메뉴 건너뛰기




Volumn 7, Issue 6, 2012, Pages

Simulation vs. reality: A comparison of in silico distance predictions with DEER and FRET measurements

Author keywords

[No Author keywords available]

Indexed keywords

NITROXIDE; PROTEIN RPO4; PROTEIN RPO7; RECOMBINANT PROTEIN; RNA POLYMERASE; UNCLASSIFIED DRUG; WATER;

EID: 84862668293     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039492     Document Type: Article
Times cited : (63)

References (69)
  • 2
    • 44649094094 scopus 로고    scopus 로고
    • Fluorescence resonance energy transfer: techniques for measuring molecular conformation and molecular proximity
    • Unit 18.10
    • Edidin M, (2003) Fluorescence resonance energy transfer: techniques for measuring molecular conformation and molecular proximity. Curr Prot Immunol Chapter 18: Unit 18.10.
    • (2003) Curr Prot Immunol Chapter , vol.18
    • Edidin, M.1
  • 3
    • 34548317408 scopus 로고    scopus 로고
    • Long-range distance determinations in biomacromolecules by EPR spectroscopy
    • Schiemann O, Prisner TF, (2007) Long-range distance determinations in biomacromolecules by EPR spectroscopy. Q Rev Biophys 40: 1-53.
    • (2007) Q Rev Biophys , vol.40 , pp. 1-53
    • Schiemann, O.1    Prisner, T.F.2
  • 4
    • 61349166815 scopus 로고    scopus 로고
    • Membrane protein structure and dynamics studied by site-directed spin labeling ESR
    • Hemminga, M. A., Berliner, L. J., Eds.; New York: Springer Science and Business Media
    • Bordignon E, Steinhoff HJ, (2007) Membrane protein structure and dynamics studied by site-directed spin labeling ESR. In ESR Spectroscopy in Membrane Biophysics, Hemminga, M. A., Berliner, L. J., Eds.; New York: Springer Science and Business Media. Pp pp. 129-164.
    • (2007) ESR Spectroscopy in Membrane Biophysics , pp. 129-164
    • Bordignon, E.1    Steinhoff, H.J.2
  • 5
    • 27744599888 scopus 로고
    • Transfer mechanisms of electronic excitation
    • Förster T, (1959) Transfer mechanisms of electronic excitation. Discuss Faraday Soc 27: 7-17.
    • (1959) Discuss Faraday Soc , vol.27 , pp. 7-17
    • Förster, T.1
  • 6
    • 79960440046 scopus 로고    scopus 로고
    • The Initiation Factor TFE and the Elongation Factor Spt4/5 Compete for the RNAP Clamp during Transcription Initiation and Elongation
    • Grohmann D, Nagy J, Chakraborty A, Klose D, Fielden D, et al. (2011) The Initiation Factor TFE and the Elongation Factor Spt4/5 Compete for the RNAP Clamp during Transcription Initiation and Elongation. Mol Cell 43: 263-274.
    • (2011) Mol Cell , vol.43 , pp. 263-274
    • Grohmann, D.1    Nagy, J.2    Chakraborty, A.3    Klose, D.4    Fielden, D.5
  • 7
    • 0029987587 scopus 로고    scopus 로고
    • Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor
    • Ha T, Enderle T, Ogletree DF, Chemla DS, Selvin PR, et al. (1996) Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc Natl Acad Sci U S A 93: 6264-6268.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 6264-6268
    • Ha, T.1    Enderle, T.2    Ogletree, D.F.3    Chemla, D.S.4    Selvin, P.R.5
  • 8
    • 77954641162 scopus 로고    scopus 로고
    • Accurate Single-Molecule FRET Studies Using Multiparameter Fluorescence Detection
    • Sisamakis E, Valeri A, Kalinin S, Rothwell PJ, Seidel CAM, (2010) Accurate Single-Molecule FRET Studies Using Multiparameter Fluorescence Detection. Method Enzymol 475: 455-514.
    • (2010) Method Enzymol , vol.475 , pp. 455-514
    • Sisamakis, E.1    Valeri, A.2    Kalinin, S.3    Rothwell, P.J.4    Seidel, C.A.M.5
  • 9
    • 34247540806 scopus 로고    scopus 로고
    • Pulsed ELDOR Determination of the Intramolecular Distance between the Metal Binding Sites in Dicupric Human Serum Transferrin and Lactoferrin
    • Kay CWM, El Mkami H, Cammack R, Evans RW, (2007) Pulsed ELDOR Determination of the Intramolecular Distance between the Metal Binding Sites in Dicupric Human Serum Transferrin and Lactoferrin. J Am Chem Soc 129: 4868-4869.
    • (2007) J Am Chem Soc , vol.129 , pp. 4868-4869
    • Kay, C.W.M.1    El Mkami, H.2    Cammack, R.3    Evans, R.W.4
  • 10
    • 30744436853 scopus 로고    scopus 로고
    • Determination of the Distance between the Two Neutral Flavin Radicals in Augmenter of Liver Regeneration by Pulsed ELDOR
    • Kay CWM, Elsässer C, Bittl R, Farrell SR, Thorpe C, (2006) Determination of the Distance between the Two Neutral Flavin Radicals in Augmenter of Liver Regeneration by Pulsed ELDOR. J Am Chem Soc 128: 76-77.
    • (2006) J Am Chem Soc , vol.128 , pp. 76-77
    • Kay, C.W.M.1    Elsässer, C.2    Bittl, R.3    Farrell, S.R.4    Thorpe, C.5
  • 11
    • 0024974071 scopus 로고
    • Structural studies on transmembrane proteins. 2. Spin labelling of bacteriorhodopsin mutants at unique cysteines
    • Altenbach C, Flitsch SL, Khorana HG, Hubbell WL, (1989) Structural studies on transmembrane proteins. 2. Spin labelling of bacteriorhodopsin mutants at unique cysteines. Biochemistry 28: 7806-7812.
    • (1989) Biochemistry , vol.28 , pp. 7806-7812
    • Altenbach, C.1    Flitsch, S.L.2    Khorana, H.G.3    Hubbell, W.L.4
  • 13
    • 33645472931 scopus 로고    scopus 로고
    • Site-directed Parallel Spin-Labeling and Paramagnetic Relaxation Enhancement in Structure Determination of Membrane Proteins by Solution NMR Spectroscopy
    • Liang B, Bushweller BH, Tamm LK, (2006) Site-directed Parallel Spin-Labeling and Paramagnetic Relaxation Enhancement in Structure Determination of Membrane Proteins by Solution NMR Spectroscopy. J Am Chem Soc 128: 4389-4397.
    • (2006) J Am Chem Soc , vol.128 , pp. 4389-4397
    • Liang, B.1    Bushweller, B.H.2    Tamm, L.K.3
  • 14
    • 78651504121 scopus 로고    scopus 로고
    • Evolution of multisubunit RNA polymerases in the three domains of life
    • Werner F, Grohmann D, (2011) Evolution of multisubunit RNA polymerases in the three domains of life. Nat Rev Microbiol 9: 85-98.
    • (2011) Nat Rev Microbiol , vol.9 , pp. 85-98
    • Werner, F.1    Grohmann, D.2
  • 15
    • 77955059733 scopus 로고    scopus 로고
    • Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif
    • Hirtreiter A, Damsma GE, Cheung ACM, Klose D, Grohmann D, et al. (2010) Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif. Nucl Acids Res 38: 4040-4051.
    • (2010) Nucl Acids Res , vol.38 , pp. 4040-4051
    • Hirtreiter, A.1    Damsma, G.E.2    Cheung, A.C.M.3    Klose, D.4    Grohmann, D.5
  • 16
    • 77951691467 scopus 로고    scopus 로고
    • RNA-Binding to Archaeal RNA Polymerase Subunits F/E: A DEER and FRET Study
    • Grohmann D, Klose D, Klare JP, Kay CWM, Steinhoff HJ, et al. (2010) RNA-Binding to Archaeal RNA Polymerase Subunits F/E: A DEER and FRET Study. J Am Chem Soc 132: 5954-5955.
    • (2010) J Am Chem Soc , vol.132 , pp. 5954-5955
    • Grohmann, D.1    Klose, D.2    Klare, J.P.3    Kay, C.W.M.4    Steinhoff, H.J.5
  • 17
    • 28544436370 scopus 로고    scopus 로고
    • Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II
    • Meka H, Werner F, Cordell SC, Onesti S, Brick P, (2005) Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II. Nucl Acids Res 33: 6435-6444.
    • (2005) Nucl Acids Res , vol.33 , pp. 6435-6444
    • Meka, H.1    Werner, F.2    Cordell, S.C.3    Onesti, S.4    Brick, P.5
  • 19
    • 70349617706 scopus 로고    scopus 로고
    • Generalized Temperature Measurement Equations for Rhodamine B Dye Solution and Its Application to Microfluidics
    • Shah JJ, Gaitan M, Geist J, (2009) Generalized Temperature Measurement Equations for Rhodamine B Dye Solution and Its Application to Microfluidics. Anal Chem 81: 8260-8263.
    • (2009) Anal Chem , vol.81 , pp. 8260-8263
    • Shah, J.J.1    Gaitan, M.2    Geist, J.3
  • 20
    • 0035930324 scopus 로고    scopus 로고
    • Structure of an Archaeal Homolog of the Eukaryotic RNA Polymerase II RPB4/RPB7 Complex
    • Todone F, Brick P, Werner F, Weinzierl ROJ, Onesti S, (2001) Structure of an Archaeal Homolog of the Eukaryotic RNA Polymerase II RPB4/RPB7 Complex. Mol Cell 8: 1137-1143.
    • (2001) Mol Cell , vol.8 , pp. 1137-1143
    • Todone, F.1    Brick, P.2    Werner, F.3    Weinzierl, R.O.J.4    Onesti, S.5
  • 21
    • 0036180593 scopus 로고    scopus 로고
    • Fluorescence resonance energy transfer (FRET) and competing processes in donor-acceptor substituted DNA strands: a comparative study of ensemble and single-molecule data
    • Dietrich A, Buschmann V, Müller C, Sauer M, (2002) Fluorescence resonance energy transfer (FRET) and competing processes in donor-acceptor substituted DNA strands: a comparative study of ensemble and single-molecule data. Rev Mol Biotechnol 82: 211-231.
    • (2002) Rev Mol Biotechnol , vol.82 , pp. 211-231
    • Dietrich, A.1    Buschmann, V.2    Müller, C.3    Sauer, M.4
  • 22
    • 0036835759 scopus 로고    scopus 로고
    • Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes
    • Marras SAE, Kramer FR, Tyagi S, (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucl Acids Res 30: e122.
    • (2002) Nucl Acids Res , vol.30
    • Marras, S.A.E.1    Kramer, F.R.2    Tyagi, S.3
  • 24
    • 0026640565 scopus 로고
    • Orientation factor in steady-state and time-resolved resonance energy transfer measurements
    • Wu P, Brand L, (1992) Orientation factor in steady-state and time-resolved resonance energy transfer measurements. Biochem 31: 7939-7947.
    • (1992) Biochem , vol.31 , pp. 7939-7947
    • Wu, P.1    Brand, L.2
  • 25
    • 0028884014 scopus 로고
    • Fluorescence Resonance Energy Transfer Spectroscopy Is a Reliable "Ruler" for Measuring Structural Changes in Proteins: Dispelling the Problem of the Unknown Orientation Factor
    • dos Remedios CG, Moens PDJ, (1995) Fluorescence Resonance Energy Transfer Spectroscopy Is a Reliable "Ruler" for Measuring Structural Changes in Proteins: Dispelling the Problem of the Unknown Orientation Factor. J Struct Biol 115: 175-185.
    • (1995) J Struct Biol , vol.115 , pp. 175-185
    • dos Remedios, C.G.1    Moens, P.D.J.2
  • 26
    • 0026687952 scopus 로고
    • Fluorescence resonance energy transfer and nucleic acids
    • Clegg RM, (1992) Fluorescence resonance energy transfer and nucleic acids. Method Enzymol 211: 353-388.
    • (1992) Method Enzymol , vol.211 , pp. 353-388
    • Clegg, R.M.1
  • 27
    • 23644433196 scopus 로고    scopus 로고
    • Measurements of Internal Distance Changes of the 30 S Ribosome Using FRET with Multiple Donor-Acceptor Pairs: Quantitative Spectroscopic Methods
    • Majumdar ZK, Hickerson R, Noller HF, Clegg RM, (2005) Measurements of Internal Distance Changes of the 30 S Ribosome Using FRET with Multiple Donor-Acceptor Pairs: Quantitative Spectroscopic Methods. J Mol Biol 351: 1123-1145.
    • (2005) J Mol Biol , vol.351 , pp. 1123-1145
    • Majumdar, Z.K.1    Hickerson, R.2    Noller, H.F.3    Clegg, R.M.4
  • 28
    • 38949171385 scopus 로고    scopus 로고
    • De Novo High-Resolution Structure Determination from Sparse Spin-Labeling EPR Data
    • Alexander N, Al-Mestarihi A, Bortolus M, Mchaourab HS, Meiler S, (2008) De Novo High-Resolution Structure Determination from Sparse Spin-Labeling EPR Data. Structure 16: 181-195.
    • (2008) Structure , vol.16 , pp. 181-195
    • Alexander, N.1    Al-Mestarihi, A.2    Bortolus, M.3    Mchaourab, H.S.4    Meiler, S.5
  • 29
    • 79251562868 scopus 로고    scopus 로고
    • Rotamer libraries of spin labelled cysteines for protein studies
    • Polyhach Y, Bordignon E, Jeschke G, (2011) Rotamer libraries of spin labelled cysteines for protein studies. Phys Chem Chem Phys 13: 2356-2366.
    • (2011) Phys Chem Chem Phys , vol.13 , pp. 2356-2366
    • Polyhach, Y.1    Bordignon, E.2    Jeschke, G.3
  • 30
    • 55549120565 scopus 로고    scopus 로고
    • Simulation of Structure, Orientation, and Energy Transfer between AlexaFluor Molecules Attached to MscL
    • Corry B, Jayatilaka D, (2008) Simulation of Structure, Orientation, and Energy Transfer between AlexaFluor Molecules Attached to MscL. Biophys J 95: 2711-2721.
    • (2008) Biophys J , vol.95 , pp. 2711-2721
    • Corry, B.1    Jayatilaka, D.2
  • 31
    • 28444473536 scopus 로고    scopus 로고
    • Simulation of Fluorescence Anisotropy Experiments: Probing Protein Dynamics
    • Schröder GF, Alexiev U, Grubmüller H, (2005) Simulation of Fluorescence Anisotropy Experiments: Probing Protein Dynamics. Biophys J 89: 3757-3770.
    • (2005) Biophys J , vol.89 , pp. 3757-3770
    • Schröder, G.F.1    Alexiev, U.2    Grubmüller, H.3
  • 33
    • 8344224484 scopus 로고    scopus 로고
    • Inter- and intra-molecular distances determined by EPR spectroscopy and site-directed spin labeling reveal protein-protein and protein-oligonucleotide interaction
    • Steinhoff HJ, (2004) Inter- and intra-molecular distances determined by EPR spectroscopy and site-directed spin labeling reveal protein-protein and protein-oligonucleotide interaction. Biol Chem 385: 913-920.
    • (2004) Biol Chem , vol.385 , pp. 913-920
    • Steinhoff, H.J.1
  • 34
    • 68349083357 scopus 로고    scopus 로고
    • Topology of the amphipathic helices of the colicin A pore-forming domain in E. coli lipid membranes studied by pulse EPR
    • Boehme S, Padmavathi PVL, Holterhues J, Ouchni F, Klare JP, et al. (2009) Topology of the amphipathic helices of the colicin A pore-forming domain in E. coli lipid membranes studied by pulse EPR. Phys Chem Chem Phys 11: 6770-6777.
    • (2009) Phys Chem Chem Phys , vol.11 , pp. 6770-6777
    • Boehme, S.1    Padmavathi, P.V.L.2    Holterhues, J.3    Ouchni, F.4    Klare, J.P.5
  • 35
    • 34147218123 scopus 로고    scopus 로고
    • Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance
    • Jeschke G, Polyhach Y, (2007) Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance. Phys Chem Chem Phys 9: 1895-1910.
    • (2007) Phys Chem Chem Phys , vol.9 , pp. 1895-1910
    • Jeschke, G.1    Polyhach, Y.2
  • 36
    • 33749426764 scopus 로고    scopus 로고
    • A Structure-Based Simulation Approach for Electron Paramagnetic Resonance Spectra Using Molecular and Stochastic Dynamics Simulations
    • Beier C, Steinhoff HJ, (2006) A Structure-Based Simulation Approach for Electron Paramagnetic Resonance Spectra Using Molecular and Stochastic Dynamics Simulations. Biophys J 91: 2647-2664.
    • (2006) Biophys J , vol.91 , pp. 2647-2664
    • Beier, C.1    Steinhoff, H.J.2
  • 37
    • 65649117362 scopus 로고    scopus 로고
    • Structural origin of weakly ordered nitroxide motion in spin-labeled proteins
    • Fleissner MR, Cascio D, Hubbell WL, (2009) Structural origin of weakly ordered nitroxide motion in spin-labeled proteins. Protein Sci pp. 893-908.
    • (2009) Protein Sci , pp. 893-908
    • Fleissner, M.R.1    Cascio, D.2    Hubbell, W.L.3
  • 39
    • 73049092277 scopus 로고    scopus 로고
    • Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex
    • Andrecka J, Treutlein B, Arcusa MAI, Muschielok A, Lewis R, et al. (2009) Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex. Nucl Acids Res 37: 5803-5809.
    • (2009) Nucl Acids Res , vol.37 , pp. 5803-5809
    • Andrecka, J.1    Treutlein, B.2    Arcusa, M.A.I.3    Muschielok, A.4    Lewis, R.5
  • 40
    • 77950366126 scopus 로고    scopus 로고
    • Combining EPR with Fluorescence Spectroscopy to Monitor Conformational Changes at the Myosin Nucleotide Pocket
    • Naber N, Malnasi-Csizmadia A, Purcell TJ, Cooke R, Pate E, (2010) Combining EPR with Fluorescence Spectroscopy to Monitor Conformational Changes at the Myosin Nucleotide Pocket. J Mol Biol 396: 937-948.
    • (2010) J Mol Biol , vol.396 , pp. 937-948
    • Naber, N.1    Malnasi-Csizmadia, A.2    Purcell, T.J.3    Cooke, R.4    Pate, E.5
  • 41
    • 0036753399 scopus 로고    scopus 로고
    • A Recombinant RNA Polymerase II-like Enzyme Capable of Promoter-Specific Transcription
    • Werner F, Weinzierl ROJ, (2002) A Recombinant RNA Polymerase II-like Enzyme Capable of Promoter-Specific Transcription. Mol Cell 10: 635-646.
    • (2002) Mol Cell , vol.10 , pp. 635-646
    • Werner, F.1    Weinzierl, R.O.J.2
  • 42
    • 84862666636 scopus 로고    scopus 로고
    • New York: Springer
    • Principles of Fluorescence Spectroscopy; 3rd edn
    • Lakowicz JR, (2006) New York: Springer. Principles of Fluorescence Spectroscopy; 3rd edn.
    • (2006)
    • Lakowicz, J.R.1
  • 43
    • 0032476844 scopus 로고    scopus 로고
    • Determination of End-to-End Distances in a Series of TEMPO Diradicals of up to 2.8 nm Length with a New Four-Pulse Double Electron Electron Resonance Experiment
    • Martin RE, Pannier M, Diederich F, Gramlich V, Hubrich M, et al. (1998) Determination of End-to-End Distances in a Series of TEMPO Diradicals of up to 2.8 nm Length with a New Four-Pulse Double Electron Electron Resonance Experiment. Angew Chem Int Ed 37: 2833-2837.
    • (1998) Angew Chem Int Ed , vol.37 , pp. 2833-2837
    • Martin, R.E.1    Pannier, M.2    Diederich, F.3    Gramlich, V.4    Hubrich, M.5
  • 44
    • 0034132251 scopus 로고    scopus 로고
    • Dead-Time Free Measurement of Dipole-Dipole Interactions between Electron Spins
    • Pannier M, Veit S, Godt A, Jeschke G, Spiess HW, (2000) Dead-Time Free Measurement of Dipole-Dipole Interactions between Electron Spins. J Magn Res 142: 331-340.
    • (2000) J Magn Res , vol.142 , pp. 331-340
    • Pannier, M.1    Veit, S.2    Godt, A.3    Jeschke, G.4    Spiess, H.W.5
  • 45
    • 33846344623 scopus 로고    scopus 로고
    • DeerAnalysis2006 - a comprehensive software package for analyzing pulsed ELDOR data
    • Jeschke G, Chechik V, Ionita P, Godt A, Zimmermann H, et al. (2006) DeerAnalysis2006- a comprehensive software package for analyzing pulsed ELDOR data. Appl Magn Reson 30: 473-498.
    • (2006) Appl Magn Reson , vol.30 , pp. 473-498
    • Jeschke, G.1    Chechik, V.2    Ionita, P.3    Godt, A.4    Zimmermann, H.5
  • 50
    • 35648987515 scopus 로고    scopus 로고
    • Practical Pulsed Dipolar ESR (DEER)
    • Hemminga, M. A., Berliner, L. J., Eds.; New York: Springer Science and Business Media
    • Fajer PG, Brown L, Song L, (2007) Practical Pulsed Dipolar ESR (DEER). In ESR Spectroscopy in Membrane Biophysics, Hemminga, M. A., Berliner, L. J., Eds.; New York: Springer Science and Business Media. Pp pp. 95-128.
    • (2007) ESR Spectroscopy in Membrane Biophysics , pp. 95-128
    • Fajer, P.G.1    Brown, L.2    Song, L.3
  • 51
    • 5944261746 scopus 로고
    • Density-functional approximation for the correlation energy of the inhomogeneous electron gas
    • Perdew JP, (1986) Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys Rev B 33: 8822.
    • (1986) Phys Rev B , vol.33 , pp. 8822
    • Perdew, J.P.1
  • 52
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic behavior
    • Becke AD, (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38: 3098.
    • (1988) Phys Rev A , vol.38 , pp. 3098
    • Becke, A.D.1
  • 53
    • 0039209924 scopus 로고
    • Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr
    • Schäfer A, Huber C, Ahlrichs R, (1994) Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr. J Chem Phys 100: 5829-5835.
    • (1994) J Chem Phys , vol.100 , pp. 5829-5835
    • Schäfer, A.1    Huber, C.2    Ahlrichs, R.3
  • 54
    • 20344365516 scopus 로고
    • Integral approximations for LCAO-SCF calculations
    • Vahtras O, Almlöf J, Feyereisen MW, (1993) Integral approximations for LCAO-SCF calculations. Chem Phys Lett 213: 514-518.
    • (1993) Chem Phys Lett , vol.213 , pp. 514-518
    • Vahtras, O.1    Almlöf, J.2    Feyereisen, M.W.3
  • 55
    • 84862639112 scopus 로고    scopus 로고
    • an ab initio, Density Functional und Semiempirical Program Package 2.6.0, version 2.6.0
    • ORCA
    • ORCA (2007) an ab initio, Density Functional und Semiempirical Program Package 2.6.0, version 2.6.0.
    • (2007)
  • 56
    • 84986513567 scopus 로고
    • Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis
    • Breneman CM, Wiberg KB, (1990) Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J Comput Chem 11: 361-373.
    • (1990) J Comput Chem , vol.11 , pp. 361-373
    • Breneman, C.M.1    Wiberg, K.B.2
  • 58
    • 48749137581 scopus 로고
    • Stochastic boundary conditions for molecular dynamics simulations of ST2 water
    • Brünger A, Brooks CL, Karplus M, (1984) Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem Phys Lett 105: 495-500.
    • (1984) Chem Phys Lett , vol.105 , pp. 495-500
    • Brünger, A.1    Brooks, C.L.2    Karplus, M.3
  • 59
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N · log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L, (1993) Particle mesh Ewald: An N · log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 60
    • 36449003554 scopus 로고
    • Constant pressure molecular dynamics algorithms
    • Martyna GJ, Tobias DJ, Klein ML, (1994) Constant pressure molecular dynamics algorithms. J Chem Phys 101: 4177-4189.
    • (1994) J Chem Phys , vol.101 , pp. 4177-4189
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3
  • 62
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P, (1995) Knowledge-based protein secondary structure assignment. Proteins 23: 566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 63
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • Sanner MF, Olson AJ, Spehner JC, (1996) Reduced surface: An efficient way to compute molecular surfaces. Biopolymers 38: 305-320.
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 64
    • 0001048849 scopus 로고
    • Stiffness and energy conservation in molecular dynamics: An improved integrator
    • Harrison RW, (1993) Stiffness and energy conservation in molecular dynamics: An improved integrator. J Comput Chem 14: 1112-1122.
    • (1993) J Comput Chem , vol.14 , pp. 1112-1122
    • Harrison, R.W.1
  • 65
    • 0036284090 scopus 로고    scopus 로고
    • VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs
    • Pedretti A, Villa L, Vistoli G, (2002) VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs. J Mol Graph Model 21: 47-49.
    • (2002) J Mol Graph Model , vol.21 , pp. 47-49
    • Pedretti, A.1    Villa, L.2    Vistoli, G.3
  • 67
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • Mackerell AD Jr, Feig M, Brooks CL III, (2004) Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25: 1400-1415.
    • (2004) J Comput Chem , vol.25 , pp. 1400-1415
    • Mackerell Jr., A.D.1    Feig, M.2    Brooks III, C.L.3
  • 68
    • 65649117362 scopus 로고    scopus 로고
    • Protein Sci
    • Fleissner M, Hubbell WL, (2009) Protein Sci. 18(5): 893-908.
    • (2009) , vol.18 , Issue.5 , pp. 893-908
    • Fleissner, M.1    Hubbell, W.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.