메뉴 건너뛰기




Volumn 131, Issue 3, 2009, Pages

The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation

Author keywords

[No Author keywords available]

Indexed keywords

ADDITIVITY; ATOMISTIC SIMULATIONS; BASIS FUNCTIONS; COARSE GRAINED MODELS; COARSE GRAINING; COARSE-GRAINED; COARSE-GRAINED POTENTIAL; COARSE-GRAINING METHOD; DETAILED MODELS; HIGH CONCENTRATION; LENNARD-JONES PARTICLES; MANY-BODY; MANY-BODY POTENTIALS; MD SIMULATION; MOLE FRACTION; MOLECULAR DYNAMICS SIMULATIONS; MULTISCALE; POTENTIAL FUNCTION; SIMPLE MODEL; SOLUTE CONCENTRATIONS; STATISTICAL SAMPLING; VARIATIONAL CALCULATION; VARIATIONAL SOLUTIONS;

EID: 67651236198     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3173812     Document Type: Article
Times cited : (61)

References (62)
  • 3
    • 0034623787 scopus 로고    scopus 로고
    • 0036-8075,. 10.1126/science.290.5498.1903
    • M. Shirts and V. S. Pande, Science 0036-8075 290, 1903 (2000). 10.1126/science.290.5498.1903
    • (2000) Science , vol.290 , pp. 1903
    • Shirts, M.1    Pande, V.S.2
  • 5
    • 0037398844 scopus 로고    scopus 로고
    • Minimalist models for protein folding and design
    • DOI 10.1016/S0959-440X(03)00030-7
    • T. Head-Gordon and S. Brown, Curr. Opin. Struct. Biol. 0959-440X 13, 160 (2003), and references therein. 10.1016/S0959-440X(03)00030-7 (Pubitemid 36515143)
    • (2003) Current Opinion in Structural Biology , vol.13 , Issue.2 , pp. 160-167
    • Head-Gordon, T.1    Brown, S.2
  • 6
    • 17044393884 scopus 로고    scopus 로고
    • 0959-440X, (), and references therein. 10.1016/j.sbi.2005.02.005
    • V. Tozzini, Curr. Opin. Struct. Biol. 0959-440X 15, 144 (2005), and references therein. 10.1016/j.sbi.2005.02.005
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 144
    • Tozzini, V.1
  • 7
    • 25844431698 scopus 로고    scopus 로고
    • Coarse-grained normal mode analysis in structural biology
    • DOI 10.1016/j.sbi.2005.08.007, PII S0959440X05001557, Carbohydrates and Glycoconjugates/Biophysical Methods
    • I. Bahar and A. Rader, Curr. Opin. Struct. Biol. 0959-440X 15, 586 (2005), and references therein. 10.1016/j.sbi.2005.08.007 (Pubitemid 41393491)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.5 , pp. 586-592
    • Bahar, I.1    Rader, A.J.2
  • 8
    • 34247098754 scopus 로고    scopus 로고
    • Multiscale modeling of biomolecular systems: in serial and in parallel
    • DOI 10.1016/j.sbi.2007.03.004, PII S0959440X07000346, Theory and Simulation / Mecromolecular Assemblages
    • G. S. Ayton, W. G. Noid, and G. A. Voth, Curr. Opin. Struct. Biol. 0959-440X 17, 192 (2007). 10.1016/j.sbi.2007.03.004 (Pubitemid 46584804)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.2 , pp. 192-198
    • Ayton, G.S.1    Noid, W.G.2    Voth, G.A.3
  • 9
    • 58149471580 scopus 로고    scopus 로고
    • 0370-1573, (), and references therein. 10.1016/j.physre2006.08.003
    • M. Müller, K. Katsov, and M. Schick, Phys. Rep. 0370-1573 434, 113 (2006), and references therein. 10.1016/j.physrep.2006.08.003
    • (2006) Phys. Rep. , vol.434 , pp. 113
    • Müller, M.1    Katsov, K.2    Schick, M.3
  • 12
    • 0017157584 scopus 로고
    • 0022-2836,. 10.1016/0022-2836(76)90004-8
    • M. Levitt, J. Mol. Biol. 0022-2836 104, 59 (1976). 10.1016/0022-2836(76) 90004-8
    • (1976) J. Mol. Biol. , vol.104 , pp. 59
    • Levitt, M.1
  • 13
    • 0019569599 scopus 로고
    • 0006-3525,. 10.1002/bi1981.360200511
    • N. G and H. Abe, Biopolymers 0006-3525 20, 991 (1981). 10.1002/bip.1981.360200511
    • (1981) Biopolymers , vol.20 , pp. 991
    • N, G.1    Abe, H.2
  • 14
    • 0019571422 scopus 로고
    • 0006-3525,. 10.1002/bi1981.360200512
    • H. Abe and N. G, Biopolymers 0006-3525 20, 1013 (1981). 10.1002/bip.1981.360200512
    • (1981) Biopolymers , vol.20 , pp. 1013
    • Abe, H.1    N, G.2
  • 15
  • 16
    • 33645078713 scopus 로고
    • 1063-651X,. 10.1103/PhysRevE.52.3730
    • A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 1063-651X 52, 3730 (1995). 10.1103/PhysRevE.52.3730
    • (1995) Phys. Rev. e , vol.52 , pp. 3730
    • Lyubartsev, A.P.1    Laaksonen, A.2
  • 21
    • 3042720018 scopus 로고    scopus 로고
    • Equation-free: The computer-aided analysis of complex multiscale systems
    • DOI 10.1002/aic.10106
    • I. G. Kevrekidis, C. W. Gear, and G. Hummer, AIChE J. 0001-1541 50, 1346 (2004). 10.1002/aic.10106 (Pubitemid 38856761)
    • (2004) AIChE Journal , vol.50 , Issue.7 , pp. 1346-1355
    • Kevrekidis, I.G.1    Gear, C.W.2    Hummer, G.3
  • 22
    • 1842454935 scopus 로고    scopus 로고
    • Orientational potentials extracted from protein structures improve native fold recognition
    • DOI 10.1110/ps.03488704
    • N. -V. Buchete, J. E. Straub, and D. Thirumalai, Protein Sci. 0961-8368 13, 862 (2004). 10.1110/ps.03488704 (Pubitemid 38429210)
    • (2004) Protein Science , vol.13 , Issue.4 , pp. 862-874
    • Buchete, N.-V.1    Straub, J.E.2    Thirumalai, D.3
  • 24
    • 55749115445 scopus 로고    scopus 로고
    • 0027-8424,. 10.1073/pnas.0806072105
    • M. Lu and J. Ma, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 105, 15358 (2008). 10.1073/pnas.0806072105
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 15358
    • Lu, M.1    Ma, J.2
  • 26
    • 59349083629 scopus 로고    scopus 로고
    • 0021-9606,. 10.1063/1.3050106
    • R. B. Pandey and B. L. Farmer, J. Chem. Phys. 0021-9606 130, 044906 (2009). 10.1063/1.3050106
    • (2009) J. Chem. Phys. , vol.130 , pp. 044906
    • Pandey, R.B.1    Farmer, B.L.2
  • 28
    • 56349126308 scopus 로고    scopus 로고
    • 1089-5647,. 10.1021/jp806291p
    • Z. Zhang and W. Wriggers, J. Phys. Chem. B 1089-5647 112, 14026 (2008). 10.1021/jp806291p
    • (2008) J. Phys. Chem. B , vol.112 , pp. 14026
    • Zhang, Z.1    Wriggers, W.2
  • 30
    • 33847242278 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of membrane proteins and peptides
    • DOI 10.1016/j.jsb.2006.10.004, PII S1047847706003108, Advanced in Molecular Dynamics Simulations
    • P. J. Bond, J. Holyoake, A. Ivetac, S. Khalid, and M. S. Sansom, J. Struct. Biol. 1047-8477 157, 593 (2007). 10.1016/j.jsb.2006.10.004 (Pubitemid 46304257)
    • (2007) Journal of Structural Biology , vol.157 , Issue.3 , pp. 593-605
    • Bond, P.J.1    Holyoake, J.2    Ivetac, A.3    Khalid, S.4    Sansom, M.S.P.5
  • 33
    • 50349098485 scopus 로고    scopus 로고
    • 0006-3495,. 10.1529/biophysj.108.131714
    • K. Moritsugu and J. C. Smith, Biophys. J. 0006-3495 95, 1639 (2008). 10.1529/biophysj.108.131714
    • (2008) Biophys. J. , vol.95 , pp. 1639
    • Moritsugu, K.1    Smith, J.C.2
  • 34
  • 35
    • 0001259264 scopus 로고    scopus 로고
    • 0163-1829,. 10.1103/PhysRevB.58.R5893
    • R. E. Rudd and J. Q. Broughton, Phys. Rev. B 0163-1829 58, R5893 (1998). 10.1103/PhysRevB.58.R5893
    • (1998) Phys. Rev. B , vol.58 , pp. 5893
    • Rudd, R.E.1    Broughton, J.Q.2
  • 36
    • 0035130082 scopus 로고    scopus 로고
    • Structure-based coarse-grained model for polymer melts
    • DOI 10.1063/1.1330744
    • R. L. C. Akkermans and W. J. Briels, J. Chem. Phys. 0021-9606 114, 1020 (2001). 10.1063/1.1330744 (Pubitemid 32138537)
    • (2001) Journal of Chemical Physics , vol.114 , Issue.2 , pp. 1020-1031
    • Akkermans, R.L.C.1    Briels, W.J.2
  • 37
    • 0037042149 scopus 로고    scopus 로고
    • A coarse-graining procedure for flexible polymer chains with bonded and nonbonded interactions
    • DOI 10.1063/1.1469609
    • H. Fukunaga, J. Takimoto, and M. Doi, J. Chem. Phys. 0021-9606 116, 8183 (2002). 10.1063/1.1469609 (Pubitemid 34555090)
    • (2002) Journal of Chemical Physics , vol.116 , Issue.18 , pp. 8183-8190
    • Fukunaga, H.1    Takimoto, J.-I.2    Doi, M.3
  • 41
    • 21644450880 scopus 로고    scopus 로고
    • Coarse-grained rigid blob model for soft matter simulations
    • DOI 10.1063/1.1938193, 234912
    • S. D. Chao, J. D. Kress, and A. Redondo, J. Chem. Phys. 0021-9606 122, 234912 (2005). 10.1063/1.1938193 (Pubitemid 40925793)
    • (2005) Journal of Chemical Physics , vol.122 , Issue.23 , pp. 1-14
    • Chao, S.D.1    Kress, J.D.2    Redondo, A.3
  • 42
    • 24344438610 scopus 로고    scopus 로고
    • A coarse grained model for the dynamics of flap opening in HIV-1 protease
    • DOI 10.1016/j.cplett.2005.07.075, PII S0009261405010663
    • V. Tozzini and J. A. McCammon, Chem. Phys. Lett. 0009-2614 413, 123 (2005). 10.1016/j.cplett.2005.07.075 (Pubitemid 41252378)
    • (2005) Chemical Physics Letters , vol.413 , Issue.1-3 , pp. 123-128
    • Tozzini, V.1    McCammon, J.A.2
  • 44
    • 33747241994 scopus 로고    scopus 로고
    • Generalized coarse-grained model based on point multipole and Gay-Berne potentials
    • DOI 10.1063/1.2244553
    • P. A. Golubkov and P. Ren, J. Chem. Phys. 0021-9606 125, 064103 (2006). 10.1063/1.2244553 (Pubitemid 44239079)
    • (2006) Journal of Chemical Physics , vol.125 , Issue.6 , pp. 064103
    • Golubkov, P.A.1    Ren, P.2
  • 45
    • 33748448490 scopus 로고    scopus 로고
    • A natural coarse graining for simulating large biomolecular motion
    • DOI 10.1529/biophysj.106.083568
    • H. Gohlke and M. Thorpe, Biophys. J. 0006-3495 91, 2115 (2006). 10.1529/biophysj.106.083568 (Pubitemid 44352394)
    • (2006) Biophysical Journal , vol.91 , Issue.6 , pp. 2115-2120
    • Gohlke, H.1    Thorpe, M.F.2
  • 46
    • 33749521415 scopus 로고    scopus 로고
    • Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data
    • DOI 10.1529/biophysj.106.085894
    • D. A. Kondrashov, Q. Cui, and G. N. Phillips, Biophys. J. 0006-3495 91, 2760 (2006). 10.1529/biophysj.106.085894 (Pubitemid 44526467)
    • (2006) Biophysical Journal , vol.91 , Issue.8 , pp. 2760-2767
    • Kondrashov, D.A.1    Cui, Q.2    Phillips Jr., G.N.3
  • 47
    • 33846106848 scopus 로고    scopus 로고
    • An automatic coarse-graining and fine-graining simulation method: Application on polyethylene
    • DOI 10.1021/jp0644558
    • L. -J. Chen, H. -J. Qian, Z. -Y. Lu, Z. -S. Li, and C. -C. Sun, J. Phys. Chem. B 1089-5647 110, 24093 (2006). 10.1021/jp0644558 (Pubitemid 46065849)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.47 , pp. 24093-24100
    • Chen, L.-J.1    Qian, H.-J.2    Lu, Z.-Y.3    Li, Z.-S.4    Sun, C.-C.5
  • 48
    • 14544291957 scopus 로고    scopus 로고
    • A multiscale coarse-graining method for biomolecular systems
    • DOI 10.1021/jp044629q
    • S. Izvekov and G. A. Voth, J. Phys. Chem. B 1089-5647 109, 2469 (2005). 10.1021/jp044629q (Pubitemid 40304419)
    • (2005) Journal of Physical Chemistry B , vol.109 , Issue.7 , pp. 2469-2473
    • Izvekov, S.1    Voth, G.A.2
  • 49
    • 33644929350 scopus 로고    scopus 로고
    • Multiscale coarse graining of liquid-state systems
    • DOI 10.1063/1.2038787, 134105
    • S. Izvekov and G. A. Voth, J. Chem. Phys. 0021-9606 123, 134105 (2005). 10.1063/1.2038787 (Pubitemid 41434694)
    • (2005) Journal of Chemical Physics , vol.123 , Issue.13 , pp. 1-13
    • Izvekov, S.1    Voth, G.A.2
  • 52
    • 34247852583 scopus 로고    scopus 로고
    • Coarse-grained peptide modeling using a systematic multiscale approach
    • DOI 10.1529/biophysj.106.094425
    • J. Zhou, I. F. Thorpe, S. Izvekov, and G. A. Voth, Biophys. J. 0006-3495 92, 4289 (2007). 10.1529/biophysj.106.094425 (Pubitemid 46910544)
    • (2007) Biophysical Journal , vol.92 , Issue.12 , pp. 4289-4303
    • Zhou, J.1    Thorpe, I.F.2    Izvekov, S.3    Voth, G.A.4
  • 54
    • 25444487536 scopus 로고    scopus 로고
    • Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation
    • DOI 10.1021/jp0530496
    • S. Izvekov, A. Violi, and G. A. Voth, J. Phys. Chem. B 1089-5647 109, 17019 (2005). 10.1021/jp0530496 (Pubitemid 41361374)
    • (2005) Journal of Physical Chemistry B , vol.109 , Issue.36 , pp. 17019-17024
    • Izvekov, S.1    Violi, A.2    Voth, G.A.3
  • 55
    • 33748266722 scopus 로고    scopus 로고
    • Mixed atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel
    • DOI 10.1021/jp062700h
    • Q. Shi, S. Izvekov, and G. A. Voth, J. Phys. Chem. B 1089-5647 110, 15045 (2006). 10.1021/jp062700h (Pubitemid 44318467)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.31 , pp. 15045-15048
    • Shi, Q.1    Izvekov, S.2    Voth, G.A.3
  • 59
    • 61949390790 scopus 로고    scopus 로고
    • 1089-5647,. 10.1021/jp809604k
    • L. Lu and G. A. Voth, J. Phys. Chem. B 1089-5647 113, 1501 (2009). 10.1021/jp809604k
    • (2009) J. Phys. Chem. B , vol.113 , pp. 1501
    • Lu, L.1    Voth, G.A.2
  • 61
    • 36749107785 scopus 로고
    • 0021-9606,. 10.1063/1.439486
    • H. C. Andersen, J. Chem. Phys. 0021-9606 72, 2384 (1980). 10.1063/1.439486
    • (1980) J. Chem. Phys. , vol.72 , pp. 2384
    • Andersen, H.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.