-
1
-
-
0021196998
-
Protein-DNA Recognition
-
Pabo, C. O.; Sauer, R. T. Protein-DNA Recognition Annu. Rev. Biochem. 1984, 53, 293-321 10.1146/annurev.bi.53.070184.001453
-
(1984)
Annu. Rev. Biochem.
, vol.53
, pp. 293-321
-
-
Pabo, C.O.1
Sauer, R.T.2
-
2
-
-
0026682657
-
Transcription Factors: Structural Families and Principles of DNA Recognition
-
Pabo, C. O.; Sauer, R. T. Transcription Factors: Structural Families and Principles of DNA Recognition Annu. Rev. Biochem. 1992, 61, 1053-1095 10.1146/annurev.bi.61.070192.005201
-
(1992)
Annu. Rev. Biochem.
, vol.61
, pp. 1053-1095
-
-
Pabo, C.O.1
Sauer, R.T.2
-
3
-
-
70350344051
-
Running in Reverse: The Structural Basis for Translocation Polarity in Hexameric Helicases
-
Thomsen, N. D.; Berger, J. M. Running in Reverse: the Structural Basis for Translocation Polarity in Hexameric Helicases Cell 2009, 139, 523-34 10.1016/j.cell.2009.08.043
-
(2009)
Cell
, vol.139
, pp. 523-534
-
-
Thomsen, N.D.1
Berger, J.M.2
-
4
-
-
1842411320
-
Crystal Structure of the Nucleosome Core Particle at 2.8 Å Resolution
-
Luger, K.; Mader, A. W.; Richmond, R. K.; Sargent, D. F.; Richmond, T. J. Crystal Structure of the Nucleosome Core Particle at 2.8 Å Resolution Nature 1997, 389, 251-260 10.1038/38444
-
(1997)
Nature
, vol.389
, pp. 251-260
-
-
Luger, K.1
Mader, A.W.2
Richmond, R.K.3
Sargent, D.F.4
Richmond, T.J.5
-
5
-
-
84869009900
-
Nucleosomal Elements That Control the Topography of the Barrier to Transcription
-
Bintu, L.; Ishibashi, T.; Dangkulwanich, M.; Wu, Y.-Y. Y.; Lubkowska, L.; Kashlev, M.; Bustamante, C. Nucleosomal Elements That Control the Topography of the Barrier to Transcription Cell 2012, 151, 738-49 10.1016/j.cell.2012.10.009
-
(2012)
Cell
, vol.151
, pp. 738-749
-
-
Bintu, L.1
Ishibashi, T.2
Dangkulwanich, M.3
Wu, Y.-Y.Y.4
Lubkowska, L.5
Kashlev, M.6
Bustamante, C.7
-
6
-
-
79851485457
-
Controlled Translocation of Individual DNA Molecules Through Protein Nanopores with Engineered Molecular Brakes
-
Rincon-Restrepo, M.; Mikhailova, E.; Bayley, H.; Maglia, G. Controlled Translocation of Individual DNA Molecules Through Protein Nanopores With Engineered Molecular Brakes Nano Lett. 2011, 11, 746-750 10.1021/nl1038874
-
(2011)
Nano Lett.
, vol.11
, pp. 746-750
-
-
Rincon-Restrepo, M.1
Mikhailova, E.2
Bayley, H.3
Maglia, G.4
-
7
-
-
84865583099
-
Molecular Dynamics Study of MspA Arginine Mutants Predicts Slow DNA Translocations and Ion Current Blockades Indicative of DNA Sequence
-
Bhattacharya, S.; Derrington, I. M.; Pavlenok, M.; Niederweis, M.; Gundlach, J. H.; Aksimentiev, A. Molecular Dynamics Study of MspA Arginine Mutants Predicts Slow DNA Translocations and Ion Current Blockades Indicative of DNA Sequence ACS Nano 2012, 6, 6960-6968 10.1021/nn3019943
-
(2012)
ACS Nano
, vol.6
, pp. 6960-6968
-
-
Bhattacharya, S.1
Derrington, I.M.2
Pavlenok, M.3
Niederweis, M.4
Gundlach, J.H.5
Aksimentiev, A.6
-
8
-
-
0018094892
-
Electrostatic Effects in Proteins
-
Perutz, M. Electrostatic Effects in Proteins Science 1978, 201, 1187-1191 10.1126/science.694508
-
(1978)
Science
, vol.201
, pp. 1187-1191
-
-
Perutz, M.1
-
9
-
-
0034039797
-
Electrostatic Aspects of Protein-Protein Interactions
-
Sheinerman, F. B.; Norel, R.; Honig, B. Electrostatic Aspects of Protein-Protein Interactions Curr. Opin. Struct. Biol. 2000, 10, 153-159 10.1016/S0959-440X(00)00065-8
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 153-159
-
-
Sheinerman, F.B.1
Norel, R.2
Honig, B.3
-
10
-
-
0037168655
-
A Structural Model for Alzheimer's β-amyloid Fibrils Based on Experimental Constraints from Solid State NMR
-
Petkova, A. T.; Ishii, Y.; Balbach, J. J.; Antzutkin, O. N.; Leapman, R. D.; Delaglio, F.; Tycko, R. A Structural Model for Alzheimer's β-amyloid Fibrils Based on Experimental Constraints From Solid State NMR Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 16742-16747 10.1073/pnas.262663499
-
(2002)
Proc. Natl. Acad. Sci. U. S. A.
, vol.99
, pp. 16742-16747
-
-
Petkova, A.T.1
Ishii, Y.2
Balbach, J.J.3
Antzutkin, O.N.4
Leapman, R.D.5
Delaglio, F.6
Tycko, R.7
-
11
-
-
0032504237
-
G Protein-coupled Receptors: I. Diversity of Receptor-ligand Interactions
-
Ji, T. H.; Grossmann, M.; Ji, I. G Protein-coupled Receptors: I. Diversity of Receptor-ligand Interactions J. Biol. Chem. 1998, 273, 17299-17302 10.1074/jbc.273.28.17299
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 17299-17302
-
-
Ji, T.H.1
Grossmann, M.2
Ji, I.3
-
12
-
-
73849149844
-
Ligand-specific Regulation of the Extracellular Surface of a G-protein-coupled receptor
-
Bokoch, M. P.; Zou, Y.; Rasmussen, S. G. F.; Liu, C. W.; Nygaard, R.; Rosenbaum, D. M.; Fung, J. J.; Choi, H.-J. J.; Thian, F. S.; Kobilka, T. S.; Puglisi, J. D.; Weis, W. I.; Pardo, L.; Prosser, R. S.; Mueller, L.; Kobilka, B. K. Ligand-specific Regulation of the Extracellular Surface of a G-protein-coupled receptor Nature 2010, 463, 108-12 10.1038/nature08650
-
(2010)
Nature
, vol.463
, pp. 108-112
-
-
Bokoch, M.P.1
Zou, Y.2
Rasmussen, S.G.F.3
Liu, C.W.4
Nygaard, R.5
Rosenbaum, D.M.6
Fung, J.J.7
Choi, H.-J.J.8
Thian, F.S.9
Kobilka, T.S.10
Puglisi, J.D.11
Weis, W.I.12
Pardo, L.13
Prosser, R.S.14
Mueller, L.15
Kobilka, B.K.16
-
13
-
-
0020475449
-
A Simple Method for Displaying the Hydropathic Character of a Protein
-
Kyte, J.; Doolittle, R. F. A Simple Method for Displaying the Hydropathic Character of a Protein J. Mol. Biol. 1982, 157, 105-132 10.1016/0022-2836(82)90515-0
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
14
-
-
13444262028
-
Recognition of Transmembrane Helices by the Endoplasmic Reticulum Translocon
-
Hessa, T.; Kim, H.; Bihlmaier, K.; Lundin, C.; Boekel, J.; Andersson, H.; Nilsson, I.; White, S. H.; von Heijne, G. Recognition of Transmembrane Helices by the Endoplasmic Reticulum Translocon Nature 2005, 433, 377-381 10.1038/nature03216
-
(2005)
Nature
, vol.433
, pp. 377-381
-
-
Hessa, T.1
Kim, H.2
Bihlmaier, K.3
Lundin, C.4
Boekel, J.5
Andersson, H.6
Nilsson, I.7
White, S.H.8
Von Heijne, G.9
-
15
-
-
33845343261
-
Membrane-protein Topology
-
von Heijne, G. Membrane-protein Topology Nat. Rev. Mol. Cell Biol. 2006, 7, 909-18 10.1038/nrm2063
-
(2006)
Nat. Rev. Mol. Cell Biol.
, vol.7
, pp. 909-918
-
-
Von Heijne, G.1
-
16
-
-
33845637597
-
Phospholipids and the Origin of Cationic Gating Charges in Voltage Sensors
-
Schmidt, D.; Jiang, Q.-X.; MacKinnon, R. Phospholipids and the Origin of Cationic Gating Charges in Voltage Sensors Nature 2006, 444, 775-779 10.1038/nature05416
-
(2006)
Nature
, vol.444
, pp. 775-779
-
-
Schmidt, D.1
Jiang, Q.-X.2
Mackinnon, R.3
-
17
-
-
28444477387
-
Plasma Membrane Phosphoinositide Organization by Protein Electrostatics
-
McLaughlin, S.; Murray, D. Plasma Membrane Phosphoinositide Organization by Protein Electrostatics Nature 2005, 438, 605-11 10.1038/nature04398
-
(2005)
Nature
, vol.438
, pp. 605-611
-
-
McLaughlin, S.1
Murray, D.2
-
18
-
-
27244444569
-
Interface connections of a transmembrane voltage sensor
-
Freites, J. A.; Tobias, D. J.; von Heijne, G.; White, S. H. Interface connections of a transmembrane voltage sensor Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 15059-15064 10.1073/pnas.0507618102
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 15059-15064
-
-
Freites, J.A.1
Tobias, D.J.2
Von Heijne, G.3
White, S.H.4
-
19
-
-
84930204469
-
Neurotransmitter and Psychostimulant Recognition by the Dopamine Transporter
-
Wang, K. H.; Penmatsa, A.; Gouaux, E. Neurotransmitter and Psychostimulant Recognition by the Dopamine Transporter Nature 2015, 521, 322-7 10.1038/nature14431
-
(2015)
Nature
, vol.521
, pp. 322-327
-
-
Wang, K.H.1
Penmatsa, A.2
Gouaux, E.3
-
20
-
-
0025119185
-
Ligand-gated Ion Channels in the Brain: The Amino Acid Receptor Superfamily
-
Betz, H. Ligand-gated Ion Channels in the Brain: The Amino Acid Receptor Superfamily Neuron 1990, 5, 383-392 10.1016/0896-6273(90)90077-S
-
(1990)
Neuron
, vol.5
, pp. 383-392
-
-
Betz, H.1
-
21
-
-
0032578635
-
Structure of a Glutamate-receptor Ligand-binding Core in Complex with Kainate
-
Armstrong, N.; Sun, Y.; Chen, G.-Q.; Gouaux, E. Structure of a Glutamate-receptor Ligand-binding Core in Complex with Kainate Nature 1998, 395, 913-917 10.1038/27692
-
(1998)
Nature
, vol.395
, pp. 913-917
-
-
Armstrong, N.1
Sun, Y.2
Chen, G.-Q.3
Gouaux, E.4
-
22
-
-
0029011701
-
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179-5197 10.1021/ja00124a002
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
23
-
-
33748518255
-
Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters Proteins: Struct., Funct., Genet. 2006, 65, 712-25 10.1002/prot.21123
-
(2006)
Proteins: Struct., Funct., Genet.
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
24
-
-
33645786604
-
Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme
-
Buck, M.; Bouguet-Bonnet, S.; Pastor, R. W.; MacKerell, A. D. Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme Biophys. J. 2006, 90, L36-38 10.1529/biophysj.105.078154
-
(2006)
Biophys. J.
, vol.90
, pp. L36-L38
-
-
Buck, M.1
Bouguet-Bonnet, S.2
Pastor, R.W.3
MacKerell, A.D.4
-
25
-
-
84865723813
-
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles
-
Best, R. B.; Zhu, X.; Shim, J.; Lopes, P. E. M.; Mittal, J.; Feig, M.; MacKerell, A. D., Jr. Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles J. Chem. Theory Comput. 2012, 8, 3257-3273 10.1021/ct300400x
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3257-3273
-
-
Best, R.B.1
Zhu, X.2
Shim, J.3
Lopes, P.E.M.4
Mittal, J.5
Feig, M.6
MacKerell, A.D.7
-
26
-
-
77953513118
-
Improved Side-chain Torsion Potentials for the Amber ff99SB Protein Force Field
-
Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Improved Side-chain Torsion Potentials for the Amber ff99SB Protein Force Field Proteins: Struct., Funct., Genet. 2010, 78, 1950-8 10.1002/prot.22711
-
(2010)
Proteins: Struct., Funct., Genet.
, vol.78
, pp. 1950-1958
-
-
Lindorff-Larsen, K.1
Piana, S.2
Palmo, K.3
Maragakis, P.4
Klepeis, J.L.5
Dror, R.O.6
Shaw, D.E.7
-
27
-
-
15744368593
-
An Ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer
-
Klauda, J. B.; Brooks, B. R.; MacKerell, A. D., Jr.; Venable, R. M.; Pastor, R. W. An Ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer J. Phys. Chem. B 2005, 109, 5300-11 10.1021/jp0468096
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 5300-5311
-
-
Klauda, J.B.1
Brooks, B.R.2
MacKerell, A.D.3
Venable, R.M.4
Pastor, R.W.5
-
28
-
-
77953377650
-
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
-
Klauda, J. B.; Venable, R. M.; Freites, J. A.; O'Connor, J. W.; Tobias, D. J.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A. D., Jr.; Pastor, R. W. Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types J. Phys. Chem. B 2010, 114, 7830-7843 10.1021/jp101759q
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 7830-7843
-
-
Klauda, J.B.1
Venable, R.M.2
Freites, J.A.3
O'Connor, J.W.4
Tobias, D.J.5
Mondragon-Ramirez, C.6
Vorobyov, I.7
MacKerell, A.D.8
Pastor, R.W.9
-
29
-
-
0000214231
-
All-atom Empirical Force Field for Nucleic Acids: II. Application to Molecular Dynamics Simulations of DNA and RNA in Solution
-
MacKerell, A. D., Jr.; Banavali, N. K. All-atom Empirical Force Field for Nucleic Acids: II. Application to Molecular Dynamics Simulations of DNA and RNA in Solution J. Comput. Chem. 2000, 21, 105-120 10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 105-120
-
-
MacKerell, A.D.1
Banavali, N.K.2
-
30
-
-
0348244547
-
All-atom Empirical Force Field for Nucleic Acids: I. Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data
-
Foloppe, N.; MacKerell, A. D., Jr. All-atom Empirical Force Field for Nucleic Acids: I. Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data J. Comput. Chem. 2000, 21, 86-104 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell, A.D.2
-
31
-
-
34250318638
-
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α /γ Conformers
-
Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E.; Laughton, C. A.; Orozco, M. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α /γ Conformers Biophys. J. 2007, 92, 3817-3829 10.1529/biophysj.106.097782
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Perez, A.1
Marchan, I.2
Svozil, D.3
Sponer, J.4
Cheatham, T.E.5
Laughton, C.A.6
Orozco, M.7
-
32
-
-
84855661433
-
Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
-
Hart, K.; Foloppe, N.; Baker, C. M.; Denning, E. J.; Nilsson, L.; MacKerell, A. D., Jr. Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium J. Chem. Theory Comput. 2012, 8, 348-362 10.1021/ct200723y
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 348-362
-
-
Hart, K.1
Foloppe, N.2
Baker, C.M.3
Denning, E.J.4
Nilsson, L.5
MacKerell, A.D.6
-
33
-
-
79955484353
-
Impact of 2′-Hydroxyl Sampling on the Conformational Properties of RNA: Update of the CHARMM All-atom Additive Force Field for RNA
-
Denning, E. J.; Priyakumar, U. D.; Nilsson, L.; MacKerell, A. D., Jr. Impact of 2′-Hydroxyl Sampling on the Conformational Properties of RNA: Update of the CHARMM All-atom Additive Force Field for RNA J. Comput. Chem. 2011, 32, 1929-1943 10.1002/jcc.21777
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 1929-1943
-
-
Denning, E.J.1
Priyakumar, U.D.2
Nilsson, L.3
MacKerell, A.D.4
-
34
-
-
80052820313
-
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
-
Zgarbová, M.; Otyepka, M.; Šponer, J.; Mládek, A.; Banás, P.; Cheatham, T. E.; Jurečka, P. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles J. Chem. Theory Comput. 2011, 7, 2886-2902 10.1021/ct200162x
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2886-2902
-
-
Zgarbová, M.1
Otyepka, M.2
Šponer, J.3
Mládek, A.4
Banás, P.5
Cheatham, T.E.6
Jurečka, P.7
-
35
-
-
73349099062
-
Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields
-
Fadrna, E.; Spackova, N.; Sarzynska, J.; Koca, J.; Orozco, M.; Cheatham, T. E.; Kulinski, T.; Šponer, J. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields J. Chem. Theory Comput. 2009, 5, 2514-2530 10.1021/ct900200k
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 2514-2530
-
-
Fadrna, E.1
Spackova, N.2
Sarzynska, J.3
Koca, J.4
Orozco, M.5
Cheatham, T.E.6
Kulinski, T.7
Šponer, J.8
-
36
-
-
0041784950
-
All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
-
MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616 10.1021/jp973084f
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiórkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
37
-
-
84901675920
-
Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
-
Petrov, D.; Zagrovic, B. Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments? PLoS Comput. Biol. 2014, 10, e1003638 10.1371/journal.pcbi.1003638
-
(2014)
PLoS Comput. Biol.
, vol.10
-
-
Petrov, D.1
Zagrovic, B.2
-
38
-
-
65249149750
-
Hydration Water Dynamics Near Biological Interfaces
-
Johnson, M. E.; Malardier-Jugroot, C.; Murarka, R. K.; Head-Gordon, T. Hydration Water Dynamics Near Biological Interfaces J. Phys. Chem. B 2009, 113, 4082-4092 10.1021/jp806183v
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 4082-4092
-
-
Johnson, M.E.1
Malardier-Jugroot, C.2
Murarka, R.K.3
Head-Gordon, T.4
-
39
-
-
84859950079
-
Optimizing Solute-Water van der Waals Interactions to Reproduce Solvation Free Energies
-
Nerenberg, P. S.; Jo, B.; So, C.; Tripathy, A.; Head-Gordon, T. Optimizing Solute-Water van der Waals Interactions to Reproduce Solvation Free Energies J. Phys. Chem. B 2012, 116, 4524-4534 10.1021/jp2118373
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 4524-4534
-
-
Nerenberg, P.S.1
Jo, B.2
So, C.3
Tripathy, A.4
Head-Gordon, T.5
-
40
-
-
84909598675
-
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
-
Best, R. B.; Zheng, W.; Mittal, J. Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association J. Chem. Theory Comput. 2014, 10, 5113-5124 10.1021/ct500569b
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 5113-5124
-
-
Best, R.B.1
Zheng, W.2
Mittal, J.3
-
41
-
-
84928503362
-
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States
-
Piana, S.; Donchev, A. G.; Robustelli, P.; Shaw, D. E. Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States J. Phys. Chem. B 2015, 119, 5113-5123 10.1021/jp508971m
-
(2015)
J. Phys. Chem. B
, vol.119
, pp. 5113-5123
-
-
Piana, S.1
Donchev, A.G.2
Robustelli, P.3
Shaw, D.E.4
-
42
-
-
84855431691
-
2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems
-
2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems J. Phys. Chem. Lett. 2012, 3, 45-50 10.1021/jz201501a
-
(2012)
J. Phys. Chem. Lett.
, vol.3
, pp. 45-50
-
-
Yoo, J.1
Aksimentiev, A.2
-
43
-
-
0001533502
-
Measurement of the Repulsive Force between Polyelectrolyte Molecules in Ionic Solution: Hydration Forces between Parallel DNA Double Helices
-
Rau, D. C.; Lee, B.; Parsegian, V. A. Measurement of the Repulsive Force Between Polyelectrolyte Molecules in Ionic Solution: Hydration Forces Between Parallel DNA Double Helices Proc. Natl. Acad. Sci. U. S. A. 1984, 81, 2621-2625 10.1073/pnas.81.9.2621
-
(1984)
Proc. Natl. Acad. Sci. U. S. A.
, vol.81
, pp. 2621-2625
-
-
Rau, D.C.1
Lee, B.2
Parsegian, V.A.3
-
44
-
-
77149136136
-
Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions
-
Luo, Y.; Roux, B. Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions J. Phys. Chem. Lett. 2009, 1, 183-9 10.1021/jz900079w
-
(2009)
J. Phys. Chem. Lett.
, vol.1
, pp. 183-189
-
-
Luo, Y.1
Roux, B.2
-
45
-
-
7244251461
-
Control of Ion Selectivity in Potassium Channels by Electrostatic and Dynamic Properties of Carbonyl Ligands
-
Noskov, S. Y.; Berneche, S.; Roux, B. Control of Ion Selectivity in Potassium Channels by Electrostatic and Dynamic Properties of Carbonyl Ligands Nature 2004, 431, 830-834 10.1038/nature02943
-
(2004)
Nature
, vol.431
, pp. 830-834
-
-
Noskov, S.Y.1
Berneche, S.2
Roux, B.3
-
46
-
-
84868242573
-
Competitive Binding of Cations to Duplex DNA Revealed Through Molecular Dynamics Simulations
-
Yoo, J.; Aksimentiev, A. Competitive Binding of Cations to Duplex DNA Revealed Through Molecular Dynamics Simulations J. Phys. Chem. B 2012, 116, 12946-12954 10.1021/jp306598y
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 12946-12954
-
-
Yoo, J.1
Aksimentiev, A.2
-
47
-
-
84907452614
-
Close Encounters with DNA
-
Maffeo, C.; Yoo, J.; Comer, J.; Wells, D. B.; Luan, B.; Aksimentiev, A. Close Encounters With DNA J. Phys.: Condens. Matter 2014, 26, 413101 10.1088/0953-8984/26/41/413101
-
(2014)
J. Phys.: Condens. Matter
, vol.26
, pp. 413101
-
-
Maffeo, C.1
Yoo, J.2
Comer, J.3
Wells, D.B.4
Luan, B.5
Aksimentiev, A.6
-
48
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935 10.1063/1.445869
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
49
-
-
10844247921
-
A Modified TIP3P Water Potential for Simulation with Ewald Summation
-
Price, D. J.; Brooks, C. L., III A Modified TIP3P Water Potential for Simulation With Ewald Summation J. Chem. Phys. 2004, 121, 10096 10.1063/1.1808117
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 10096
-
-
Price, D.J.1
Brooks, C.L.2
-
50
-
-
0001655657
-
Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations
-
Beglov, D.; Roux, B. Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations J. Chem. Phys. 1994, 100, 9050-9063 10.1063/1.466711
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9050-9063
-
-
Beglov, D.1
Roux, B.2
-
51
-
-
0001274151
-
Sulfate Anion in Water - Model Structural, Thermodynamic, and Dynamic Properties
-
Cannon, W. R.; Pettitt, B. M.; McCammon, J. A. Sulfate Anion in Water-Model Structural, Thermodynamic, and Dynamic Properties J. Phys. Chem. 1994, 98, 6225-6230 10.1021/j100075a027
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 6225-6230
-
-
Cannon, W.R.1
Pettitt, B.M.2
McCammon, J.A.3
-
52
-
-
84865124149
-
Thermodynamics of Transport Through the Ammonium Transporter Amt-1 Investigated with Free Energy Calculations
-
Ullmann, R. T.; Andrade, S. L. A.; Ullmann, G. M. Thermodynamics of Transport Through the Ammonium Transporter Amt-1 Investigated with Free Energy Calculations J. Phys. Chem. B 2012, 116, 9690-9703 10.1021/jp305440f
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 9690-9703
-
-
Ullmann, R.T.1
Andrade, S.L.A.2
Ullmann, G.M.3
-
53
-
-
79954518426
-
Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides
-
Nerenberg, P. S.; Head-Gordon, T. Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides J. Chem. Theory Comput. 2011, 7, 1220-1230 10.1021/ct2000183
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1220-1230
-
-
Nerenberg, P.S.1
Head-Gordon, T.2
-
54
-
-
84859611714
-
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements
-
Beauchamp, K. A.; Lin, Y.-S. S.; Das, R.; Pande, V. S. Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements J. Chem. Theory Comput. 2012, 8, 1409-1414 10.1021/ct2007814
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1409-1414
-
-
Beauchamp, K.A.1
Lin, Y.-S.S.2
Das, R.3
Pande, V.S.4
-
55
-
-
49449085241
-
Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
-
Joung, I. S.; Cheatham, T. E. Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations J. Phys. Chem. B 2008, 112, 9020-9041 10.1021/jp8001614
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9020-9041
-
-
Joung, I.S.1
Cheatham, T.E.2
-
56
-
-
27344436659
-
Scalable Molecular Dynamics with NAMD
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802 10.1002/jcc.20289
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
57
-
-
33645542434
-
The Electromechanics of DNA in a Synthetic Nanopore
-
Heng, J. B.; Aksimentiev, A.; Ho, C.; Marks, P.; Grinkova, Y. V.; Sligar, S.; Schulten, K.; Timp, G. The Electromechanics of DNA in a Synthetic Nanopore Biophys. J. 2006, 90, 1098-1106 10.1529/biophysj.105.070672
-
(2006)
Biophys. J.
, vol.90
, pp. 1098-1106
-
-
Heng, J.B.1
Aksimentiev, A.2
Ho, C.3
Marks, P.4
Grinkova, Y.V.5
Sligar, S.6
Schulten, K.7
Timp, G.8
-
58
-
-
34547925931
-
Advantages of a Lowe-Andersen Thermostat in Molecular Dynamics Simulations
-
Koopman, E. A.; Lowe, C. P. Advantages of a Lowe-Andersen Thermostat in Molecular Dynamics Simulations J. Chem. Phys. 2006, 124, 204103 10.1063/1.2198824
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 204103
-
-
Koopman, E.A.1
Lowe, C.P.2
-
59
-
-
46249092554
-
GROMACS 4: Algorithms for Highly Efficient, Load-balanced, and Scalable Molecular Simulation
-
Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 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
-
60
-
-
84926811618
-
Constant Pressure Molecular Dynamics for Molecular Systems
-
Nose, S.; Klein, M. L. Constant Pressure Molecular Dynamics for Molecular Systems Mol. Phys. 1983, 50, 1055-76 10.1080/00268978300102851
-
(1983)
Mol. Phys.
, vol.50
, pp. 1055-1076
-
-
Nose, S.1
Klein, M.L.2
-
61
-
-
0001538909
-
Canonical Dynamics: Equilibrium Phase-space Distributions
-
Hoover, W. G. Canonical Dynamics: Equilibrium Phase-space Distributions Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695-1697 10.1103/PhysRevA.31.1695
-
(1985)
Phys. Rev. A: At., Mol., Opt. Phys.
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
62
-
-
0019707626
-
Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method
-
Parrinello, M.; Rahman, A. Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method J. Appl. Phys. 1981, 52, 7182-90 10.1063/1.328693
-
(1981)
J. Appl. Phys.
, vol.52
, pp. 7182-7190
-
-
Parrinello, M.1
Rahman, A.2
-
63
-
-
33846823909
-
Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems
-
Darden, T. A.; York, D.; Pedersen, L. Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-92 10.1063/1.464397
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.A.1
York, D.2
Pedersen, L.3
-
64
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
-
Miyamoto, S.; Kollman, P. A. SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models J. Comput. Chem. 1992, 13, 952-62 10.1002/jcc.540130805
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
65
-
-
0000388705
-
LINCS: A Linear Constraint Solver for Molecular Simulations
-
Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463-72 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.C.3
Fraaije, J.G.E.M.4
-
66
-
-
45849137851
-
Attractive Forces between Cation Condensed DNA Double Helices
-
Todd, B. A.; Parsegian, V. A.; Shirahata, A.; Thomas, T. J.; Rau, D. C. Attractive Forces Between Cation Condensed DNA Double Helices Biophys. J. 2008, 94, 4775-82 10.1529/biophysj.107.127332
-
(2008)
Biophys. J.
, vol.94
, pp. 4775-4782
-
-
Todd, B.A.1
Parsegian, V.A.2
Shirahata, A.3
Thomas, T.J.4
Rau, D.C.5
-
67
-
-
84986519238
-
The Weighted Histogram Analysis Method for Free-energy Calculations on Biomolecules. I. the Method
-
Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. The Weighted Histogram Analysis Method for Free-energy Calculations on Biomolecules. I. The Method J. Comput. Chem. 1992, 13, 1011-1021 10.1002/jcc.540130812
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Rosenberg, J.M.2
Bouzida, D.3
Swendsen, R.H.4
Kollman, P.A.5
-
68
-
-
67650500988
-
CHARMM: The Biomolecular Simulation Program
-
Brooks, B. R.; Brooks, C. L.; MacKerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: the Biomolecular Simulation Program J. Comput. Chem. 2009, 30, 1545-614 10.1002/jcc.21287
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks, C.L.2
MacKerell, A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
69
-
-
84892868149
-
New Faster CHARMM Molecular Dynamics Engine
-
Hynninen, A.-P.; Crowley, M. F. New Faster CHARMM Molecular Dynamics Engine J. Comput. Chem. 2014, 35, 406-413 10.1002/jcc.23501
-
(2014)
J. Comput. Chem.
, vol.35
, pp. 406-413
-
-
Hynninen, A.-P.1
Crowley, M.F.2
-
70
-
-
84954459096
-
-
accessed January 15
-
Klauda, J. B. http://terpconnect.umd.edu/~jbklauda/research/download.html (accessed January 15, 2015).
-
(2015)
-
-
Klauda, J.B.1
-
71
-
-
34249652309
-
Water Activity and Osmotic Coefficients in Solutions of Glycine, Glutamic Acid, Histidine and Their Salts at 298.15 and 310.15 K
-
Tsurko, E.; Neueder, R.; Kunz, W. Water Activity and Osmotic Coefficients in Solutions of Glycine, Glutamic Acid, Histidine and Their Salts at 298.15 and 310.15 K J. Solution Chem. 2007, 36, 651-672 10.1007/s10953-007-9131-8
-
(2007)
J. Solution Chem.
, vol.36
, pp. 651-672
-
-
Tsurko, E.1
Neueder, R.2
Kunz, W.3
-
72
-
-
0037442915
-
Potentials of Mean Force between Ionizable Amino Acid Side Chains in Water
-
Masunov, A.; Lazaridis, T. Potentials of Mean Force Between Ionizable Amino Acid Side Chains in Water J. Am. Chem. Soc. 2003, 125, 1722-30 10.1021/ja025521w
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 1722-1730
-
-
Masunov, A.1
Lazaridis, T.2
-
75
-
-
33748591572
-
Enzymatic Mechanisms of Phosphate and Sulfate Transfer
-
Cleland, W. W.; Hengge, A. C. Enzymatic Mechanisms of Phosphate and Sulfate Transfer Chem. Rev. 2006, 106, 3252-78 10.1021/cr050287o
-
(2006)
Chem. Rev.
, vol.106
, pp. 3252-3278
-
-
Cleland, W.W.1
Hengge, A.C.2
-
76
-
-
34247842883
-
Sulfate Acts as Phosphate Analog on the Monomeric Catalytic Fragment of the CPx-ATPase CopB from Sulfolobus Solfataricus
-
Lübben, M.; Güldenhaupt, J.; Zoltner, M.; Deigweiher, K.; Haebel, P.; Urbanke, C.; Scheidig, A. J. Sulfate Acts as Phosphate Analog on the Monomeric Catalytic Fragment of the CPx-ATPase CopB from Sulfolobus Solfataricus J. Mol. Biol. 2007, 369, 368-85 10.1016/j.jmb.2007.03.029
-
(2007)
J. Mol. Biol.
, vol.369
, pp. 368-385
-
-
Lübben, M.1
Güldenhaupt, J.2
Zoltner, M.3
Deigweiher, K.4
Haebel, P.5
Urbanke, C.6
Scheidig, A.J.7
-
77
-
-
0027943884
-
A Structural Analysis of Phosphate and Sulphate Binding Sites in Proteins: Estimation of Propensities for Binding and Conservation of Phosphate Binding Sites
-
Copley, R. R.; Barton, G. J. A Structural Analysis of Phosphate and Sulphate Binding Sites in Proteins: Estimation of Propensities for Binding and Conservation of Phosphate Binding Sites J. Mol. Biol. 1994, 242, 321-329 10.1006/jmbi.1994.1583
-
(1994)
J. Mol. Biol.
, vol.242
, pp. 321-329
-
-
Copley, R.R.1
Barton, G.J.2
-
78
-
-
35848935027
-
Crystal Structure of Monofunctional Histidinol Phosphate Phosphatase from Thermus Thermophilus HB8
-
Omi, R.; Goto, M.; Miyahara, I.; Manzoku, M.; Ebihara, A.; Hirotsu, K. Crystal Structure of Monofunctional Histidinol Phosphate Phosphatase from Thermus Thermophilus HB8 Biochemistry 2007, 46, 12618-12627 10.1021/bi701204r
-
(2007)
Biochemistry
, vol.46
, pp. 12618-12627
-
-
Omi, R.1
Goto, M.2
Miyahara, I.3
Manzoku, M.4
Ebihara, A.5
Hirotsu, K.6
-
79
-
-
78349236903
-
Potential Anti-bacterial Drug Target: Structural Characterization of 3.4-dihydroxy-2-butanone-4-phosphate Synthase from Salmonella Typhimurium LT2
-
Kumar, P.; Singh, M.; Gautam, R.; Karthikeyan, S. Potential Anti-bacterial Drug Target: Structural Characterization of 3.4-dihydroxy-2-butanone-4-phosphate Synthase from Salmonella Typhimurium LT2 Proteins: Struct., Funct., Genet. 2010, 78, 3292-303 10.1002/prot.22837
-
(2010)
Proteins: Struct., Funct., Genet.
, vol.78
, pp. 3292-3303
-
-
Kumar, P.1
Singh, M.2
Gautam, R.3
Karthikeyan, S.4
-
80
-
-
84873667995
-
Structural and Mechanistic Characterization of l-Histidinol Phosphate Phosphatase from the Polymerase and Histidinol Phosphatase Family of Proteins
-
Ghodge, S. V.; Fedorov, A. A.; Fedorov, E. V.; Hillerich, B.; Seidel, R.; Almo, S. C.; Raushel, F. M. Structural and Mechanistic Characterization of l-Histidinol Phosphate Phosphatase from the Polymerase and Histidinol Phosphatase Family of Proteins Biochemistry 2013, 52, 1101-1112 10.1021/bi301496p
-
(2013)
Biochemistry
, vol.52
, pp. 1101-1112
-
-
Ghodge, S.V.1
Fedorov, A.A.2
Fedorov, E.V.3
Hillerich, B.4
Seidel, R.5
Almo, S.C.6
Raushel, F.M.7
-
81
-
-
76249087938
-
CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields
-
Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; MacKerell, A. D., Jr. CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields J. Comput. Chem. 2010, 31, 671-690 10.1002/jcc.21367
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 671-690
-
-
Vanommeslaeghe, K.1
Hatcher, E.2
Acharya, C.3
Kundu, S.4
Zhong, S.5
Shim, J.6
Darian, E.7
Guvench, O.8
Lopes, P.9
Vorobyov, I.10
MacKerell, A.D.11
-
82
-
-
41149115685
-
Molecular Dynamics Simulation of Multivalent-ion Mediated Attraction between DNA Molecules
-
Dai, L.; Mu, Y.; Nordenskiöld, L.; van der Maarel, J. R. C. Molecular Dynamics Simulation of Multivalent-ion Mediated Attraction Between DNA Molecules Phys. Rev. Lett. 2008, 100, 118301 10.1103/PhysRevLett.100.118301
-
(2008)
Phys. Rev. Lett.
, vol.100
, pp. 118301
-
-
Dai, L.1
Mu, Y.2
Nordenskiöld, L.3
Van Der Maarel, J.R.C.4
-
83
-
-
84857393452
-
Volume Exclusion and H-Bonding Dominate the Thermodynamics and Solvation of Trimethylamine-N-oxide in Aqueous Urea
-
Rösgen, J.; Jackson-Atogi, R. Volume Exclusion and H-Bonding Dominate the Thermodynamics and Solvation of Trimethylamine-N-oxide in Aqueous Urea J. Am. Chem. Soc. 2012, 134, 3590-3597 10.1021/ja211530n
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 3590-3597
-
-
Rösgen, J.1
Jackson-Atogi, R.2
-
84
-
-
84877011320
-
A Comparison of DNA Compaction by Arginine and Lysine Peptides: A Physical Basis for Arginine Rich Protamines
-
DeRouchey, J.; Hoover, B.; Rau, D. C. A Comparison of DNA Compaction by Arginine and Lysine Peptides: A Physical Basis for Arginine Rich Protamines Biochemistry 2013, 52, 3000-3009 10.1021/bi4001408
-
(2013)
Biochemistry
, vol.52
, pp. 3000-3009
-
-
DeRouchey, J.1
Hoover, B.2
Rau, D.C.3
-
85
-
-
84861375893
-
End-to-end Attraction of Duplex DNA
-
Maffeo, C.; Luan, B.; Aksimentiev, A. End-to-end Attraction of Duplex DNA Nucleic Acids Res. 2012, 40, 3812-3821 10.1093/nar/gkr1220
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 3812-3821
-
-
Maffeo, C.1
Luan, B.2
Aksimentiev, A.3
-
86
-
-
56749160319
-
DNA Attraction in Monovalent and Divalent Electrolytes
-
Luan, B.; Aksimentiev, A. DNA Attraction in Monovalent and Divalent Electrolytes J. Am. Chem. Soc. 2008, 130, 15754-15755 10.1021/ja804802u
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 15754-15755
-
-
Luan, B.1
Aksimentiev, A.2
-
87
-
-
77957562056
-
DNA-DNA Interactions in Tight Supercoils Are Described by a Small Effective Charge Density
-
Maffeo, C.; Schöpflin, R.; Brutzer, H.; Stehr, R.; Aksimentiev, A.; Wedemann, G.; Seidel, R. DNA-DNA Interactions in Tight Supercoils Are Described by a Small Effective Charge Density Phys. Rev. Lett. 2010, 105, 158101 10.1103/PhysRevLett.105.158101
-
(2010)
Phys. Rev. Lett.
, vol.105
, pp. 158101
-
-
Maffeo, C.1
Schöpflin, R.2
Brutzer, H.3
Stehr, R.4
Aksimentiev, A.5
Wedemann, G.6
Seidel, R.7
-
88
-
-
0033637460
-
Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by (2)H NMR Spectroscopy
-
Petrache, H. I.; Dodd, S. W.; Brown, M. F. Area Per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by (2)H NMR Spectroscopy Biophys. J. 2000, 79, 3172-92 10.1016/S0006-3495(00)76551-9
-
(2000)
Biophys. J.
, vol.79
, pp. 3172-3192
-
-
Petrache, H.I.1
Dodd, S.W.2
Brown, M.F.3
-
89
-
-
1542289943
-
Structure and Fluctuations of Charged Phosphatidylserine Bilayers in the Absence of Salt
-
Petrache, H. I.; Tristram-Nagle, S.; Gawrisch, K.; Harries, D.; Parsegian, V. A.; Nagle, J. F. Structure and Fluctuations of Charged Phosphatidylserine Bilayers in the Absence of Salt Biophys. J. 2004, 86, 1574 10.1016/S0006-3495(04)74225-3
-
(2004)
Biophys. J.
, vol.86
, pp. 1574
-
-
Petrache, H.I.1
Tristram-Nagle, S.2
Gawrisch, K.3
Harries, D.4
Parsegian, V.A.5
Nagle, J.F.6
-
90
-
-
45849126131
-
-
Feller, S. E. Elsevier
-
Klauda, J. B.; Venable, R. M.; MacKerell, A. D., Jr.; Pastor, R. W. In Current Topics in Membranes; Feller, S. E., Ed.; Elsevier, 2008; Vol. 60, pp 1-48.
-
(2008)
Current Topics in Membranes
, vol.60
, pp. 1-48
-
-
Klauda, J.B.1
Venable, R.M.2
MacKerell, A.D.3
Pastor, R.W.4
-
91
-
-
0032421354
-
Functions of Lipid Rafts in Biological Membranes
-
Brown, D. A.; London, E. Functions of Lipid Rafts in Biological Membranes Annu. Rev. Cell Dev. Biol. 1998, 14, 111-136 10.1146/annurev.cellbio.14.1.111
-
(1998)
Annu. Rev. Cell Dev. Biol.
, vol.14
, pp. 111-136
-
-
Brown, D.A.1
London, E.2
|