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
Hoover, W. (1985) Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A: At., Mol., Opt. Phys. 31, 1695-1697 10.1103/PhysRevA.31.1695
-
(1985)
Phys. Rev. A: At., Mol., Opt. Phys.
, vol.31
, pp. 1695-1697
-
-
Hoover, W.1
-
42
-
-
84926811618
-
Constant pressure molecular dynamics for molecular systems
-
Nosé, S. and Klein, M. L. (1983) Constant pressure molecular dynamics for molecular systems Mol. Phys. 50, 1055-1076 10.1080/00268978300102851
-
(1983)
Mol. Phys.
, vol.50
, pp. 1055-1076
-
-
Nosé, S.1
Klein, M.L.2
-
43
-
-
0019707626
-
Polymorphic transitions in single crystals: A new molecular dynamics method
-
Parrinello, M. and Rahman, A. (1981) Polymorphic transitions in single crystals: A new molecular dynamics method J. Appl. Phys. 52, 7182-7190 10.1063/1.328693
-
(1981)
J. Appl. Phys.
, vol.52
, pp. 7182-7190
-
-
Parrinello, M.1
Rahman, A.2
-
44
-
-
0000388705
-
LINCS: A linear constraint solver for molecular simulations
-
Hess, B., Bekker, H., Berendsen, H. J., and Fraaije, J. G. E. M. (1997) LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 18, 1463-1472 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.3.CO;2-L
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.3
Fraaije, J.G.E.M.4
-
45
-
-
38749123962
-
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
-
Hess, B. (2008) P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation J. Chem. Theory Comput. 4, 116-122 10.1021/ct700200b
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 116-122
-
-
Hess, B.1
-
46
-
-
84986440341
-
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
Miyamoto, S. and Kollman, P. A. (1992) Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 13, 952-962 10.1002/jcc.540130805
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
47
-
-
33846823909
-
Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
-
Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems J. Chem. Phys. 98, 10089-10092 10.1063/1.464397
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
48
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A smooth particle mesh Ewald method J. Chem. Phys. 103, 8577-8593 10.1063/1.470117
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
49
-
-
84941130416
-
A series of PDB-related databanks for everyday needs
-
Touw, W. G., Baakman, C., Black, J., Te Beek, T. A. H., Krieger, E., Joosten, R. P., and Vriend, G. (2015) A series of PDB-related databanks for everyday needs Nucleic Acids Res. 43, D364-D368 10.1093/nar/gku1028
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D364-D368
-
-
Touw, W.G.1
Baakman, C.2
Black, J.3
Te Beek, T.A.H.4
Krieger, E.5
Joosten, R.P.6
Vriend, G.7
-
50
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22, 2577-2637 10.1002/bip.360221211
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
51
-
-
79957788878
-
ProDy: Protein dynamics inferred from theory and experiments
-
Bakan, A., Meireles, L. M., and Bahar, I. (2011) ProDy: protein dynamics inferred from theory and experiments Bioinformatics 27, 1575-1577 10.1093/bioinformatics/btr168
-
(2011)
Bioinformatics
, vol.27
, pp. 1575-1577
-
-
Bakan, A.1
Meireles, L.M.2
Bahar, I.3
-
52
-
-
77949634796
-
Normal mode analysis of biomolecular structures: Functional mechanisms of membrane proteins
-
Bahar, I., Lezon, T. R., Bakan, A., and Shrivastava, I. H. (2010) Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins Chem. Rev. 110, 1463-1497 10.1021/cr900095e
-
(2010)
Chem. Rev.
, vol.110
, pp. 1463-1497
-
-
Bahar, I.1
Lezon, T.R.2
Bakan, A.3
Shrivastava, I.H.4
-
53
-
-
0027995683
-
Detection, delineation, measurement and display of cavities in macromolecular structures
-
Kleywegt, G. J. and Jones, T. a. (1994) Detection, delineation, measurement and display of cavities in macromolecular structures Acta Crystallogr., Sect. D: Biol. Crystallogr. 50, 178-185 10.1107/S0907444993011333
-
(1994)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.50
, pp. 178-185
-
-
Kleywegt, G.J.1
Jones, T.A.2
-
54
-
-
84888295649
-
G-contacts: Fast contact search in bio-molecular ensemble data
-
Blau, C. and Grubmuller, H. (2013) g-contacts: Fast contact search in bio-molecular ensemble data Comput. Phys. Commun. 184, 2856-2859 10.1016/j.cpc.2013.07.018
-
(2013)
Comput. Phys. Commun.
, vol.184
, pp. 2856-2859
-
-
Blau, C.1
Grubmuller, H.2
-
55
-
-
84904964377
-
G-mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations
-
Kumari, R., Kumar, R., and Lynn, A. (2014) g-mmpbsa-A GROMACS Tool for High-Throughput MM-PBSA Calculations J. Chem. Inf. Model. 54, 1951-1962 10.1021/ci500020m
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 1951-1962
-
-
Kumari, R.1
Kumar, R.2
Lynn, A.3
-
56
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker, N. A., Sept, D., Joseph, S., Holst, M. J., and McCammon, J. A. (2001) Electrostatics of nanosystems: application to microtubules and the ribosome Proc. Natl. Acad. Sci. U. S. A. 98, 10037-10041 10.1073/pnas.181342398
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
57
-
-
33645678321
-
Thermodynamics of Hydrogen Bonding in Hydrophilic and Hydrophobic Media
-
van der Spoel, D., van Maaren, P. J., Larsson, P., and Tîmneanu, N. N. (2006) Thermodynamics of Hydrogen Bonding in Hydrophilic and Hydrophobic Media J. Phys. Chem. B 110, 4393-4398 10.1021/jp0572535
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 4393-4398
-
-
Van Der Spoel, D.1
Van Maaren, P.J.2
Larsson, P.3
Tîmneanu, N.N.4
-
58
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: visual molecular dynamics J. Mol. Graphics 14, 33-38 10.1016/0263-7855(96)00018-5
-
(1996)
J. Mol. Graphics
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
59
-
-
84954198602
-
Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase
-
Peng, Y., Norris, J., Schwartz, C., and Alexov, E. (2016) Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase Int. J. Mol. Sci. 17, 77 10.3390/ijms17010077
-
(2016)
Int. J. Mol. Sci.
, vol.17
, pp. 77
-
-
Peng, Y.1
Norris, J.2
Schwartz, C.3
Alexov, E.4
-
60
-
-
77956276773
-
Computational analysis of missense mutations causing Snyder-Robinson syndrome
-
Zhang, Z., Teng, S., Wang, L., Schwartz, C. E., and Alexov, E. (2010) Computational analysis of missense mutations causing Snyder-Robinson syndrome Hum. Mutat. 31, 1043-1049 10.1002/humu.21310
-
(2010)
Hum. Mutat.
, vol.31
, pp. 1043-1049
-
-
Zhang, Z.1
Teng, S.2
Wang, L.3
Schwartz, C.E.4
Alexov, E.5
-
61
-
-
0034504583
-
Resolving the hydrogen bond dynamics conundrum
-
Luzar, A. (2000) Resolving the hydrogen bond dynamics conundrum J. Chem. Phys. 113, 10663-10675 10.1063/1.1320826
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 10663-10675
-
-
Luzar, A.1
-
62
-
-
0002300553
-
Hydrogen-bond kinetics in liquid water
-
Luzar, A. and Chandler, D. (1996) Hydrogen-bond kinetics in liquid water Nature 379, 55-57 10.1038/379055a0
-
(1996)
Nature
, vol.379
, pp. 55-57
-
-
Luzar, A.1
Chandler, D.2
-
63
-
-
80054078305
-
Cofactors and metabolites as potential stabilizers of mitochondrial acyl-CoA dehydrogenases
-
Lucas, T. G., Henriques, B. J., Rodrigues, J. V., Bross, P., Gregersen, N., and Gomes, C. M. (2011) Cofactors and metabolites as potential stabilizers of mitochondrial acyl-CoA dehydrogenases Biochim. Biophys. Acta, Mol. Basis Dis. 1812, 1658-1663 10.1016/j.bbadis.2011.09.009
-
(2011)
Biochim. Biophys. Acta, Mol. Basis Dis.
, vol.1812
, pp. 1658-1663
-
-
Lucas, T.G.1
Henriques, B.J.2
Rodrigues, J.V.3
Bross, P.4
Gregersen, N.5
Gomes, C.M.6
-
64
-
-
4344567022
-
Sensitivity of molecular dynamics simulations to the choice of the X-ray structure used to model an enzymatic reaction
-
Garcia-Viloca, M., Poulsen, T. D., Truhlar, D. G., and Gao, J. (2004) Sensitivity of molecular dynamics simulations to the choice of the X-ray structure used to model an enzymatic reaction Protein Sci. 13, 2341-2354 10.1110/ps.03504104
-
(2004)
Protein Sci.
, vol.13
, pp. 2341-2354
-
-
Garcia-Viloca, M.1
Poulsen, T.D.2
Truhlar, D.G.3
Gao, J.4
|