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Volumn 2, Issue C, 2006, Pages 233-261

Chapter 13 Principal Components Analysis: A Review of its Application on Molecular Dynamics Data

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EID: 40949107037     PISSN: 15741400     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1574-1400(06)02013-5     Document Type: Review
Times cited : (109)

References (268)
  • 1
    • 18744371588 scopus 로고    scopus 로고
    • Molecular dynamics and protein function
    • Karplus M., and Kuriyan J. Molecular dynamics and protein function. Proc. Natl. Acad. Sci. 102 (2005) 6679-6685
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 6679-6685
    • Karplus, M.1    Kuriyan, J.2
  • 3
    • 0036285985 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M. Molecular dynamics simulations of biomolecules. Acc. Chem. Res. 35 (2002) 321-323
    • (2002) Acc. Chem. Res. , vol.35 , pp. 321-323
    • Karplus, M.1
  • 4
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M., and McCammon J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9 (2002) 646-652
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 6
    • 0025048105 scopus 로고
    • Molecular dynamics simulations in biology
    • Karplus M., and Petsko G.A. Molecular dynamics simulations in biology. Nature 347 (1990) 631-639
    • (1990) Nature , vol.347 , pp. 631-639
    • Karplus, M.1    Petsko, G.A.2
  • 7
    • 4244215365 scopus 로고
    • Molecular dynamics simulations of proteins
    • Karplus M. Molecular dynamics simulations of proteins. Phys. Today 40 (1987) 68-70
    • (1987) Phys. Today , vol.40 , pp. 68-70
    • Karplus, M.1
  • 8
    • 18544381108 scopus 로고    scopus 로고
    • Modified replica exchange simulation methods for local structure refinement
    • Cheng X., Cui G., Hornak V., and Simmerling C. Modified replica exchange simulation methods for local structure refinement. J. Phys. Chem. B 109 (2005) 8220-8230
    • (2005) J. Phys. Chem. B , vol.109 , pp. 8220-8230
    • Cheng, X.1    Cui, G.2    Hornak, V.3    Simmerling, C.4
  • 10
    • 19644401067 scopus 로고    scopus 로고
    • Long time molecular dynamics for enhanced conformational sampling in biomolecular systems
    • Minary P., Tuckerman M.E., and Martyna G.T. Long time molecular dynamics for enhanced conformational sampling in biomolecular systems. Phys. Rev. Lett. 93 (2004) 1520201/1-1520201/4
    • (2004) Phys. Rev. Lett. , vol.93
    • Minary, P.1    Tuckerman, M.E.2    Martyna, G.T.3
  • 11
    • 0037439853 scopus 로고    scopus 로고
    • Self-guided enhanced sampling methods for thermodynamic averages
    • Andricioaei I., Dinner A.R., and Karplus M. Self-guided enhanced sampling methods for thermodynamic averages. J. Chem. Phys. 118 (2003) 1074-1084
    • (2003) J. Chem. Phys. , vol.118 , pp. 1074-1084
    • Andricioaei, I.1    Dinner, A.R.2    Karplus, M.3
  • 13
    • 19044377596 scopus 로고    scopus 로고
    • Using novel variable transformations to enhance conformational sampling in molecular dynamics
    • Zhu Z., Tuckerman M.E., Samuelson S.O., and Martyna G.T. Using novel variable transformations to enhance conformational sampling in molecular dynamics. Phys. Rev. Lett. 88 (2002) 100201/1-100201/4
    • (2002) Phys. Rev. Lett. , vol.88
    • Zhu, Z.1    Tuckerman, M.E.2    Samuelson, S.O.3    Martyna, G.T.4
  • 14
    • 0000689085 scopus 로고
    • Predicting slow structural transitions in macromolecular systems: Conformational Flooding
    • Grubmuller H. Predicting slow structural transitions in macromolecular systems: Conformational Flooding. Phys. Rev. E 52 (1995) 2893-2906
    • (1995) Phys. Rev. E , vol.52 , pp. 2893-2906
    • Grubmuller, H.1
  • 17
    • 0007048141 scopus 로고    scopus 로고
    • Femtochemistry, Atomic-scale dynamics of the chemical bond using ultrafast lasers Nobel lecture
    • Frangsmyr T. (Ed), Almqvist and Wiksell International, Stockholm
    • Zewail A.H. Femtochemistry, Atomic-scale dynamics of the chemical bond using ultrafast lasers Nobel lecture. In: Frangsmyr T. (Ed). Les Prix Nobel (2000), Almqvist and Wiksell International, Stockholm 110-203
    • (2000) Les Prix Nobel , pp. 110-203
    • Zewail, A.H.1
  • 18
    • 0000161584 scopus 로고    scopus 로고
    • Ultrafast spectroscopy of protein dynamics
    • Hochstrasser R.M. Ultrafast spectroscopy of protein dynamics. J. Chem. Educ. 75 (1998) 559-564
    • (1998) J. Chem. Educ. , vol.75 , pp. 559-564
    • Hochstrasser, R.M.1
  • 19
    • 0032574723 scopus 로고    scopus 로고
    • Dynamics of different functional parts of bacteriorhodopsin: H-2 H labeling and neutron scattering
    • Reat V., Patzelt H., Ferrand M., Pfister C., Oesterhelt D., and Zaccai G. Dynamics of different functional parts of bacteriorhodopsin: H-2 H labeling and neutron scattering. Proc. Natl. Acad. Sci. 95 (1998) 4970-4975
    • (1998) Proc. Natl. Acad. Sci. , vol.95 , pp. 4970-4975
    • Reat, V.1    Patzelt, H.2    Ferrand, M.3    Pfister, C.4    Oesterhelt, D.5    Zaccai, G.6
  • 20
    • 5744241809 scopus 로고    scopus 로고
    • Ultrafast X-ray and electron diffraction: Theoretical considerations
    • Ben-Nun M., Cao J., and Wilson K.R. Ultrafast X-ray and electron diffraction: Theoretical considerations. J. Phys. Chem. A 101 (1997) 8743-8761
    • (1997) J. Phys. Chem. A , vol.101 , pp. 8743-8761
    • Ben-Nun, M.1    Cao, J.2    Wilson, K.R.3
  • 22
    • 0030918284 scopus 로고    scopus 로고
    • Biomolecular dynamics at long timesteps: Bridging the timescale gap between simulation and experimentation
    • Schlick T., Barth E., and Mandziuk M. Biomolecular dynamics at long timesteps: Bridging the timescale gap between simulation and experimentation. Annu. Rev. Biophys. Biomol. Struct. 26 (1997) 181-222
    • (1997) Annu. Rev. Biophys. Biomol. Struct. , vol.26 , pp. 181-222
    • Schlick, T.1    Barth, E.2    Mandziuk, M.3
  • 23
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan Y., and Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282 (1998) 740-744
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 24
    • 0000793139 scopus 로고
    • Cramming more components onto integrated circuits
    • Moore G.E. Cramming more components onto integrated circuits. Electronics 38 (1965) 114-117
    • (1965) Electronics , vol.38 , pp. 114-117
    • Moore, G.E.1
  • 25
  • 26
    • 0037067102 scopus 로고    scopus 로고
    • Water rotational relaxation and diffusion in hydrated lysozyme
    • Marchi M., Sterpone F., and Ceccarelli M. Water rotational relaxation and diffusion in hydrated lysozyme. J. Am. Chem. Soc. 124 (2002) 6787-6791
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 6787-6791
    • Marchi, M.1    Sterpone, F.2    Ceccarelli, M.3
  • 27
    • 28444490422 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
    • Dixit S.B., Beveridge D.L., Case D.A., Cheatham III T.E., Giudice E., Lankas F., Lavery R., Maddocks J.H., Osman R., Sklenar H., Thayer K.M., and Varnai P. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys. J. 89 (2005) 3721-3740
    • (2005) Biophys. J. , vol.89 , pp. 3721-3740
    • Dixit, S.B.1    Beveridge, D.L.2    Case, D.A.3    Cheatham III, T.E.4    Giudice, E.5    Lankas, F.6    Lavery, R.7    Maddocks, J.H.8    Osman, R.9    Sklenar, H.10    Thayer, K.M.11    Varnai, P.12
  • 31
    • 0035305518 scopus 로고    scopus 로고
    • Statistical analysis of the fractal gating motions of the enzyme acetylcholinesterase
    • Shen T.Y., Kaihsu T., and McCammon J.A. Statistical analysis of the fractal gating motions of the enzyme acetylcholinesterase. Phys. Rev. E 63 (2001) 041902/1-041902/6
    • (2001) Phys. Rev. E , vol.63
    • Shen, T.Y.1    Kaihsu, T.2    McCammon, J.A.3
  • 32
    • 0000114327 scopus 로고    scopus 로고
    • Non-Boltzmann rate distributions in stochastically gated reactions
    • Baker N.A., and McCammon J.A. Non-Boltzmann rate distributions in stochastically gated reactions. J. Phys. Chem. B 103 (1999) 615-617
    • (1999) J. Phys. Chem. B , vol.103 , pp. 615-617
    • Baker, N.A.1    McCammon, J.A.2
  • 33
    • 0032482925 scopus 로고    scopus 로고
    • Conformation gating as a mechanism for enzyme specificity
    • Zhou H.-X., Wlodek S.T., and McCammon J.A. Conformation gating as a mechanism for enzyme specificity. Proc. Natl. Acad. Sci. 95 (1998) 9280-9283
    • (1998) Proc. Natl. Acad. Sci. , vol.95 , pp. 9280-9283
    • Zhou, H.-X.1    Wlodek, S.T.2    McCammon, J.A.3
  • 34
    • 0033621030 scopus 로고    scopus 로고
    • Understanding protein lids: Kinetic analysis of active hinge mutants in triosephosphate isomerase
    • Sun J., and Sampson N.S. Understanding protein lids: Kinetic analysis of active hinge mutants in triosephosphate isomerase. Biochemistry 38 (1999) 11474-11481
    • (1999) Biochemistry , vol.38 , pp. 11474-11481
    • Sun, J.1    Sampson, N.S.2
  • 35
    • 0031972864 scopus 로고    scopus 로고
    • The loop opening/closing motion of the enzyme triosephosphate isomerase
    • Derreumaux P., and Schlick T. The loop opening/closing motion of the enzyme triosephosphate isomerase. Biophys. J. 74 (1998) 72-81
    • (1998) Biophys. J. , vol.74 , pp. 72-81
    • Derreumaux, P.1    Schlick, T.2
  • 36
    • 0028041588 scopus 로고
    • The hinged lid of yeast triose-phosphate isomerase. Determination of the energy barrier between the two conformations
    • Yuksel K., Sun A., Gracy R., and Schnackerz K. The hinged lid of yeast triose-phosphate isomerase. Determination of the energy barrier between the two conformations. J. Biol. Chem. 269 (1994) 5005-5008
    • (1994) J. Biol. Chem. , vol.269 , pp. 5005-5008
    • Yuksel, K.1    Sun, A.2    Gracy, R.3    Schnackerz, K.4
  • 37
    • 0026782489 scopus 로고
    • Segmental motion in catalysis: Investigation of a hydrogen bond critical for loop closure in the reaction of triosephosphate isomerase
    • Sampson N.S., and Knowles J.R. Segmental motion in catalysis: Investigation of a hydrogen bond critical for loop closure in the reaction of triosephosphate isomerase. Biochemistry 31 (1992) 8488-8494
    • (1992) Biochemistry , vol.31 , pp. 8488-8494
    • Sampson, N.S.1    Knowles, J.R.2
  • 38
    • 0025015392 scopus 로고
    • Anatomy of a conformational change: Hinged "lid" motion of the triosephosphate isomerase loop
    • Joseph D., Petsko G.A., and Karplus M. Anatomy of a conformational change: Hinged "lid" motion of the triosephosphate isomerase loop. Science 249 (1990) 1425-1428
    • (1990) Science , vol.249 , pp. 1425-1428
    • Joseph, D.1    Petsko, G.A.2    Karplus, M.3
  • 39
    • 0040488445 scopus 로고    scopus 로고
    • Functional significance of hierarchical tiers in carbonmonoxy myoglobin: Conformational substates and transitions studied by conformational flooding simulations
    • Schulze B.G., Grubmuller H., and Evanseck J.D. Functional significance of hierarchical tiers in carbonmonoxy myoglobin: Conformational substates and transitions studied by conformational flooding simulations. J. Am. Chem. Soc. 122 (2000) 8700-8711
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 8700-8711
    • Schulze, B.G.1    Grubmuller, H.2    Evanseck, J.D.3
  • 40
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular motions
    • Gerstein M., and Krebs W. A database of macromolecular motions. Nucleic Acids Res 26 (1998) 4280-4290
    • (1998) Nucleic Acids Res , vol.26 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.2
  • 45
    • 0003976358 scopus 로고
    • M.S. Lewis-Beck Ed, 1st Ed, Sage, Newbury Park
    • G. H. Dunteman, In: M.S. Lewis-Beck (Ed.), Principal Components Analysis, 1st Ed., vol. 69, Sage, Newbury Park, 1989, p. 96-97.
    • (1989) Principal Components Analysis , vol.69 , pp. 96-97
    • Dunteman, G.H.1
  • 46
    • 25144437529 scopus 로고    scopus 로고
    • Dynamite extended: Two new services to simplify protein dynamic analysis
    • Barrett C.P., and Noble M.E.M. Dynamite extended: Two new services to simplify protein dynamic analysis. Bioinformatics 21 (2005) 3174-3175
    • (2005) Bioinformatics , vol.21 , pp. 3174-3175
    • Barrett, C.P.1    Noble, M.E.M.2
  • 47
    • 17844362986 scopus 로고    scopus 로고
    • A directed essential dynamics simulation of peptide folding
    • Chen C., Xiao Y., and Zhang L. A directed essential dynamics simulation of peptide folding. Biophys. J. 88 (2005) 3276-3285
    • (2005) Biophys. J. , vol.88 , pp. 3276-3285
    • Chen, C.1    Xiao, Y.2    Zhang, L.3
  • 48
  • 49
    • 17844380512 scopus 로고    scopus 로고
    • Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: Toward an understanding of Kir channel gating
    • Haider S., Grottesi A., Hall B.A., Ashcroft F.M., and Sansom M.S.P. Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: Toward an understanding of Kir channel gating. Biophys. J. 88 (2005) 3310-3320
    • (2005) Biophys. J. , vol.88 , pp. 3310-3320
    • Haider, S.1    Grottesi, A.2    Hall, B.A.3    Ashcroft, F.M.4    Sansom, M.S.P.5
  • 50
    • 15044346071 scopus 로고    scopus 로고
    • Characterization and classification of lanthanides by multivariate analysis methods
    • Horovitz O., and Sarbu C. Characterization and classification of lanthanides by multivariate analysis methods. J. Chem. Ed. 82 (2005) 473-483
    • (2005) J. Chem. Ed. , vol.82 , pp. 473-483
    • Horovitz, O.1    Sarbu, C.2
  • 51
    • 17844364634 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the M2 helices within the nicotinic acetylcholine receptor transmembrane domain: Structure and collective motions
    • Hung A., Tai K., and Sansom M.S.P. Molecular dynamics simulation of the M2 helices within the nicotinic acetylcholine receptor transmembrane domain: Structure and collective motions. Biophys. J. 88 (2005) 3321-3333
    • (2005) Biophys. J. , vol.88 , pp. 3321-3333
    • Hung, A.1    Tai, K.2    Sansom, M.S.P.3
  • 53
    • 19644383795 scopus 로고    scopus 로고
    • Dissociation of an antiviral compound from the internal pocket of human rhinovirus 14 capsid
    • Li Y., Zhou Z., and Post C.B. Dissociation of an antiviral compound from the internal pocket of human rhinovirus 14 capsid. Proc. Natl. Acad. Sci. 102 (2005) 7529-7534
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 7529-7534
    • Li, Y.1    Zhou, Z.2    Post, C.B.3
  • 54
    • 17744391285 scopus 로고    scopus 로고
    • Unfolding crystallins: The destabilizing role of a β-hairpin cysteine in βB2-crystallin by simulation and experiment
    • MacDonald J.T., Purkiss A.G., Smith M.A., Evans P., Goodfellow J.M., and Slingsby C. Unfolding crystallins: The destabilizing role of a β-hairpin cysteine in βB2-crystallin by simulation and experiment. Protein Sci 14 (2005) 1282-1292
    • (2005) Protein Sci , vol.14 , pp. 1282-1292
    • MacDonald, J.T.1    Purkiss, A.G.2    Smith, M.A.3    Evans, P.4    Goodfellow, J.M.5    Slingsby, C.6
  • 56
    • 34548098038 scopus 로고    scopus 로고
    • Functionally relevant protein motions: Extracting basin-specific collective coordinates from molecular dynamics trajectories
    • Pan P.W., Dickson R.J., Gordon H.L., Rothstein S.M., and Tanaka S. Functionally relevant protein motions: Extracting basin-specific collective coordinates from molecular dynamics trajectories. J. Chem. Phys. 122 (2005) 034904
    • (2005) J. Chem. Phys. , vol.122 , pp. 034904
    • Pan, P.W.1    Dickson, R.J.2    Gordon, H.L.3    Rothstein, S.M.4    Tanaka, S.5
  • 57
    • 15244355250 scopus 로고    scopus 로고
    • The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking
    • Smith G.R., Sternberg M.J., and Bates P.A. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J. Mol. Biol. 347 (2005) 1077-1101
    • (2005) J. Mol. Biol. , vol.347 , pp. 1077-1101
    • Smith, G.R.1    Sternberg, M.J.2    Bates, P.A.3
  • 58
    • 29144436035 scopus 로고    scopus 로고
    • Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase
    • Zhou Z., Madrid M., Evanseck J.D., and Madura J.D. Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase. J. Am. Chem. Soc. 127 (2005) 17253-17260
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 17253-17260
    • Zhou, Z.1    Madrid, M.2    Evanseck, J.D.3    Madura, J.D.4
  • 60
    • 4544353149 scopus 로고    scopus 로고
    • Application of time series analysis on molecular dynamics simulations of proteins: A study of different conformational spaces by principal component analysis
    • Alakent B., Doruker P., and Camurdan M.C. Application of time series analysis on molecular dynamics simulations of proteins: A study of different conformational spaces by principal component analysis. J. Chem. Phys. 121 (2004) 4759-4769
    • (2004) J. Chem. Phys. , vol.121 , pp. 4759-4769
    • Alakent, B.1    Doruker, P.2    Camurdan, M.C.3
  • 61
    • 0842311616 scopus 로고    scopus 로고
    • Time series analysis of collective motions in proteins
    • Alakent B., Doruker P., and Camurdan M.C. Time series analysis of collective motions in proteins. J. Chem. Phys. 120 (2004) 1072-1088
    • (2004) J. Chem. Phys. , vol.120 , pp. 1072-1088
    • Alakent, B.1    Doruker, P.2    Camurdan, M.C.3
  • 62
    • 16644370327 scopus 로고    scopus 로고
    • Dynamite: A simple way to gain insight into protein motions
    • Barrett C.P., Hall B.A., and Noble M.E.M. Dynamite: A simple way to gain insight into protein motions. Acta Cryst. D. 60 (2004) 2280-2287
    • (2004) Acta Cryst. D. , vol.60 , pp. 2280-2287
    • Barrett, C.P.1    Hall, B.A.2    Noble, M.E.M.3
  • 64
    • 1442300068 scopus 로고    scopus 로고
    • Flexibility of β-sheets: Principal component analysis of database protein structures
    • Emberly E.G., Mukhopadhyay R., Tang C., and Wingreen N.S. Flexibility of β-sheets: Principal component analysis of database protein structures. Proteins 55 (2004) 91-98
    • (2004) Proteins , vol.55 , pp. 91-98
    • Emberly, E.G.1    Mukhopadhyay, R.2    Tang, C.3    Wingreen, N.S.4
  • 65
    • 10844270511 scopus 로고    scopus 로고
    • A molecular dynamics study of acylphosphatase in aggregation-promoting conditions: The influence of trifluoroethanol/water solvent
    • Flock D., Daidone I., and Di Nola A. A molecular dynamics study of acylphosphatase in aggregation-promoting conditions: The influence of trifluoroethanol/water solvent. Biopolymers 75 (2004) 491-496
    • (2004) Biopolymers , vol.75 , pp. 491-496
    • Flock, D.1    Daidone, I.2    Di Nola, A.3
  • 66
    • 4644357714 scopus 로고    scopus 로고
    • The folding pathway of ubiquitin from all-atom molecular dynamics simulations
    • Marianayagam N.J., and Jackson S.E. The folding pathway of ubiquitin from all-atom molecular dynamics simulations. Biophys. Chem. 111 (2004) 159-171
    • (2004) Biophys. Chem. , vol.111 , pp. 159-171
    • Marianayagam, N.J.1    Jackson, S.E.2
  • 67
    • 12844268201 scopus 로고    scopus 로고
    • Folding dynamics of proteins from denatured to native state: Principal component analysis
    • Palazoglu A., Gursoy A., Arkun Y., and Erman B. Folding dynamics of proteins from denatured to native state: Principal component analysis. J. Comp. Biol. 11 (2004) 1149-1168
    • (2004) J. Comp. Biol. , vol.11 , pp. 1149-1168
    • Palazoglu, A.1    Gursoy, A.2    Arkun, Y.3    Erman, B.4
  • 68
    • 9244235496 scopus 로고    scopus 로고
    • A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor
    • Tatsumi R., Fukunishi Y., and Nakamura H.K. A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor. J. Comp. Chem. 25 (2004) 1995-2005
    • (2004) J. Comp. Chem. , vol.25 , pp. 1995-2005
    • Tatsumi, R.1    Fukunishi, Y.2    Nakamura, H.K.3
  • 69
    • 4344661682 scopus 로고    scopus 로고
    • Modelling of third cytoplasmic loop of bovine rhodopsin by multicanonical molecular dynamics
    • Watanabe Y.S., Fukunishi Y., and Nakamura H.K. Modelling of third cytoplasmic loop of bovine rhodopsin by multicanonical molecular dynamics. J. Mol. Graph. Model 23 (2004) 59-68
    • (2004) J. Mol. Graph. Model , vol.23 , pp. 59-68
    • Watanabe, Y.S.1    Fukunishi, Y.2    Nakamura, H.K.3
  • 70
    • 1542316339 scopus 로고    scopus 로고
    • Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP
    • Zacharias M. Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP. Proteins 54 (2004) 759-767
    • (2004) Proteins , vol.54 , pp. 759-767
    • Zacharias, M.1
  • 71
    • 0037338421 scopus 로고    scopus 로고
    • Protein concerted motions in the DNA-human topoisomerase I complex
    • Chillemi G., Fiorani P., Benedetti P., and Desideri A. Protein concerted motions in the DNA-human topoisomerase I complex. Nucleic Acids Res. 31 (2003) 1525-1535
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1525-1535
    • Chillemi, G.1    Fiorani, P.2    Benedetti, P.3    Desideri, A.4
  • 72
    • 0038617472 scopus 로고    scopus 로고
    • Molecular dynamics study of [2]rotaxanes: Influence of solvation and cation on co-conformation
    • Fradera X., Marquez M., Smith B.D., Orozco M., and Luque F.J. Molecular dynamics study of [2]rotaxanes: Influence of solvation and cation on co-conformation. J. Org. Chem. 68 (2003) 4663-4673
    • (2003) J. Org. Chem. , vol.68 , pp. 4663-4673
    • Fradera, X.1    Marquez, M.2    Smith, B.D.3    Orozco, M.4    Luque, F.J.5
  • 73
    • 0037508925 scopus 로고    scopus 로고
    • Self-consistency analysis of dipolar couplings in multiple alignments of ubiquitin
    • Hus J.-C., Peti W., Griesinger C., and Bruschweiler R. Self-consistency analysis of dipolar couplings in multiple alignments of ubiquitin. J. Am. Chem. Soc. 125 (2003) 5596-5597
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 5596-5597
    • Hus, J.-C.1    Peti, W.2    Griesinger, C.3    Bruschweiler, R.4
  • 74
    • 0037337008 scopus 로고    scopus 로고
    • Comparing the fine specificity of DNA binding by NF-κB p50 and p52 using principal coordinates analysis
    • Nijnik A., Mott R., Kwiatkowski D.P., and Udalova I.R. Comparing the fine specificity of DNA binding by NF-κB p50 and p52 using principal coordinates analysis. Nucleic Acids Res. 31 (2003) 1497-1501
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1497-1501
    • Nijnik, A.1    Mott, R.2    Kwiatkowski, D.P.3    Udalova, I.R.4
  • 75
    • 0344413575 scopus 로고    scopus 로고
    • Optimal spectrum estimation in statistical mechanics
    • Wheeler R.A., and Dong H. Optimal spectrum estimation in statistical mechanics. ChemPhysChem 4 (2003) 1227-1230
    • (2003) ChemPhysChem , vol.4 , pp. 1227-1230
    • Wheeler, R.A.1    Dong, H.2
  • 76
    • 0037437247 scopus 로고    scopus 로고
    • Quasiharmonic vibrations of water, water dimer, and liquid water from principal component analysis of quantum and QM/MM trajectories
    • Wheeler R.A., Dong H., and Boesch S.E. Quasiharmonic vibrations of water, water dimer, and liquid water from principal component analysis of quantum and QM/MM trajectories. ChemPhysChem 4 (2003) 382-384
    • (2003) ChemPhysChem , vol.4 , pp. 382-384
    • Wheeler, R.A.1    Dong, H.2    Boesch, S.E.3
  • 77
    • 0037168294 scopus 로고    scopus 로고
    • Inherent flexibility of calmodulin domains: A normal-mode analysis study
    • Barton N.P., Verma C.S., and Caves L.S.D. Inherent flexibility of calmodulin domains: A normal-mode analysis study. J. Phys. Chem. B. 106 (2002) 11036-11040
    • (2002) J. Phys. Chem. B. , vol.106 , pp. 11036-11040
    • Barton, N.P.1    Verma, C.S.2    Caves, L.S.D.3
  • 78
    • 0036533472 scopus 로고    scopus 로고
    • Congruent qualitative behavior of complete and reconstructed phase space trajectories from biomolecular dynamics simulation
    • Caves L.S.D., and Verma C.S. Congruent qualitative behavior of complete and reconstructed phase space trajectories from biomolecular dynamics simulation. Proteins Struct. Funct. Genet. 47 (2002) 25-30
    • (2002) Proteins Struct. Funct. Genet. , vol.47 , pp. 25-30
    • Caves, L.S.D.1    Verma, C.S.2
  • 81
    • 0036245097 scopus 로고    scopus 로고
    • Molecular dynamics simulation of 7,8-dihydro-8-oxoguanine DNA
    • Ishida H. Molecular dynamics simulation of 7,8-dihydro-8-oxoguanine DNA. J. Biomol. Struct. Dyn. 19 (2002) 839-851
    • (2002) J. Biomol. Struct. Dyn. , vol.19 , pp. 839-851
    • Ishida, H.1
  • 82
    • 0036827811 scopus 로고    scopus 로고
    • Differential actions of anti-Parkinson agents at multiple classes of monoaminergic receptor. 1. A multivariate analysis of the binding profiles of 14 drugs at 21 native and cloned human receptor subtypes
    • Millan M.J., Maiofiss L., Cussac D., Audinot V., Boutin J.A., and Newman-Tancredi A. Differential actions of anti-Parkinson agents at multiple classes of monoaminergic receptor. 1. A multivariate analysis of the binding profiles of 14 drugs at 21 native and cloned human receptor subtypes. J. Pharm. Exp. Ther. 303 (2002) 791-804
    • (2002) J. Pharm. Exp. Ther. , vol.303 , pp. 791-804
    • Millan, M.J.1    Maiofiss, L.2    Cussac, D.3    Audinot, V.4    Boutin, J.A.5    Newman-Tancredi, A.6
  • 83
    • 0037061982 scopus 로고    scopus 로고
    • Molecular dynamics of the tRNA Ala acceptor stem: Comparison between continuum reaction field and Particle-Mesh Ewald electrostatic treatments
    • Nina M., and Simonson T. Molecular dynamics of the tRNA Ala acceptor stem: Comparison between continuum reaction field and Particle-Mesh Ewald electrostatic treatments. J. Phys. Chem. B. 106 (2002) 3696-3705
    • (2002) J. Phys. Chem. B. , vol.106 , pp. 3696-3705
    • Nina, M.1    Simonson, T.2
  • 84
    • 0037160546 scopus 로고    scopus 로고
    • Correlative motions and memory effects in molecular dynamics simulations of molecules: Principal components and rescaled range analysis suggest that the motions of native BPTI are more correlated than those of its mutants
    • Saarala J.T.A., Tuppurainen K., Perakyla M., Santa H., and Laatikainen. Correlative motions and memory effects in molecular dynamics simulations of molecules: Principal components and rescaled range analysis suggest that the motions of native BPTI are more correlated than those of its mutants. Biophys. Chem. 95 (2002) 49-57
    • (2002) Biophys. Chem. , vol.95 , pp. 49-57
    • Saarala, J.T.A.1    Tuppurainen, K.2    Perakyla, M.3    Santa, H.4    Laatikainen5
  • 85
    • 0034966704 scopus 로고    scopus 로고
    • Enzyme specificity under dynamic control II. Principal components analysis of a-lytic protease using global and local solvent boundary conditions
    • Ota N., and Agard D.A. Enzyme specificity under dynamic control II. Principal components analysis of a-lytic protease using global and local solvent boundary conditions,. Protein Sci. 10 (2001) 1403-1414
    • (2001) Protein Sci. , vol.10 , pp. 1403-1414
    • Ota, N.1    Agard, D.A.2
  • 86
    • 0034321622 scopus 로고    scopus 로고
    • Temperature effects on protein motions: A molecular dynamics study of RNase-Sa
    • Dvorsky R., Sevcik J., Caves L.S.D., Hubbard R.E., and Verma C.S. Temperature effects on protein motions: A molecular dynamics study of RNase-Sa. J. Phys. Chem. B 104 (2000) 10387-10397
    • (2000) J. Phys. Chem. B , vol.104 , pp. 10387-10397
    • Dvorsky, R.1    Sevcik, J.2    Caves, L.S.D.3    Hubbard, R.E.4    Verma, C.S.5
  • 87
    • 0034083950 scopus 로고    scopus 로고
    • Nonlinear methods in the analysis of protein sequences: A case study in rubredoxins
    • Giuliani A., Benigni R., Sirabella P., Zbilut J.P., and Colosimo A. Nonlinear methods in the analysis of protein sequences: A case study in rubredoxins. Biophys. J. 78 (2000) 136-148
    • (2000) Biophys. J. , vol.78 , pp. 136-148
    • Giuliani, A.1    Benigni, R.2    Sirabella, P.3    Zbilut, J.P.4    Colosimo, A.5
  • 88
    • 0034500645 scopus 로고    scopus 로고
    • Similarities between principal components of protein dynamics and random diffusion
    • Hess B. Similarities between principal components of protein dynamics and random diffusion. Phys. Rev. E 62 (2000) 8438-8448
    • (2000) Phys. Rev. E , vol.62 , pp. 8438-8448
    • Hess, B.1
  • 89
    • 0032901423 scopus 로고    scopus 로고
    • Mechanics and dynamics of B1 domain of Protein G: Role of packing and surface hydrophobic residues
    • Ceruso M.A., Amadei A., and Di Nola A. Mechanics and dynamics of B1 domain of Protein G: Role of packing and surface hydrophobic residues. Protein Sci. 8 (1999) 147-160
    • (1999) Protein Sci. , vol.8 , pp. 147-160
    • Ceruso, M.A.1    Amadei, A.2    Di Nola, A.3
  • 90
    • 0033557175 scopus 로고    scopus 로고
    • Major structural determinants of transmembrane proteins identified by principal components analysis
    • Koshi J.M., and Bruno W.J. Major structural determinants of transmembrane proteins identified by principal components analysis. Proteins 34 (1999) 333-340
    • (1999) Proteins , vol.34 , pp. 333-340
    • Koshi, J.M.1    Bruno, W.J.2
  • 91
    • 0037575221 scopus 로고    scopus 로고
    • Conformational analysis of tetracycline using molecular mechanical and semiempirical MO-calculations
    • Lanig H., Gottschalk M., Schneider S., and Clark T.W. Conformational analysis of tetracycline using molecular mechanical and semiempirical MO-calculations. J. Mol. Mod. 5 (1999) 46-62
    • (1999) J. Mol. Mod. , vol.5 , pp. 46-62
    • Lanig, H.1    Gottschalk, M.2    Schneider, S.3    Clark, T.W.4
  • 92
    • 0033554018 scopus 로고    scopus 로고
    • Cooperative role of Arg45 and His64 in the spectroscopic A3 state of carbonmonoxy myoglobin: Molecular dynamics simulations, multivariate anlaysis and quantum mechanical computations
    • Schulze B.G., and Evanseck J.D. Cooperative role of Arg45 and His64 in the spectroscopic A3 state of carbonmonoxy myoglobin: Molecular dynamics simulations, multivariate anlaysis and quantum mechanical computations. J. Am. Chem. Soc. 121 (1999) 6444-6454
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 6444-6454
    • Schulze, B.G.1    Evanseck, J.D.2
  • 95
    • 0031827402 scopus 로고    scopus 로고
    • High-performance size-exclusion chromatographic behavior of substituted benzoylpoly L-lysines by principal component analysis and molecular dynamics simulations
    • Bolzacchini E., Consonni V., Lucini R., Orlandi M., and Rindone B. High-performance size-exclusion chromatographic behavior of substituted benzoylpoly L-lysines by principal component analysis and molecular dynamics simulations. J. Chromatogr. A 813 (1998) 255-265
    • (1998) J. Chromatogr. A , vol.813 , pp. 255-265
    • Bolzacchini, E.1    Consonni, V.2    Lucini, R.3    Orlandi, M.4    Rindone, B.5
  • 96
    • 0031910020 scopus 로고    scopus 로고
    • Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin
    • Caves L.S.D., Evanseck J.D., and Karplus M. Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin. Protein Sci. 7 (1998) 649-666
    • (1998) Protein Sci. , vol.7 , pp. 649-666
    • Caves, L.S.D.1    Evanseck, J.D.2    Karplus, M.3
  • 97
    • 0032514113 scopus 로고    scopus 로고
    • Internal motions of native lysozyme are more organized than those of mutants: A principal component analysis of molecular dynamics data
    • Laatikainen R., Saarala J.T.A., Tuppurainen K., and Hassinen T. Internal motions of native lysozyme are more organized than those of mutants: A principal component analysis of molecular dynamics data. Biophys. Chem. 73 (1998) 1-5
    • (1998) Biophys. Chem. , vol.73 , pp. 1-5
    • Laatikainen, R.1    Saarala, J.T.A.2    Tuppurainen, K.3    Hassinen, T.4
  • 98
    • 0030888546 scopus 로고    scopus 로고
    • Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme
    • Hayward S., Kitao A., and Berendsen H.J.C. Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 27 (1997) 425-437
    • (1997) Proteins , vol.27 , pp. 425-437
    • Hayward, S.1    Kitao, A.2    Berendsen, H.J.C.3
  • 99
    • 0031467464 scopus 로고    scopus 로고
    • Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin
    • Lazaridis T., Lee I., and Karplus M. Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin. Protein Sci 6 (1997) 2589-2605
    • (1997) Protein Sci , vol.6 , pp. 2589-2605
    • Lazaridis, T.1    Lee, I.2    Karplus, M.3
  • 100
    • 0030955505 scopus 로고    scopus 로고
    • Prediction of protein side-chain conformations by principal component analysis for fixed main-chain atoms
    • Ogata K., and Umeyama H. Prediction of protein side-chain conformations by principal component analysis for fixed main-chain atoms. Protein Eng. 10 (1997) 353-359
    • (1997) Protein Eng. , vol.10 , pp. 353-359
    • Ogata, K.1    Umeyama, H.2
  • 101
    • 0030728865 scopus 로고    scopus 로고
    • Molecular dynamics of acetylcholinase dimer complexed wtih tacrine
    • Wlodek S.T., Clark T.W., Scott L.R., and McCammon J.A. Molecular dynamics of acetylcholinase dimer complexed wtih tacrine. J. Am. Chem. Soc. 119 (1997) 9513-9522
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 9513-9522
    • Wlodek, S.T.1    Clark, T.W.2    Scott, L.R.3    McCammon, J.A.4
  • 102
    • 0001295503 scopus 로고    scopus 로고
    • Principal component analysis and long time protein dynamics
    • Balsera M.A., Wriggers W., Oono Y., and Schulten K. Principal component analysis and long time protein dynamics. J. Phys. Chem. 100 (1996) 2567-2572
    • (1996) J. Phys. Chem. , vol.100 , pp. 2567-2572
    • Balsera, M.A.1    Wriggers, W.2    Oono, Y.3    Schulten, K.4
  • 103
    • 0028292635 scopus 로고
    • Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis
    • Hayward S., Kitao A., and Go N. Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis. Protein Sci. 3 (1994) 936-943
    • (1994) Protein Sci. , vol.3 , pp. 936-943
    • Hayward, S.1    Kitao, A.2    Go, N.3
  • 104
    • 0000577041 scopus 로고
    • Large-amplitude nonlinear motions in proteins
    • Garcia A.E. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68 (1992) 2696-2699
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 2696-2699
    • Garcia, A.E.1
  • 106
    • 0035944933 scopus 로고    scopus 로고
    • I. Rosenberg and M. Petrova-Endova, -CH2-lengthening of the internucleotide linkage in the ApA dimer can improve its conformational compatibility with its natural polynucleotide counterpart
    • Hanus J., Barvik I., Ruszovz-Chmelova K., Stepanek J., Turpin P.-Y., and Bok J. I. Rosenberg and M. Petrova-Endova, -CH2-lengthening of the internucleotide linkage in the ApA dimer can improve its conformational compatibility with its natural polynucleotide counterpart. Nucleic Acids Res. 29 (2001) 5182-5194
    • (2001) Nucleic Acids Res. , vol.29 , pp. 5182-5194
    • Hanus, J.1    Barvik, I.2    Ruszovz-Chmelova, K.3    Stepanek, J.4    Turpin, P.-Y.5    Bok, J.6
  • 107
    • 0034877118 scopus 로고    scopus 로고
    • Decomposition of protein tryptophan fluorescence spectra into log-normal components. III. Correlation between fluorescence and microenvironment parameters of individual tryptophan residues
    • Reshetnyak Y.K., Koshevnik Y., and Burstein E.A. Decomposition of protein tryptophan fluorescence spectra into log-normal components. III. Correlation between fluorescence and microenvironment parameters of individual tryptophan residues. Biophys. J. 81 (2001) 1735-1758
    • (2001) Biophys. J. , vol.81 , pp. 1735-1758
    • Reshetnyak, Y.K.1    Koshevnik, Y.2    Burstein, E.A.3
  • 108
    • 0037627715 scopus 로고    scopus 로고
    • The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35
    • Gsponer J., Haberthur U., and Caflisch A. The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proc. Natl. Acad. Sci. 100 (2003) 5154-5159
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 5154-5159
    • Gsponer, J.1    Haberthur, U.2    Caflisch, A.3
  • 109
    • 0036499409 scopus 로고    scopus 로고
    • Folding and stability of the three-stranded β-sheet peptide Betanova: Insights from molecular dynamics simulations
    • Colombo G., Roccatano D., and Mark A.E. Folding and stability of the three-stranded β-sheet peptide Betanova: Insights from molecular dynamics simulations. Proteins 46 (2002) 380-392
    • (2002) Proteins , vol.46 , pp. 380-392
    • Colombo, G.1    Roccatano, D.2    Mark, A.E.3
  • 110
    • 0034804341 scopus 로고    scopus 로고
    • Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation
    • Best R.B., Li B., Steward A., Daggett V., and Clarke J. Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. Biophys. J. 81 (2001) 2344-2356
    • (2001) Biophys. J. , vol.81 , pp. 2344-2356
    • Best, R.B.1    Li, B.2    Steward, A.3    Daggett, V.4    Clarke, J.5
  • 111
    • 0035960060 scopus 로고    scopus 로고
    • Quantitative structure-antitumor activity relationships of camptothecin analogues: Cluster analysis and genetic algorithm-based studies
    • Fan Y., Shi L.M., Kohn K.W., Pommier Y., and Weinstein J.N. Quantitative structure-antitumor activity relationships of camptothecin analogues: Cluster analysis and genetic algorithm-based studies. J. Med. Chem. 44 (2001) 3254-3263
    • (2001) J. Med. Chem. , vol.44 , pp. 3254-3263
    • Fan, Y.1    Shi, L.M.2    Kohn, K.W.3    Pommier, Y.4    Weinstein, J.N.5
  • 112
    • 0034825161 scopus 로고    scopus 로고
    • A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization
    • Hamprecht F.A., Peter C., Daura X., Thiel W., and van Gunsteren W.F. A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization. J. Chem. Phys. 114 (2001) 2079-2089
    • (2001) J. Chem. Phys. , vol.114 , pp. 2079-2089
    • Hamprecht, F.A.1    Peter, C.2    Daura, X.3    Thiel, W.4    van Gunsteren, W.F.5
  • 113
    • 0035789124 scopus 로고    scopus 로고
    • New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical chemical properties
    • Vankatarajan M., and Braun W. New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical chemical properties. J. Mol. Mod. 7 (2001) 445-453
    • (2001) J. Mol. Mod. , vol.7 , pp. 445-453
    • Vankatarajan, M.1    Braun, W.2
  • 114
    • 0035865543 scopus 로고    scopus 로고
    • Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue
    • Zhang Z., Zhu Y., and Shi Y. Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue. Biophys. Chem. 89 (2001) 145-162
    • (2001) Biophys. Chem. , vol.89 , pp. 145-162
    • Zhang, Z.1    Zhu, Y.2    Shi, Y.3
  • 115
    • 0034050785 scopus 로고    scopus 로고
    • Conformational analysis of a farnesyltransferase peptide inhibitor
    • Carlacci L. Conformational analysis of a farnesyltransferase peptide inhibitor. CVIM, J. Comput.-Aided Mol. Des. 14 (2000) 369-382
    • (2000) CVIM, J. Comput.-Aided Mol. Des. , vol.14 , pp. 369-382
    • Carlacci, L.1
  • 116
    • 0001767031 scopus 로고    scopus 로고
    • Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations
    • Ferrara P., Apostolakis J., and Caflisch A. Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations. J. Phys. Chem. B 104 (2000) 5000-5010
    • (2000) J. Phys. Chem. B , vol.104 , pp. 5000-5010
    • Ferrara, P.1    Apostolakis, J.2    Caflisch, A.3
  • 117
    • 0034646218 scopus 로고    scopus 로고
    • Mechanisms and kinetics of β-hairpin formation
    • Klimov D.K., and Thirumalai D. Mechanisms and kinetics of β-hairpin formation. Proc. Natl. Acad. Sci. 97 (2000) 2544-2549
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 2544-2549
    • Klimov, D.K.1    Thirumalai, D.2
  • 118
    • 0029963345 scopus 로고    scopus 로고
    • Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
    • Li A., and Daggett V. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J. Mol. Biol. 247 (1996) 412-419
    • (1996) J. Mol. Biol. , vol.247 , pp. 412-419
    • Li, A.1    Daggett, V.2
  • 119
    • 0029965463 scopus 로고    scopus 로고
    • Structure and dynamics of the DNA hairpins formed by tandemly repeated CTG triplets associated with myotonic dystrophy
    • Mariappan S., Garcoa A., and Gupta G. Structure and dynamics of the DNA hairpins formed by tandemly repeated CTG triplets associated with myotonic dystrophy. Nucleic Acids Res. 24 (1996) 775-783
    • (1996) Nucleic Acids Res. , vol.24 , pp. 775-783
    • Mariappan, S.1    Garcoa, A.2    Gupta, G.3
  • 120
    • 0029151245 scopus 로고
    • First-principle calculation of the folding free energy of a three-helix bundle protein
    • Boczko E.M., and Brooks III C.L. First-principle calculation of the folding free energy of a three-helix bundle protein. Science 269 (1995) 393-396
    • (1995) Science , vol.269 , pp. 393-396
    • Boczko, E.M.1    Brooks III, C.L.2
  • 121
    • 0028143603 scopus 로고
    • Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2
    • Li A., and Daggett V. Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci. 91 (1994) 10430-10434
    • (1994) Proc. Natl. Acad. Sci. , vol.91 , pp. 10430-10434
    • Li, A.1    Daggett, V.2
  • 122
    • 0027393187 scopus 로고
    • Statistical clustering techniques for the analysis of long molecular dynamics trajectories: Analysis of 2.2 ns trajectories of YPGDV
    • Karpen M.E., Tobias D.J., and Brooks III C.L. Statistical clustering techniques for the analysis of long molecular dynamics trajectories: Analysis of 2.2 ns trajectories of YPGDV. Biochemistry 32 (1993) 412-420
    • (1993) Biochemistry , vol.32 , pp. 412-420
    • Karpen, M.E.1    Tobias, D.J.2    Brooks III, C.L.3
  • 123
    • 0032735433 scopus 로고    scopus 로고
    • From atomic to mesoscopic descriptions of the internal dynamics of DNA
    • Bruant N., Flatters D., Lavery R., and Genest D. From atomic to mesoscopic descriptions of the internal dynamics of DNA. Biophys. J. 77 (1999) 2366-2376
    • (1999) Biophys. J. , vol.77 , pp. 2366-2376
    • Bruant, N.1    Flatters, D.2    Lavery, R.3    Genest, D.4
  • 124
    • 5244253992 scopus 로고    scopus 로고
    • Correlated motions analysis from molecular dynamics trajectories: Statistical accuracy on the determination of canonical correlation coefficients
    • Genest D. Correlated motions analysis from molecular dynamics trajectories: Statistical accuracy on the determination of canonical correlation coefficients. J. Comp. Chem. 20 (1999) 1571-1576
    • (1999) J. Comp. Chem. , vol.20 , pp. 1571-1576
    • Genest, D.1
  • 125
    • 0031896634 scopus 로고    scopus 로고
    • Motion of groups of atoms in DNA studied by molecular dynamics simulation
    • Genest D. Motion of groups of atoms in DNA studied by molecular dynamics simulation. Eur. Biophys. J. 27 (1998) 283-289
    • (1998) Eur. Biophys. J. , vol.27 , pp. 283-289
    • Genest, D.1
  • 126
    • 1442324641 scopus 로고    scopus 로고
    • Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution
    • Xia Y., and Levitt M. Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution. Proteins 55 (2004) 107-114
    • (2004) Proteins , vol.55 , pp. 107-114
    • Xia, Y.1    Levitt, M.2
  • 127
    • 0037251966 scopus 로고    scopus 로고
    • SDAP: Database and computational tools for allergenic proteins
    • Ivanciuc O., Schein C.H., and Braun W. SDAP: Database and computational tools for allergenic proteins. Nucleic Acids Res. 31 (2003) 359-362
    • (2003) Nucleic Acids Res. , vol.31 , pp. 359-362
    • Ivanciuc, O.1    Schein, C.H.2    Braun, W.3
  • 128
    • 0141995485 scopus 로고    scopus 로고
    • Convergence in peptide folding simulation: Multiple trajectories of a potential AIDS pharmacophore
    • Mihailescu D., Reed J., and Smith J.C. Convergence in peptide folding simulation: Multiple trajectories of a potential AIDS pharmacophore. Biopolymers 70 (2003) 121-133
    • (2003) Biopolymers , vol.70 , pp. 121-133
    • Mihailescu, D.1    Reed, J.2    Smith, J.C.3
  • 129
    • 0141974927 scopus 로고    scopus 로고
    • Global mapping of nucleic acid conformational space: Dinucleoside monophosphate conformations and transition pathways among conformational classes
    • Sims G.E., and Kim S.-H. Global mapping of nucleic acid conformational space: Dinucleoside monophosphate conformations and transition pathways among conformational classes. Nucleic Acids Res. 31 (2003) 5607-5616
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5607-5616
    • Sims, G.E.1    Kim, S.-H.2
  • 130
    • 0035263411 scopus 로고    scopus 로고
    • Metric and multidimensional scaling: Efficient tools for clustering molecular conformations
    • Feher M., and Schmidt J.M. Metric and multidimensional scaling: Efficient tools for clustering molecular conformations. J. Chem. Inf. Comput. Sci. 41 (2001) 346-353
    • (2001) J. Chem. Inf. Comput. Sci. , vol.41 , pp. 346-353
    • Feher, M.1    Schmidt, J.M.2
  • 131
    • 0000325341 scopus 로고
    • On lines and planes of closest fit to a system of points in space
    • Pearson K. On lines and planes of closest fit to a system of points in space. Phil. Mag. 2 (1901) 559-572
    • (1901) Phil. Mag. , vol.2 , pp. 559-572
    • Pearson, K.1
  • 132
    • 0001710505 scopus 로고
    • Analysis of a complex of statistical variables into principal components
    • Hotelling H. Analysis of a complex of statistical variables into principal components. J. Educ. Psych. 24 (1933) 417-441
    • (1933) J. Educ. Psych. , vol.24 , pp. 417-441
    • Hotelling, H.1
  • 133
    • 19544385241 scopus 로고    scopus 로고
    • Structure alignment via Delauney tetrahedralization
    • Roach J., Sharma S., Kapustina M., and Carter C.W. Structure alignment via Delauney tetrahedralization. Proteins 60 (2005) 66-81
    • (2005) Proteins , vol.60 , pp. 66-81
    • Roach, J.1    Sharma, S.2    Kapustina, M.3    Carter, C.W.4
  • 134
    • 2942547529 scopus 로고    scopus 로고
    • Using 3D hidden Markov models that explicitly represent spatial coordinates to model and compare protein structures
    • V. Alexandrov and M. Gerstein, Using 3D hidden Markov models that explicitly represent spatial coordinates to model and compare protein structures, BMC Bioinform., 2004, 5(2).
    • (2004) BMC Bioinform , vol.5 , Issue.2
    • Alexandrov, V.1    Gerstein, M.2
  • 135
    • 16644386895 scopus 로고    scopus 로고
    • Domain identification by iterative analysis of error-scaled difference distance matrices
    • Scheider T.R. Domain identification by iterative analysis of error-scaled difference distance matrices. Acta Cryst. D 60 (2004) 2269-2275
    • (2004) Acta Cryst. D , vol.60 , pp. 2269-2275
    • Scheider, T.R.1
  • 136
    • 3042533398 scopus 로고    scopus 로고
    • Database searching by flexible protein structure alignment
    • Ye Y., and Godzik A. Database searching by flexible protein structure alignment. Protein Sci. 13 (2004) 1841-1850
    • (2004) Protein Sci. , vol.13 , pp. 1841-1850
    • Ye, Y.1    Godzik, A.2
  • 137
    • 0037460952 scopus 로고    scopus 로고
    • MINRMS: An efficient algorithm for determining protein structure similarity using root-mean-squared-distance
    • Jewett A.I., Huang C.C., and Ferrin T.E. MINRMS: An efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinformatics 19 (2003) 625-634
    • (2003) Bioinformatics , vol.19 , pp. 625-634
    • Jewett, A.I.1    Huang, C.C.2    Ferrin, T.E.3
  • 138
    • 0141448920 scopus 로고    scopus 로고
    • Protein structural alignment for detection of maximally conserved regions
    • Kotlovyi V., Nichols W.L., and Eyck L.F.T. Protein structural alignment for detection of maximally conserved regions. Biophys. Chem. 105 (2003) 595-608
    • (2003) Biophys. Chem. , vol.105 , pp. 595-608
    • Kotlovyi, V.1    Nichols, W.L.2    Eyck, L.F.T.3
  • 139
    • 0036008503 scopus 로고    scopus 로고
    • A genetic algorithm for the identification of conformationally invariant regions in protein molecules
    • Scheider T.R. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta Cryst. D 58 (2002) 195-208
    • (2002) Acta Cryst. D , vol.58 , pp. 195-208
    • Scheider, T.R.1
  • 140
    • 0036681439 scopus 로고    scopus 로고
    • Flexible protein alignment and hinge detection
    • Shatsky M., Nussinov R., and Wolfson H.J. Flexible protein alignment and hinge detection. Proteins 48 (2002) 242-256
    • (2002) Proteins , vol.48 , pp. 242-256
    • Shatsky, M.1    Nussinov, R.2    Wolfson, H.J.3
  • 141
    • 0035865982 scopus 로고    scopus 로고
    • Protein structural alignments and functional genomics
    • Irving J.A., Whisstock J.C., and Lesk A.M. Protein structural alignments and functional genomics. Proteins 42 (2001) 378-382
    • (2001) Proteins , vol.42 , pp. 378-382
    • Irving, J.A.1    Whisstock, J.C.2    Lesk, A.M.3
  • 142
    • 0034663597 scopus 로고    scopus 로고
    • Application of multiple sequence alignment profiles to improve protein secondary structure prediction
    • Cuff J.A., and Barton G.J. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 40 (2000) 502-511
    • (2000) Proteins , vol.40 , pp. 502-511
    • Cuff, J.A.1    Barton, G.J.2
  • 143
    • 0034655949 scopus 로고    scopus 로고
    • The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework
    • Krebs W.G., and Gerstein M. The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 28 (2000) 1665-1675
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1665-1675
    • Krebs, W.G.1    Gerstein, M.2
  • 144
    • 0034623005 scopus 로고    scopus 로고
    • T-coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C., Higgins D.G., and Heringa J. T-coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302 (2000) 205-217
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 145
    • 0030788541 scopus 로고    scopus 로고
    • Extracting protein alignment models from the sequence database
    • Neuwald A.F., Liu J.S., Lipman D.J., and Lawrence C.E. Extracting protein alignment models from the sequence database. Nucl. Acids Res. 25 (1997) 1665-1677
    • (1997) Nucl. Acids Res. , vol.25 , pp. 1665-1677
    • Neuwald, A.F.1    Liu, J.S.2    Lipman, D.J.3    Lawrence, C.E.4
  • 146
    • 0031586213 scopus 로고    scopus 로고
    • Conformation-invariant structures of the a1b1 human hemoglobin dimmer
    • Nichols W.L., Zimm B.H., and Eyck L.F.T. Conformation-invariant structures of the a1b1 human hemoglobin dimmer. J. Mol. Biol. 270 (1997) 598-615
    • (1997) J. Mol. Biol. , vol.270 , pp. 598-615
    • Nichols, W.L.1    Zimm, B.H.2    Eyck, L.F.T.3
  • 147
    • 0030883755 scopus 로고    scopus 로고
    • Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
    • Wriggers W., and Schulten K. Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 29 (1997) 1-14
    • (1997) Proteins , vol.29 , pp. 1-14
    • Wriggers, W.1    Schulten, K.2
  • 148
    • 0029091249 scopus 로고
    • Average core structures and variability measures for protein families: Application to the immunoglobins
    • Gerstein M., and Altman R.B. Average core structures and variability measures for protein families: Application to the immunoglobins. J. Mol. Biol. 251 (1995) 161-175
    • (1995) J. Mol. Biol. , vol.251 , pp. 161-175
    • Gerstein, M.1    Altman, R.B.2
  • 149
    • 0028303880 scopus 로고
    • An algorithm combining DNA and protein alignment
    • Hein J. An algorithm combining DNA and protein alignment. J. Theor. Biol. 167 (1994) 169-174
    • (1994) J. Theor. Biol. , vol.167 , pp. 169-174
    • Hein, J.1
  • 150
    • 77956775086 scopus 로고    scopus 로고
    • Personal Communication
    • H. Carlson, Personal Communication, 2005.
    • (2005)
    • Carlson, H.1
  • 151
    • 0029762039 scopus 로고    scopus 로고
    • Ligand binding to heme proteins. VI. Interconversion of taxonomic substates in carbonmonoxymyoglobin
    • Johnson J., Lamb D., Frauenfelder H., Muller J., McMahon B., Nienhaus G., and Young R. Ligand binding to heme proteins. VI. Interconversion of taxonomic substates in carbonmonoxymyoglobin. Biophys. J. 71 (1996) 1563-1573
    • (1996) Biophys. J. , vol.71 , pp. 1563-1573
    • Johnson, J.1    Lamb, D.2    Frauenfelder, H.3    Muller, J.4    McMahon, B.5    Nienhaus, G.6    Young, R.7
  • 152
    • 0000379278 scopus 로고    scopus 로고
    • Probing heme protein conformational equilibration rates with kinetic selection
    • Tian W.D., Sage J.T., Champion P.M., Chien E., and Sligar S.G. Probing heme protein conformational equilibration rates with kinetic selection. Biochemistry 35 (1996) 3487-3502
    • (1996) Biochemistry , vol.35 , pp. 3487-3502
    • Tian, W.D.1    Sage, J.T.2    Champion, P.M.3    Chien, E.4    Sligar, S.G.5
  • 153
    • 0028328331 scopus 로고
    • Structural determinants of the stretching frequency of CO bound to myoglobin
    • Li T., Quillin M.L., Phillips Jr. G.N., and Olson J.S. Structural determinants of the stretching frequency of CO bound to myoglobin. Biochemistry 33 (1994) 1433-1446
    • (1994) Biochemistry , vol.33 , pp. 1433-1446
    • Li, T.1    Quillin, M.L.2    Phillips Jr., G.N.3    Olson, J.S.4
  • 154
    • 0027502033 scopus 로고
    • Carbon monoxide recombination to human myoglobin mutants in glycerol-water solutions
    • Balasubramanian S., Lambright D.G., Marden M.C., and Boxer S.G. Carbon monoxide recombination to human myoglobin mutants in glycerol-water solutions. Biochemistry 32 (1993) 2202-2212
    • (1993) Biochemistry , vol.32 , pp. 2202-2212
    • Balasubramanian, S.1    Lambright, D.G.2    Marden, M.C.3    Boxer, S.G.4
  • 156
    • 26944458918 scopus 로고    scopus 로고
    • The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA
    • Elsawy K.M., Hodgson M.K., and Caves L.S.D. The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA. Nucleic Acids Res 33 (2005) 5749-5762
    • (2005) Nucleic Acids Res , vol.33 , pp. 5749-5762
    • Elsawy, K.M.1    Hodgson, M.K.2    Caves, L.S.D.3
  • 157
    • 0002979498 scopus 로고
    • The meaning and strategic use of factor analysis
    • Cattell R.B. (Ed), Rand McNally, Chicago
    • Cattell R. The meaning and strategic use of factor analysis. In: Cattell R.B. (Ed). Handbook of Multivariate Experimental Psychology (1966), Rand McNally, Chicago 174-243
    • (1966) Handbook of Multivariate Experimental Psychology , pp. 174-243
    • Cattell, R.1
  • 158
    • 84937549955 scopus 로고
    • The scree test for the number of factors
    • Cattell R.B. The scree test for the number of factors. Multivar. Behav. Res. 1 (1966) 245-276
    • (1966) Multivar. Behav. Res. , vol.1 , pp. 245-276
    • Cattell, R.B.1
  • 160
    • 2342668583 scopus 로고    scopus 로고
    • Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories
    • Kazmierkiewicz R., Czaplewski C., Lammek B., and Ciarkowski J. Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories. J. Comput.-Aided Mol. Des. 13 (1999) 21-33
    • (1999) J. Comput.-Aided Mol. Des. , vol.13 , pp. 21-33
    • Kazmierkiewicz, R.1    Czaplewski, C.2    Lammek, B.3    Ciarkowski, J.4
  • 163
    • 31544456090 scopus 로고    scopus 로고
    • Insight into catalytically relevant correlated motions in human purine nucleoside phosphorylase
    • Nunez S., Wing C., Antoniou D., Schramm V.L., and Schwartz S.D. Insight into catalytically relevant correlated motions in human purine nucleoside phosphorylase. J. Phys. Chem. A 110 (2006) 463-472
    • (2006) J. Phys. Chem. A , vol.110 , pp. 463-472
    • Nunez, S.1    Wing, C.2    Antoniou, D.3    Schramm, V.L.4    Schwartz, S.D.5
  • 164
    • 33746907105 scopus 로고    scopus 로고
    • Native-state dynamics of the ubiquitin family: Implications for function and evolution
    • Marianayagam N.J., and Jackson S.E. Native-state dynamics of the ubiquitin family: Implications for function and evolution. J. Royal Soc. Interface 2 (2005) 47-54
    • (2005) J. Royal Soc. Interface , vol.2 , pp. 47-54
    • Marianayagam, N.J.1    Jackson, S.E.2
  • 166
    • 15744396923 scopus 로고    scopus 로고
    • In silico evidence for DNA polymerase-beta's substrate-induced conformational change
    • Arora K., and Schlick T. In silico evidence for DNA polymerase-beta's substrate-induced conformational change. Biophys. J. 87 (2004) 3088-3099
    • (2004) Biophys. J. , vol.87 , pp. 3088-3099
    • Arora, K.1    Schlick, T.2
  • 167
    • 6944250414 scopus 로고    scopus 로고
    • Sparsely populated folding intermediates of the Fyn SH3 domain: Matching native-centric essential dynamics and experiment
    • Ollerenshaw J.E., Kaya H., Chan H.S., and Kay L.E. Sparsely populated folding intermediates of the Fyn SH3 domain: Matching native-centric essential dynamics and experiment. Proc. Natl. Acad. Sci. 101 (2004) 14748-14753
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , pp. 14748-14753
    • Ollerenshaw, J.E.1    Kaya, H.2    Chan, H.S.3    Kay, L.E.4
  • 168
    • 0037183993 scopus 로고    scopus 로고
    • Structure and flexibility of Streptococcus agalactiae hyaluronate lyase complex with its substrate. Insights into the mechanism of processive degradation of hyaluronan
    • Mello L.V., De Groot B.L., Li S., and Jedrzejas M.J. Structure and flexibility of Streptococcus agalactiae hyaluronate lyase complex with its substrate. Insights into the mechanism of processive degradation of hyaluronan. J. Biol. Chem. 277 (2002) 36678-36688
    • (2002) J. Biol. Chem. , vol.277 , pp. 36678-36688
    • Mello, L.V.1    De Groot, B.L.2    Li, S.3    Jedrzejas, M.J.4
  • 169
    • 23244433046 scopus 로고    scopus 로고
    • Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP
    • Yang R., Lee M.C., Yan H., and Duan Y. Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP. Biophys. J. 89 (2005) 95-106
    • (2005) Biophys. J. , vol.89 , pp. 95-106
    • Yang, R.1    Lee, M.C.2    Yan, H.3    Duan, Y.4
  • 171
    • 0036882097 scopus 로고    scopus 로고
    • Helix motion in protein C12A-p8MTCP1: Comparison of molecular dynamics simulations and multifield NMR relaxation data
    • Barthe P., Roumestand C., Demene H., and Chiche L. Helix motion in protein C12A-p8MTCP1: Comparison of molecular dynamics simulations and multifield NMR relaxation data. J. Comp. Chem. 23 (2002) 1577-1586
    • (2002) J. Comp. Chem. , vol.23 , pp. 1577-1586
    • Barthe, P.1    Roumestand, C.2    Demene, H.3    Chiche, L.4
  • 172
    • 0037102153 scopus 로고    scopus 로고
    • High resolution crystal structure of the human PDK1 catalytic domain defines the regulatory phosphopeptide docking site
    • Biondi R.M., Komander D., Thomas C.C., Lizcano J.M., Deak M., Alessi D.R., and van Aalten D.M.F. High resolution crystal structure of the human PDK1 catalytic domain defines the regulatory phosphopeptide docking site. EMBO J. 21 (2002) 4219-4228
    • (2002) EMBO J. , vol.21 , pp. 4219-4228
    • Biondi, R.M.1    Komander, D.2    Thomas, C.C.3    Lizcano, J.M.4    Deak, M.5    Alessi, D.R.6    van Aalten, D.M.F.7
  • 173
    • 0034702768 scopus 로고    scopus 로고
    • Crystal structure of carboxypeptidase A complexed with D-cysteine at 1.75-Å--inhibitor-induced conformational changes
    • van Aalten D.M.F., Chong C.R., and Joshua-Tor L. Crystal structure of carboxypeptidase A complexed with D-cysteine at 1.75-Å--inhibitor-induced conformational changes,. Biochemistry 39 (2000) 10082-10089
    • (2000) Biochemistry , vol.39 , pp. 10082-10089
    • van Aalten, D.M.F.1    Chong, C.R.2    Joshua-Tor, L.3
  • 174
    • 0033974163 scopus 로고    scopus 로고
    • Conformational substates in different crystal forms of the photoactive yellow protein - Correlation with theoretical and experimental flexibility
    • van Aalten D.M.F., Crielaard W., Hellingwerf K.J., and Joshua-Tor L. Conformational substates in different crystal forms of the photoactive yellow protein - Correlation with theoretical and experimental flexibility. Protein Sci. 9 (2000) 64-72
    • (2000) Protein Sci. , vol.9 , pp. 64-72
    • van Aalten, D.M.F.1    Crielaard, W.2    Hellingwerf, K.J.3    Joshua-Tor, L.4
  • 175
    • 0032769661 scopus 로고    scopus 로고
    • Structural principles governing domain motions in proteins
    • Hayward S. Structural principles governing domain motions in proteins. Proteins 36 (1999) 425-435
    • (1999) Proteins , vol.36 , pp. 425-435
    • Hayward, S.1
  • 176
    • 0032101346 scopus 로고    scopus 로고
    • Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap
    • Abseher R., Horstink L., Hilbers C.W., and Nilges M. Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap. Proteins 31 (1998) 370-382
    • (1998) Proteins , vol.31 , pp. 370-382
    • Abseher, R.1    Horstink, L.2    Hilbers, C.W.3    Nilges, M.4
  • 177
    • 0032080528 scopus 로고    scopus 로고
    • Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data
    • de Groot B.L., Hayward S., van Aalten D.M., Amadei A., and Berendsen H.J. Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data. Proteins 31 (1998) 116-127
    • (1998) Proteins , vol.31 , pp. 116-127
    • de Groot, B.L.1    Hayward, S.2    van Aalten, D.M.3    Amadei, A.4    Berendsen, H.J.5
  • 178
    • 26444556851 scopus 로고    scopus 로고
    • Determinants of protein stability and folding: Comparative analysis of β-lactoglobulins and liver basic fatty acid binding protein
    • Ragona L., Colombo G., Catalano M., and Molinari H. Determinants of protein stability and folding: Comparative analysis of β-lactoglobulins and liver basic fatty acid binding protein. Proteins 61 (2005) 366-376
    • (2005) Proteins , vol.61 , pp. 366-376
    • Ragona, L.1    Colombo, G.2    Catalano, M.3    Molinari, H.4
  • 179
    • 17844365851 scopus 로고    scopus 로고
    • Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent
    • Sugita Y., and Okamoto Y. Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent. Biophys. J. 88 (2005) 3180-3190
    • (2005) Biophys. J. , vol.88 , pp. 3180-3190
    • Sugita, Y.1    Okamoto, Y.2
  • 180
    • 10344222093 scopus 로고    scopus 로고
    • Structural and dynamic effects of α-helix deletion in Sso7d: Implications for protein thermal stability
    • Merlino A., Graziano G., and Mazzarella L. Structural and dynamic effects of α-helix deletion in Sso7d: Implications for protein thermal stability. Proteins 57 (2004) 692-701
    • (2004) Proteins , vol.57 , pp. 692-701
    • Merlino, A.1    Graziano, G.2    Mazzarella, L.3
  • 181
    • 0037339403 scopus 로고    scopus 로고
    • Selective excitation of native fluctuations during thermal unfolding simulations: Horse heart cytochrome c as a case study
    • Roccatano D., Daidone I., Ceruso M.-A., Bossa C., and Nola Alfredo D. Selective excitation of native fluctuations during thermal unfolding simulations: Horse heart cytochrome c as a case study. Biophys. J. 84 (2003) 1876-1883
    • (2003) Biophys. J. , vol.84 , pp. 1876-1883
    • Roccatano, D.1    Daidone, I.2    Ceruso, M.-A.3    Bossa, C.4    Nola Alfredo, D.5
  • 182
    • 0037194967 scopus 로고    scopus 로고
    • Two-dimensional correlation analysis of peptide unfolding: Molecular dynamics simulations of β hairpins
    • Lee J., and Shin S. Two-dimensional correlation analysis of peptide unfolding: Molecular dynamics simulations of β hairpins. J. Phys. Chem. B 106 (2002) 8796-8802
    • (2002) J. Phys. Chem. B , vol.106 , pp. 8796-8802
    • Lee, J.1    Shin, S.2
  • 183
    • 0035946983 scopus 로고    scopus 로고
    • Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds
    • de Groot B.L., Daura X., Mark A.E., and Grubmuller H. Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds. J. Mol. Biol. 309 (2001) 299-313
    • (2001) J. Mol. Biol. , vol.309 , pp. 299-313
    • de Groot, B.L.1    Daura, X.2    Mark, A.E.3    Grubmuller, H.4
  • 184
    • 0031686334 scopus 로고    scopus 로고
    • Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations
    • Creveld L.D., Amadei A., van Schaik R.C., Pepermans H.A., de Vlieg J., and Berendsen H.J. Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations. Proteins 33 (1998) 253-264
    • (1998) Proteins , vol.33 , pp. 253-264
    • Creveld, L.D.1    Amadei, A.2    van Schaik, R.C.3    Pepermans, H.A.4    de Vlieg, J.5    Berendsen, H.J.6
  • 185
    • 18744363916 scopus 로고    scopus 로고
    • A gating mechanism proposed from a simulation of a human α7 nicotinic acetylcholine receptor
    • Law R.J., Henchman R.H., and McCammon J.A. A gating mechanism proposed from a simulation of a human α7 nicotinic acetylcholine receptor. Proc. Natl. Acad. Sci. 102 (2005) 6813-6818
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 6813-6818
    • Law, R.J.1    Henchman, R.H.2    McCammon, J.A.3
  • 186
    • 0037472629 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a K+ channel blocker: Tc1 toxin from Tityus cambridgei
    • Grottesi A., and Sansom Mark S.P. Molecular dynamics simulations of a K+ channel blocker: Tc1 toxin from Tityus cambridgei. FEBS lett 535 (2003) 29-33
    • (2003) FEBS lett , vol.535 , pp. 29-33
    • Grottesi, A.1    Sansom Mark, S.P.2
  • 187
    • 0036841855 scopus 로고    scopus 로고
    • Analysis and evaluation of channel models: Simulations of alamethicin
    • Tieleman D.P., Hess B., and Sansom M.S.P. Analysis and evaluation of channel models: Simulations of alamethicin. Biophys. J. 83 (2002) 2393-2407
    • (2002) Biophys. J. , vol.83 , pp. 2393-2407
    • Tieleman, D.P.1    Hess, B.2    Sansom, M.S.P.3
  • 188
    • 0034907678 scopus 로고    scopus 로고
    • Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa
    • Lins R.D., and Straatsma T.P. Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa. Biophys. J. 81 (2001) 1037-1046
    • (2001) Biophys. J. , vol.81 , pp. 1037-1046
    • Lins, R.D.1    Straatsma, T.P.2
  • 189
    • 0035193287 scopus 로고    scopus 로고
    • Influence of a lipid interface on protein dynamics in a fungal lipase
    • Peters G.H., and Bywater R.P. Influence of a lipid interface on protein dynamics in a fungal lipase. Biophys. J. 81 (2001) 3052-3065
    • (2001) Biophys. J. , vol.81 , pp. 3052-3065
    • Peters, G.H.1    Bywater, R.P.2
  • 190
    • 0034030664 scopus 로고    scopus 로고
    • Structure and dynamics of K channel pore-lining helices: A comparative simulation study
    • Shrivastava I.H., Capener C.E., Forrest L.R., and Sansom M.S.P. Structure and dynamics of K channel pore-lining helices: A comparative simulation study. Biophys. J. 78 (2000) 79-92
    • (2000) Biophys. J. , vol.78 , pp. 79-92
    • Shrivastava, I.H.1    Capener, C.E.2    Forrest, L.R.3    Sansom, M.S.P.4
  • 191
    • 0031788690 scopus 로고    scopus 로고
    • Hinge-bending motions in annexins: Molecular dynamics and essential dynamics of apo-annexin V and of calcium bound annexin V and I
    • Cregut D., Drin G., Liautard J.P., and Chiche L. Hinge-bending motions in annexins: Molecular dynamics and essential dynamics of apo-annexin V and of calcium bound annexin V and I. Protein Eng. 11 (1998) 891-900
    • (1998) Protein Eng. , vol.11 , pp. 891-900
    • Cregut, D.1    Drin, G.2    Liautard, J.P.3    Chiche, L.4
  • 192
    • 17844406393 scopus 로고    scopus 로고
    • Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutants
    • Lee M.C., Deng J., Briggs J.M., and Duan Y. Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutants. Biophys. J. 88 (2005) 3133-3146
    • (2005) Biophys. J. , vol.88 , pp. 3133-3146
    • Lee, M.C.1    Deng, J.2    Briggs, J.M.3    Duan, Y.4
  • 193
    • 2442612037 scopus 로고    scopus 로고
    • Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling
    • Daidone I., Roccatano D., and Hayward S. Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling. J. Mol. Biol. 339 (2004) 515-525
    • (2004) J. Mol. Biol. , vol.339 , pp. 515-525
    • Daidone, I.1    Roccatano, D.2    Hayward, S.3
  • 194
    • 2442674051 scopus 로고    scopus 로고
    • Solvent interactions and protein dynamics in spin-labeled T4 lysozyme
    • Stoica I. Solvent interactions and protein dynamics in spin-labeled T4 lysozyme. J. Biomol. Struct. Dyn. 21 (2004) 745-760
    • (2004) J. Biomol. Struct. Dyn. , vol.21 , pp. 745-760
    • Stoica, I.1
  • 195
    • 0035881490 scopus 로고    scopus 로고
    • Functional and structural roles of the glutathione-binding residues in maize (Zea mays) glutathione S-transferase I
    • Labrou N.E., Mello L.V., and Clonis Y.D. Functional and structural roles of the glutathione-binding residues in maize (Zea mays) glutathione S-transferase I. Biochem. J. 358 (2001) 101-110
    • (2001) Biochem. J. , vol.358 , pp. 101-110
    • Labrou, N.E.1    Mello, L.V.2    Clonis, Y.D.3
  • 196
    • 0035958660 scopus 로고    scopus 로고
    • Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation
    • Roccatano D., Mark A.E., and Hayward S. Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation. J. Mol. Biol. 310 (2001) 1039-1053
    • (2001) J. Mol. Biol. , vol.310 , pp. 1039-1053
    • Roccatano, D.1    Mark, A.E.2    Hayward, S.3
  • 197
    • 0035576304 scopus 로고    scopus 로고
    • Revisiting the structural flexibility of the complex p21ras-GTP: The catalytic conformation of the molecular switch II
    • Soares T.A., Miller J.H., and Straatsma T.P. Revisiting the structural flexibility of the complex p21ras-GTP: The catalytic conformation of the molecular switch II. Proteins 45 (2001) 297-312
    • (2001) Proteins , vol.45 , pp. 297-312
    • Soares, T.A.1    Miller, J.H.2    Straatsma, T.P.3
  • 198
    • 0035862926 scopus 로고    scopus 로고
    • Domain movement in the epidermal growth factor family of peptides
    • Watts C.R., Toth G., Murphy R.F., and Lovas S. Domain movement in the epidermal growth factor family of peptides. Theochemistry 535 (2001) 171-182
    • (2001) Theochemistry , vol.535 , pp. 171-182
    • Watts, C.R.1    Toth, G.2    Murphy, R.F.3    Lovas, S.4
  • 199
    • 0031019423 scopus 로고    scopus 로고
    • Engineering protein mechanics: Inhibition of concerted motions of the cellular retinol binding protein by site-directed mutagenesis
    • van Aalten D.M.F., Jones P.C., De Sousa M., and Findlay J.B.C. Engineering protein mechanics: Inhibition of concerted motions of the cellular retinol binding protein by site-directed mutagenesis. Protein Eng. 10 (1997) 31-37
    • (1997) Protein Eng. , vol.10 , pp. 31-37
    • van Aalten, D.M.F.1    Jones, P.C.2    De Sousa, M.3    Findlay, J.B.C.4
  • 200
    • 0035908899 scopus 로고    scopus 로고
    • Molecular dynamics simulation and essential dynamics study of mutated plastocyanin: Structural, dynamical and functional effects of a disulfide bridge insertion at the protein surface
    • Arcangeli C., Bizzarri A.R., and Cannistraro S. Molecular dynamics simulation and essential dynamics study of mutated plastocyanin: Structural, dynamical and functional effects of a disulfide bridge insertion at the protein surface. Biophys. Chem. 92 (2001) 183-199
    • (2001) Biophys. Chem. , vol.92 , pp. 183-199
    • Arcangeli, C.1    Bizzarri, A.R.2    Cannistraro, S.3
  • 201
    • 0033214379 scopus 로고    scopus 로고
    • Molecular dynamics simulations of human glutathione transferase P1-1: Conformational fluctuations of the apo-structure
    • Stella L., Di Iorio E.E., Nicotra M., and Ricci G. Molecular dynamics simulations of human glutathione transferase P1-1: Conformational fluctuations of the apo-structure. Proteins 37 (1999) 10-19
    • (1999) Proteins , vol.37 , pp. 10-19
    • Stella, L.1    Di Iorio, E.E.2    Nicotra, M.3    Ricci, G.4
  • 202
    • 18344395352 scopus 로고    scopus 로고
    • Conservation and specialization in PAS domain dynamics
    • Pandini A., and Bonati L. Conservation and specialization in PAS domain dynamics. Prot. Eng. Des. Sel. 18 (2005) 127-137
    • (2005) Prot. Eng. Des. Sel. , vol.18 , pp. 127-137
    • Pandini, A.1    Bonati, L.2
  • 203
    • 0042821730 scopus 로고    scopus 로고
    • Subtle functional collective motions in pancreatic-like ribonucleases: From ribonuclease A to angiogenin
    • Merlino A., Vitagliano L., Ceruso Marc A., and Mazzarella L. Subtle functional collective motions in pancreatic-like ribonucleases: From ribonuclease A to angiogenin. Proteins 53 (2003) 101-110
    • (2003) Proteins , vol.53 , pp. 101-110
    • Merlino, A.1    Vitagliano, L.2    Ceruso Marc, A.3    Mazzarella, L.4
  • 204
    • 0037380948 scopus 로고    scopus 로고
    • Molecular dynamics studies of caspase-3
    • Sulpizi M., Rothlisberger U., and Carloni P. Molecular dynamics studies of caspase-3. Biophys. J. 84 (2003) 2207-2215
    • (2003) Biophys. J. , vol.84 , pp. 2207-2215
    • Sulpizi, M.1    Rothlisberger, U.2    Carloni, P.3
  • 205
    • 0037083630 scopus 로고    scopus 로고
    • Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin
    • Grottesi A., Ceruso M.-A., Colosimo A., and Di Nola A. Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin. Proteins 46 (2002) 287-294
    • (2002) Proteins , vol.46 , pp. 287-294
    • Grottesi, A.1    Ceruso, M.-A.2    Colosimo, A.3    Di Nola, A.4
  • 206
    • 0037008738 scopus 로고    scopus 로고
    • Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase
    • Jedrzejas M.J., Mello L.V., de Groot B., and Li S. Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. J. Biol. Chem. 277 (2002) 28287-28297
    • (2002) J. Biol. Chem. , vol.277 , pp. 28287-28297
    • Jedrzejas, M.J.1    Mello, L.V.2    de Groot, B.3    Li, S.4
  • 207
    • 0036226117 scopus 로고    scopus 로고
    • Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domain
    • Otyepka M., and Damborsky J. Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domain. Protein Sci. 11 (2002) 1206-1217
    • (2002) Protein Sci. , vol.11 , pp. 1206-1217
    • Otyepka, M.1    Damborsky, J.2
  • 208
    • 0036769569 scopus 로고    scopus 로고
    • Essential dynamics and sidechain hydrogen bond cluster studies on eosinophil cationic protein
    • Sanjeev B.S., and Vishveshwara S. Essential dynamics and sidechain hydrogen bond cluster studies on eosinophil cationic protein. Eur. Phys. J. D. 20 (2002) 601-608
    • (2002) Eur. Phys. J. D. , vol.20 , pp. 601-608
    • Sanjeev, B.S.1    Vishveshwara, S.2
  • 209
    • 0035869698 scopus 로고    scopus 로고
    • Concerted motions in copper plastocyanin and azurin: An essential dynamics study
    • Arcangeli C., Bizzarri A.R., and Cannistraro S. Concerted motions in copper plastocyanin and azurin: An essential dynamics study. Biophys. Chem. 90 (2001) 45-56
    • (2001) Biophys. Chem. , vol.90 , pp. 45-56
    • Arcangeli, C.1    Bizzarri, A.R.2    Cannistraro, S.3
  • 210
    • 0034607413 scopus 로고    scopus 로고
    • Similarities in the HIV-1 and ASV integrase active sites upon metal cofactor binding
    • Lins R.D., Straatsma T.P., and Briggs J.M. Similarities in the HIV-1 and ASV integrase active sites upon metal cofactor binding. Biopolymers 53 (2000) 308-315
    • (2000) Biopolymers , vol.53 , pp. 308-315
    • Lins, R.D.1    Straatsma, T.P.2    Briggs, J.M.3
  • 212
    • 0033525835 scopus 로고    scopus 로고
    • Conformational changes in the chaperonin GroEL: New insights into the allosteric mechanism
    • de Groot B.L., Vriend G., and Berendsen H.J. Conformational changes in the chaperonin GroEL: New insights into the allosteric mechanism. J. Mol. Biol. 286 (1999) 1241-1249
    • (1999) J. Mol. Biol. , vol.286 , pp. 1241-1249
    • de Groot, B.L.1    Vriend, G.2    Berendsen, H.J.3
  • 213
    • 0033515432 scopus 로고    scopus 로고
    • Functionally important correlated motions in the single-stranded DNA-binding protein encoded by filamentous phage Pf3
    • Horstink L., Abseher R., Nilges M., and Hilbers C.W. Functionally important correlated motions in the single-stranded DNA-binding protein encoded by filamentous phage Pf3. J. Mol. Biol. 287 (1999) 569-577
    • (1999) J. Mol. Biol. , vol.287 , pp. 569-577
    • Horstink, L.1    Abseher, R.2    Nilges, M.3    Hilbers, C.W.4
  • 216
    • 1942519384 scopus 로고    scopus 로고
    • Dynamic properties of the N-terminal swapped dimer of ribonuclease A
    • Merlino A., Vitagliano L., Ceruso M.A., and Mazzarella L. Dynamic properties of the N-terminal swapped dimer of ribonuclease A. Biophys. J. 86 (2004) 2383-2391
    • (2004) Biophys. J. , vol.86 , pp. 2383-2391
    • Merlino, A.1    Vitagliano, L.2    Ceruso, M.A.3    Mazzarella, L.4
  • 217
    • 0037295565 scopus 로고    scopus 로고
    • Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa
    • Ceruso M.A., Grottesi A., and Di Nola A. Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa. Proteins 50 (2003) 222-229
    • (2003) Proteins , vol.50 , pp. 222-229
    • Ceruso, M.A.1    Grottesi, A.2    Di Nola, A.3
  • 218
    • 0037380951 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the NGF-TrkA domain 5 complex and comparison with biological data
    • Settanni G., Cattaneo A., and Carloni P. Molecular dynamics simulations of the NGF-TrkA domain 5 complex and comparison with biological data. Biophys. J. 84 (2003) 2282-2292
    • (2003) Biophys. J. , vol.84 , pp. 2282-2292
    • Settanni, G.1    Cattaneo, A.2    Carloni, P.3
  • 219
    • 0034106349 scopus 로고    scopus 로고
    • Theoretical studies of the response of a protein structure to cavity-creating mutations
    • Lee J., Lee K., and Shin S. Theoretical studies of the response of a protein structure to cavity-creating mutations. Biophys. J. 78 (2000) 1665-1671
    • (2000) Biophys. J. , vol.78 , pp. 1665-1671
    • Lee, J.1    Lee, K.2    Shin, S.3
  • 220
    • 17844395966 scopus 로고    scopus 로고
    • Comparison of multiple molecular dynamics trajectories calculated for the drug-resistant HIV-1 integrase T66I/M154I catalytic domain
    • Brigo A., Lee K.W., Mustata G.I., and Briggs J.M. Comparison of multiple molecular dynamics trajectories calculated for the drug-resistant HIV-1 integrase T66I/M154I catalytic domain. Biophys. J. 88 (2005) 3072-3082
    • (2005) Biophys. J. , vol.88 , pp. 3072-3082
    • Brigo, A.1    Lee, K.W.2    Mustata, G.I.3    Briggs, J.M.4
  • 221
    • 33745470047 scopus 로고    scopus 로고
    • Stability and dynamics of domain-swapped bovine-seminal ribonuclease
    • Chakrabarti K.S., Sanjeev B.S., and Vishveshwara S. Stability and dynamics of domain-swapped bovine-seminal ribonuclease. Chem. Biodiv. 1 (2004) 802-818
    • (2004) Chem. Biodiv. , vol.1 , pp. 802-818
    • Chakrabarti, K.S.1    Sanjeev, B.S.2    Vishveshwara, S.3
  • 222
    • 4344703330 scopus 로고    scopus 로고
    • Molecular modelling of the nucleotide-binding domain of Wilson's disease protein: Location of the ATP-binding site, domain dynamics, and potential effects of the major disease mutations
    • Efremov R.G., Kosinsky Y.A., Nolde D.E., Tsivkovskii R., Arseniev A.S., and Lutsenko S. Molecular modelling of the nucleotide-binding domain of Wilson's disease protein: Location of the ATP-binding site, domain dynamics, and potential effects of the major disease mutations. Biochem. J. 382 (2004) 293-305
    • (2004) Biochem. J. , vol.382 , pp. 293-305
    • Efremov, R.G.1    Kosinsky, Y.A.2    Nolde, D.E.3    Tsivkovskii, R.4    Arseniev, A.S.5    Lutsenko, S.6
  • 223
    • 0038695001 scopus 로고    scopus 로고
    • Effects of pathological mutations on the stability of a conserved amino acid triad in retinoschisin
    • Fraternali F., Cavallo L., and Musco G. Effects of pathological mutations on the stability of a conserved amino acid triad in retinoschisin. FEBS Lett. 544 (2003) 21-26
    • (2003) FEBS Lett. , vol.544 , pp. 21-26
    • Fraternali, F.1    Cavallo, L.2    Musco, G.3
  • 226
    • 23044435795 scopus 로고    scopus 로고
    • Flexibility of prolyl oligopeptidase: Molecular dynamics and molecular framework analysis of the potential substrate pathways
    • Fuxreiter M., Magyar C., Juhasz T., Szeltner Z., Polgar L., and Simon I. Flexibility of prolyl oligopeptidase: Molecular dynamics and molecular framework analysis of the potential substrate pathways. Proteins 60 (2005) 504-512
    • (2005) Proteins , vol.60 , pp. 504-512
    • Fuxreiter, M.1    Magyar, C.2    Juhasz, T.3    Szeltner, Z.4    Polgar, L.5    Simon, I.6
  • 227
    • 2942655520 scopus 로고    scopus 로고
    • Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin
    • Bossa C., Anselmi M., Roccatano D., Amadei A., Vallone B., Brunori M., and Di Nola A. Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin. Biophys. J. 86 (2004) 3855-3862
    • (2004) Biophys. J. , vol.86 , pp. 3855-3862
    • Bossa, C.1    Anselmi, M.2    Roccatano, D.3    Amadei, A.4    Vallone, B.5    Brunori, M.6    Di Nola, A.7
  • 228
    • 0037339235 scopus 로고    scopus 로고
    • Molecular dynamics studies of the wild-type and double mutant HIV-1 integrase complexed with the 5CITEP inhibitor: Mechanism for inhibition and drug resistance
    • Barreca M.L., Lee K.W., Chimirri A., and Briggs J.M. Molecular dynamics studies of the wild-type and double mutant HIV-1 integrase complexed with the 5CITEP inhibitor: Mechanism for inhibition and drug resistance. Biophys. J. 84 (2003) 1450-1463
    • (2003) Biophys. J. , vol.84 , pp. 1450-1463
    • Barreca, M.L.1    Lee, K.W.2    Chimirri, A.3    Briggs, J.M.4
  • 229
    • 0141891817 scopus 로고    scopus 로고
    • Molecular dynamics studies of alanine racemase: A structural model for drug design
    • Mustata G.I., Soares T.A., and Briggs J.M. Molecular dynamics studies of alanine racemase: A structural model for drug design. Biopolymers 70 (2003) 186-200
    • (2003) Biopolymers , vol.70 , pp. 186-200
    • Mustata, G.I.1    Soares, T.A.2    Briggs, J.M.3
  • 230
    • 0037671391 scopus 로고    scopus 로고
    • Interdomain dynamics and ligand binding: Molecular dynamics simulations of glutamine binding protein
    • Pang A., Arinaminpathy Y., Sansom Mark S.P., and Biggin Philip C. Interdomain dynamics and ligand binding: Molecular dynamics simulations of glutamine binding protein. FEBS lett. 550 (2003) 168-174
    • (2003) FEBS lett. , vol.550 , pp. 168-174
    • Pang, A.1    Arinaminpathy, Y.2    Sansom Mark, S.P.3    Biggin Philip, C.4
  • 231
    • 0034634391 scopus 로고    scopus 로고
    • How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways
    • Ludemann S.K., Lounnas V., and Wade R.C. How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways. J. Mol. Biol. 303 (2000) 813-830
    • (2000) J. Mol. Biol. , vol.303 , pp. 813-830
    • Ludemann, S.K.1    Lounnas, V.2    Wade, R.C.3
  • 232
    • 0034026757 scopus 로고    scopus 로고
    • Molecular dynamics simulations of protein-tyrosine phosphatase 1B. II. Substrate-enzyme interactions and dynamics
    • Peters G.H., Frimurer T.M., Andersen J.N., and Olsen O.H. Molecular dynamics simulations of protein-tyrosine phosphatase 1B. II. Substrate-enzyme interactions and dynamics. Biophys. J. 78 (2000) 2191-2200
    • (2000) Biophys. J. , vol.78 , pp. 2191-2200
    • Peters, G.H.1    Frimurer, T.M.2    Andersen, J.N.3    Olsen, O.H.4
  • 233
    • 0031042565 scopus 로고    scopus 로고
    • Essential dynamics of lipase binding sites: The effect of inhibitors of different chain length
    • Peters G.H., van Aalten D.M., Svendsen A., and Bywater R. Essential dynamics of lipase binding sites: The effect of inhibitors of different chain length. Protein Eng. 10 (1997) 149-158
    • (1997) Protein Eng. , vol.10 , pp. 149-158
    • Peters, G.H.1    van Aalten, D.M.2    Svendsen, A.3    Bywater, R.4
  • 234
    • 1542316338 scopus 로고    scopus 로고
    • Reorganization in apo- and holo-β-lactoglobulin upon protonation of Glu89: Molecular dynamics and pKa calculations
    • Eberini I., Baptista A.M., Gianazza E., Fraternali F., and Beringhelli T. Reorganization in apo- and holo-β-lactoglobulin upon protonation of Glu89: Molecular dynamics and pKa calculations. Proteins 54 (2004) 744-758
    • (2004) Proteins , vol.54 , pp. 744-758
    • Eberini, I.1    Baptista, A.M.2    Gianazza, E.3    Fraternali, F.4    Beringhelli, T.5
  • 235
    • 0141524056 scopus 로고    scopus 로고
    • Molecular dynamics simulation of highly charged proteins: Comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions
    • Gargallo R., Huenenberger P.H., Aviles F.X., and Oliva B. Molecular dynamics simulation of highly charged proteins: Comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions. Protein Sci. 12 (2003) 2161-2172
    • (2003) Protein Sci. , vol.12 , pp. 2161-2172
    • Gargallo, R.1    Huenenberger, P.H.2    Aviles, F.X.3    Oliva, B.4
  • 236
    • 21644460933 scopus 로고    scopus 로고
    • Docking essential dynamics eigenstructures
    • Mustard D., and Ritchie David W. Docking essential dynamics eigenstructures. Proteins 60 (2005) 269-274
    • (2005) Proteins , vol.60 , pp. 269-274
    • Mustard, D.1    Ritchie David, W.2
  • 238
    • 0346434954 scopus 로고    scopus 로고
    • Inhibitor specificity via protein dynamics insights from the design of antibacterial agents targeted against thymidylate synthase
    • Ferrari S., Costi P.M., and Wade R.C. Inhibitor specificity via protein dynamics insights from the design of antibacterial agents targeted against thymidylate synthase. Chem. Biol. 10 (2003) 1183-1193
    • (2003) Chem. Biol. , vol.10 , pp. 1183-1193
    • Ferrari, S.1    Costi, P.M.2    Wade, R.C.3
  • 239
    • 4744350893 scopus 로고    scopus 로고
    • Relative flexibility of DNA and RNA: A molecular dynamcis study
    • Noy A., Perez A., Lankas F., Luque F.J., and Orozco M. Relative flexibility of DNA and RNA: A molecular dynamcis study. J. Mol. Biol. 343 (2004) 627-638
    • (2004) J. Mol. Biol. , vol.343 , pp. 627-638
    • Noy, A.1    Perez, A.2    Lankas, F.3    Luque, F.J.4    Orozco, M.5
  • 240
    • 11444267252 scopus 로고    scopus 로고
    • The relative flexibility of B-DNA and A-RNA duplexes: Database analysis
    • Perez A., Noy A., Lankas F., Luque F.J., and Orozco M. The relative flexibility of B-DNA and A-RNA duplexes: Database analysis. Nucleic Acids Res. 32 (2004) 6144-6151
    • (2004) Nucleic Acids Res. , vol.32 , pp. 6144-6151
    • Perez, A.1    Noy, A.2    Lankas, F.3    Luque, F.J.4    Orozco, M.5
  • 241
    • 1242347628 scopus 로고    scopus 로고
    • Theoretical methods for the simulation of nucleic acids
    • Orozco M., Perez A., Noy A., and Luque F.J. Theoretical methods for the simulation of nucleic acids. Chem. Soc. Rev. 32 (2003) 350-364
    • (2003) Chem. Soc. Rev. , vol.32 , pp. 350-364
    • Orozco, M.1    Perez, A.2    Noy, A.3    Luque, F.J.4
  • 242
    • 20444464100 scopus 로고    scopus 로고
    • Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif
    • Cojocaru V., Klement R., and Jovin T.M. Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif. Nucleic Acids Res. 33 (2005) 3435-3446
    • (2005) Nucleic Acids Res. , vol.33 , pp. 3435-3446
    • Cojocaru, V.1    Klement, R.2    Jovin, T.M.3
  • 243
    • 16844365511 scopus 로고    scopus 로고
    • Structure, recognition properties, and flexibility of the DNA.RNA hybrid
    • Noy A., Perez A., Marquez M., Luque F.J., and Orozco M. Structure, recognition properties, and flexibility of the DNA.RNA hybrid. J. Am. Chem. Soc. 127 (2005) 4910-4920
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 4910-4920
    • Noy, A.1    Perez, A.2    Marquez, M.3    Luque, F.J.4    Orozco, M.5
  • 246
  • 249
    • 27844545326 scopus 로고    scopus 로고
    • Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer
    • Jha S., Coveney P.V., and Laughton C.A. Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer. J. Comp. Chem. 26 (2005) 1617-1627
    • (2005) J. Comp. Chem. , vol.26 , pp. 1617-1627
    • Jha, S.1    Coveney, P.V.2    Laughton, C.A.3
  • 250
    • 0037526621 scopus 로고    scopus 로고
    • The structure and dynamics of DNA in the gas phase
    • Rueda M., Kalko S.G., Luque F.J., and Orozco M. The structure and dynamics of DNA in the gas phase. J. Am. Chem. Soc. 125 (2003) 8007-8014
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 8007-8014
    • Rueda, M.1    Kalko, S.G.2    Luque, F.J.3    Orozco, M.4
  • 251
    • 0034701222 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acids with a generalized born model
    • Tsui V., and Case D.A. Molecular dynamics simulations of nucleic acids with a generalized born model. J. Am. Chem. Soc. 122 (2000) 2489-2498
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2489-2498
    • Tsui, V.1    Case, D.A.2
  • 252
    • 26944462733 scopus 로고    scopus 로고
    • Independent component analysis yields chemically interpretable latent variables in multivariate regression
    • Gustafsson M.G. Independent component analysis yields chemically interpretable latent variables in multivariate regression. J. Chem. Inf. Model. 45 (2005) 1244-1255
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 1244-1255
    • Gustafsson, M.G.1
  • 254
    • 0000466122 scopus 로고    scopus 로고
    • Survey on independent component analysis
    • Hyvarinen A. Survey on independent component analysis. Neural Comput. Surveys 2 (1999) 94-128
    • (1999) Neural Comput. Surveys , vol.2 , pp. 94-128
    • Hyvarinen, A.1
  • 255
    • 29244474352 scopus 로고    scopus 로고
    • Solvation Transduction and independent component analysis for pattern recognition in SAW electronic nose
    • Yadava R.D.S., and Chaudhary R. Solvation Transduction and independent component analysis for pattern recognition in SAW electronic nose. Sens. Actuators B 113 (2006) 1-21
    • (2006) Sens. Actuators B , vol.113 , pp. 1-21
    • Yadava, R.D.S.1    Chaudhary, R.2
  • 256
    • 0142102591 scopus 로고    scopus 로고
    • Cross validation and uncertainty estimates in independent component analysis
    • Westad F., and Kermit M. Cross validation and uncertainty estimates in independent component analysis. Anal. Chim. Acta. 490 (2003) 341-354
    • (2003) Anal. Chim. Acta. , vol.490 , pp. 341-354
    • Westad, F.1    Kermit, M.2
  • 257
    • 20444478373 scopus 로고    scopus 로고
    • Application of independent component analysis to 1H MR spectroscopic imaging exams of brain tumors
    • de Edelenyi F.S., Simonetti A.W., Postma G., Huo R., and Buydens L.M.C. Application of independent component analysis to 1H MR spectroscopic imaging exams of brain tumors. Anal. Chim. Acta. 544 (2005) 36-46
    • (2005) Anal. Chim. Acta. , vol.544 , pp. 36-46
    • de Edelenyi, F.S.1    Simonetti, A.W.2    Postma, G.3    Huo, R.4    Buydens, L.M.C.5
  • 258
    • 24944488551 scopus 로고    scopus 로고
    • Blind phase projection as an effective means of recovering pure component spectra from phase modulated photoacoustic spectra
    • Pichler A., and Sowa M.G. Blind phase projection as an effective means of recovering pure component spectra from phase modulated photoacoustic spectra. Vib. Spectrosc. 39 (2005) 163-168
    • (2005) Vib. Spectrosc. , vol.39 , pp. 163-168
    • Pichler, A.1    Sowa, M.G.2
  • 259
    • 27644550602 scopus 로고    scopus 로고
    • Three-dimensional optical tomographic imaging of scattering objects in tissue-simulating turbid media using independent component analysis
    • Alrubaiee M., Xu M., Gayen S.K., Brito M., and Alfano R.R. Three-dimensional optical tomographic imaging of scattering objects in tissue-simulating turbid media using independent component analysis. Appl. Phys. Lett. 87 (2005) 191112-191113
    • (2005) Appl. Phys. Lett. , vol.87 , pp. 191112-191113
    • Alrubaiee, M.1    Xu, M.2    Gayen, S.K.3    Brito, M.4    Alfano, R.R.5
  • 260
    • 28844501729 scopus 로고    scopus 로고
    • Complexity of time series associated to dynamical systems inferred from independent component analysis
    • De Lauro E., De Martino S., Falanga M., Ciaramella A., and Tagliaferri R. Complexity of time series associated to dynamical systems inferred from independent component analysis. Phys. Rev. E 72 (2005) 046712/1-046712/14
    • (2005) Phys. Rev. E , vol.72
    • De Lauro, E.1    De Martino, S.2    Falanga, M.3    Ciaramella, A.4    Tagliaferri, R.5
  • 261
    • 0037120477 scopus 로고    scopus 로고
    • Stochastic resonance mechanism in aerosol index dynamics
    • De Martino S., Falanga M., and Mona L. Stochastic resonance mechanism in aerosol index dynamics. Phys. Rev. Lett. 89 (2002) 128501/1-128501/4
    • (2002) Phys. Rev. Lett. , vol.89
    • De Martino, S.1    Falanga, M.2    Mona, L.3
  • 262
    • 0027879547 scopus 로고
    • On the early history of the singular value decomposition
    • Stewart G.W. On the early history of the singular value decomposition. SIAM Rev 35 (1993) 551-566
    • (1993) SIAM Rev , vol.35 , pp. 551-566
    • Stewart, G.W.1
  • 263
    • 2542430932 scopus 로고    scopus 로고
    • Singular value decomposition and principal component analysis
    • Berrar D.P., Dubitzky W., and Granzow M. (Eds), Kluwer, Norwell, MA
    • Wall M.E., Rechtsteiner A., and Rocha L.M. Singular value decomposition and principal component analysis. In: Berrar D.P., Dubitzky W., and Granzow M. (Eds). A Practical Approach to Microarray Data Analysis (2003), Kluwer, Norwell, MA 91-109
    • (2003) A Practical Approach to Microarray Data Analysis , pp. 91-109
    • Wall, M.E.1    Rechtsteiner, A.2    Rocha, L.M.3
  • 264
    • 25444472585 scopus 로고    scopus 로고
    • Pathway level analysis of gene expression using singular value decomposition
    • J. Tomfohr, J. Lu and T. B. Kepler, Pathway level analysis of gene expression using singular value decomposition, BMC Bioinform. 6 (2005).
    • (2005) BMC Bioinform , vol.6
    • Tomfohr, J.1    Lu, J.2    Kepler, T.B.3
  • 265
    • 18544362653 scopus 로고    scopus 로고
    • Noise reduction in X-ray photoelectron spectromicroscopy by a singular value decomposition sorting procedure
    • Walton J., and Fairley N. Noise reduction in X-ray photoelectron spectromicroscopy by a singular value decomposition sorting procedure. J. Electr. Spectr. Relat. Phenom. 148 (2005) 29-40
    • (2005) J. Electr. Spectr. Relat. Phenom. , vol.148 , pp. 29-40
    • Walton, J.1    Fairley, N.2
  • 266
    • 9544254860 scopus 로고    scopus 로고
    • Covariance NMR spectroscopy by singular value decomposition
    • Trbovic N., Smirnov S., Zhang F., and Bruschweiler R. Covariance NMR spectroscopy by singular value decomposition. J. Magn. Reson. 171 (2004) 277-283
    • (2004) J. Magn. Reson. , vol.171 , pp. 277-283
    • Trbovic, N.1    Smirnov, S.2    Zhang, F.3    Bruschweiler, R.4
  • 267
    • 23244450294 scopus 로고    scopus 로고
    • Exploring the common dynamics of homologous proteins. Application to the globin family
    • Maguid S., Fernandez-Alberti S., Ferrelli L., and Echave J. Exploring the common dynamics of homologous proteins. Application to the globin family. Biophys. J. 89 (2005) 3-13
    • (2005) Biophys. J. , vol.89 , pp. 3-13
    • Maguid, S.1    Fernandez-Alberti, S.2    Ferrelli, L.3    Echave, J.4
  • 268
    • 0020679552 scopus 로고
    • Appropriate uses of multivariate analysis
    • Hanley J.A. Appropriate uses of multivariate analysis. Annu. Rev. Public Health 4 (1983) 155-180
    • (1983) Annu. Rev. Public Health , vol.4 , pp. 155-180
    • Hanley, J.A.1


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