메뉴 건너뛰기




Volumn 9, Issue 9, 2013, Pages 4026-4034

Exploring energy landscapes: Metrics, pathways, and normal-mode analysis for rigid-body molecules

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84884181253     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct400403y     Document Type: Article
Times cited : (21)

References (59)
  • 2
    • 77954960270 scopus 로고    scopus 로고
    • Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials
    • Price, S. L.; Leslie, M.; Welch, G. W. A.; Habgood, M.; Price, L. S.; Karamertzanis, P. G.; Day, G. M. Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials Phys. Chem. Chem. Phys. 2010, 12, 8478
    • (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 8478
    • Price, S.L.1    Leslie, M.2    Welch, G.W.A.3    Habgood, M.4    Price, L.S.5    Karamertzanis, P.G.6    Day, G.M.7
  • 4
    • 78651389319 scopus 로고    scopus 로고
    • Current approaches to predicting molecular organic crystal structures
    • Day, G. M. Current approaches to predicting molecular organic crystal structures Crystallogr. Rev. 2011, 17, 3-52
    • (2011) Crystallogr. Rev. , vol.17 , pp. 3-52
    • Day, G.M.1
  • 5
    • 84870916588 scopus 로고    scopus 로고
    • A Local Rigid Body Framework for Global Optimization of Biomolecules
    • Kusumaatmaja, H.; Whittleston, C. S.; Wales, D. J. A Local Rigid Body Framework for Global Optimization of Biomolecules J. Chem. Theory Comput. 2012, 8, 5159-5165
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 5159-5165
    • Kusumaatmaja, H.1    Whittleston, C.S.2    Wales, D.J.3
  • 6
    • 84856489322 scopus 로고    scopus 로고
    • Understanding the EF-hand closing pathway using non-biased interatomic potentials
    • Dupuis, L.; Mousseau, N. Understanding the EF-hand closing pathway using non-biased interatomic potentials J. Chem. Phys. 2012, 136, 035101
    • (2012) J. Chem. Phys. , vol.136 , pp. 035101
    • Dupuis, L.1    Mousseau, N.2
  • 7
    • 36849125573 scopus 로고
    • Second Virial Coefficients of Polar Gas Mixtures
    • Stockmayer, W. H. Second Virial Coefficients of Polar Gas Mixtures J. Chem. Phys. 1941, 9, 863-870
    • (1941) J. Chem. Phys. , vol.9 , pp. 863-870
    • Stockmayer, W.H.1
  • 8
    • 6744234112 scopus 로고
    • Modification of the overlap potential to mimic a linear site-site potential
    • Gay, J. G.; Berne, B. J. Modification of the overlap potential to mimic a linear site-site potential J. Chem. Phys. 1981, 74, 3316-3319
    • (1981) J. Chem. Phys. , vol.74 , pp. 3316-3319
    • Gay, J.G.1    Berne, B.J.2
  • 9
    • 12944264524 scopus 로고    scopus 로고
    • The energy landscape as a unifying theme in molecular science
    • Wales, D. J. The energy landscape as a unifying theme in molecular science Philos. Trans. R. Soc. London, Ser. A 2005, 363, 357-377
    • (2005) Philos. Trans. R. Soc. London, Ser. A , vol.363 , pp. 357-377
    • Wales, D.J.1
  • 10
    • 33745787907 scopus 로고    scopus 로고
    • Dynamic Pathways for Viral Capsid Assembly
    • Hagan, M. F.; Chandler, D. Dynamic Pathways for Viral Capsid Assembly Biophys. J. 2006, 91, 42-54
    • (2006) Biophys. J. , vol.91 , pp. 42-54
    • Hagan, M.F.1    Chandler, D.2
  • 11
    • 34547604210 scopus 로고    scopus 로고
    • Anisotropy of building blocks and their assembly into complex structures
    • Glotzer, S. C.; Solomon, M. J. Anisotropy of building blocks and their assembly into complex structures Nat. Mater. 2007, 6, 557-562
    • (2007) Nat. Mater. , vol.6 , pp. 557-562
    • Glotzer, S.C.1    Solomon, M.J.2
  • 12
    • 79952091255 scopus 로고    scopus 로고
    • Structural, mechanical, and thermodynamic properties of a coarsegrained DNA model
    • Ouldridge, T. E.; Louis, A. A.; Doye, J. P. K. Structural, mechanical, and thermodynamic properties of a coarsegrained DNA model J. Chem. Phys. 2011, 134, 085101
    • (2011) J. Chem. Phys. , vol.134 , pp. 085101
    • Ouldridge, T.E.1    Louis, A.A.2    Doye, J.P.K.3
  • 13
    • 0000623669 scopus 로고
    • On the representatation of orientation space
    • Evans, D. J. On the representatation of orientation space Mol. Phys. 1977, 34, 317-325
    • (1977) Mol. Phys. , vol.34 , pp. 317-325
    • Evans, D.J.1
  • 14
    • 62349137229 scopus 로고    scopus 로고
    • Simulations of rigid bodies in an angle-axis framework
    • Chakrabarti, D.; Wales, D. J. Simulations of rigid bodies in an angle-axis framework Phys. Chem. Chem. Phys. 2009, 11, 1970
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 1970
    • Chakrabarti, D.1    Wales, D.J.2
  • 15
    • 0000603016 scopus 로고
    • A method for determining reaction paths in large molecules: Application to myoglobin
    • Elber, R.; Karplus, M. A method for determining reaction paths in large molecules: Application to myoglobin Chem. Phys. Lett. 1987, 139, 375-380
    • (1987) Chem. Phys. Lett. , vol.139 , pp. 375-380
    • Elber, R.1    Karplus, M.2
  • 16
    • 0000191981 scopus 로고
    • Reaction path study of conformational transitions in flexible systems: Applications to peptides
    • Czerminski, R.; Elber, R. Reaction path study of conformational transitions in flexible systems: Applications to peptides J. Chem. Phys. 1990, 92, 5580-5601
    • (1990) J. Chem. Phys. , vol.92 , pp. 5580-5601
    • Czerminski, R.1    Elber, R.2
  • 17
    • 1442282189 scopus 로고    scopus 로고
    • A doubly nudged elastic band method for finding transition states
    • Trygubenko, S. A.; Wales, D. J. A doubly nudged elastic band method for finding transition states J. Chem. Phys. 2004, 120, 2082-2094
    • (2004) J. Chem. Phys. , vol.120 , pp. 2082-2094
    • Trygubenko, S.A.1    Wales, D.J.2
  • 18
    • 0034513054 scopus 로고    scopus 로고
    • A climbing image nudged elastic band method for finding saddle points and minimum energy paths
    • Henkelman, G.; Uberuaga, B. P.; Jónsson, H. A climbing image nudged elastic band method for finding saddle points and minimum energy paths J. Chem. Phys. 2000, 113, 9901-9904
    • (2000) J. Chem. Phys. , vol.113 , pp. 9901-9904
    • Henkelman, G.1    Uberuaga, B.P.2    Jónsson, H.3
  • 19
    • 1242329035 scopus 로고    scopus 로고
    • Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points
    • Henkelman, G.; Jónsson, H. Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points J. Chem. Phys. 2000, 113, 9978-9985
    • (2000) J. Chem. Phys. , vol.113 , pp. 9978-9985
    • Henkelman, G.1    Jónsson, H.2
  • 20
    • 84860754879 scopus 로고    scopus 로고
    • Normal mode analysis of molecular motions in curvilinear coordinates on a non-Eckart body-frame: An application to protein torsion dynamics
    • Pesonen, J.; Henriksson, K. O. E.; López-Blanco, J. R.; Chacón, P. Normal mode analysis of molecular motions in curvilinear coordinates on a non-Eckart body-frame: an application to protein torsion dynamics J. Math. Chem. 2012, 50, 1521-1549
    • (2012) J. Math. Chem. , vol.50 , pp. 1521-1549
    • Pesonen, J.1    Henriksson, K.O.E.2    López-Blanco, J.R.3    Chacón, P.4
  • 21
    • 77953560530 scopus 로고
    • Coexistence in small inert gas clusters
    • Wales, D. J. Coexistence in small inert gas clusters Mol. Phys. 1993, 78, 151-171
    • (1993) Mol. Phys. , vol.78 , pp. 151-171
    • Wales, D.J.1
  • 22
    • 0037460544 scopus 로고    scopus 로고
    • Free energy landscapes of model peptides and proteins
    • Evans, D. A.; Wales, D. J. Free energy landscapes of model peptides and proteins J. Chem. Phys. 2003, 118, 3891-3897
    • (2003) J. Chem. Phys. , vol.118 , pp. 3891-3897
    • Evans, D.A.1    Wales, D.J.2
  • 23
    • 56649088054 scopus 로고    scopus 로고
    • Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide
    • Strodel, B.; Wales, D. J. Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide Chem. Phys. Lett. 2008, 466, 105-115
    • (2008) Chem. Phys. Lett. , vol.466 , pp. 105-115
    • Strodel, B.1    Wales, D.J.2
  • 24
    • 0000560869 scopus 로고    scopus 로고
    • Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard- Jones Clusters Containing up to 110 Atoms
    • Wales, D. J.; Doye, J. P. K. Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard- Jones Clusters Containing up to 110 Atoms J. Phys. Chem. A 1997, 101, 5111-5116
    • (1997) J. Phys. Chem. A , vol.101 , pp. 5111-5116
    • Wales, D.J.1    Doye, J.P.K.2
  • 25
    • 0001476184 scopus 로고    scopus 로고
    • Defect migration in crystalline silicon
    • Munro, L. J.; Wales, D. J. Defect migration in crystalline silicon Phys. Rev. B 1999, 59, 3969-3980
    • (1999) Phys. Rev. B , vol.59 , pp. 3969-3980
    • Munro, L.J.1    Wales, D.J.2
  • 26
    • 0000327364 scopus 로고    scopus 로고
    • A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives
    • Henkelman, G.; Jónsson, H. A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives J. Chem. Phys. 1999, 111, 7010-7022
    • (1999) J. Chem. Phys. , vol.111 , pp. 7010-7022
    • Henkelman, G.1    Jónsson, H.2
  • 27
    • 0000370391 scopus 로고    scopus 로고
    • The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
    • Becker, O. M.; Karplus, M. The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics J. Chem. Phys. 1997, 106, 1495-1517
    • (1997) J. Chem. Phys. , vol.106 , pp. 1495-1517
    • Becker, O.M.1    Karplus, M.2
  • 28
    • 0032552138 scopus 로고    scopus 로고
    • Archetypal energy landscapes
    • Wales, D. J.; Miller, M. A.; Walsh, T. R. Archetypal energy landscapes Nature 1998, 394, 758-760
    • (1998) Nature , vol.394 , pp. 758-760
    • Wales, D.J.1    Miller, M.A.2    Walsh, T.R.3
  • 29
    • 0037115811 scopus 로고    scopus 로고
    • Free energy disconnectivity graphs: Application to peptide models
    • Krivov, S. V.; Karplus, M. Free energy disconnectivity graphs: Application to peptide models J. Chem. Phys. 2002, 117, 10894-10903
    • (2002) J. Chem. Phys. , vol.117 , pp. 10894-10903
    • Krivov, S.V.1    Karplus, M.2
  • 30
    • 0001482877 scopus 로고
    • Optimal sampling of the rotation function
    • Lattman, E. E. Optimal sampling of the rotation function Acta Crystallogr., Sect. B 1972, 28, 1065-1068
    • (1972) Acta Crystallogr., Sect. B , vol.28 , pp. 1065-1068
    • Lattman, E.E.1
  • 31
    • 33846216327 scopus 로고    scopus 로고
    • The directional contact distance of two ellipsoids: Coarse-grained potentials for anisotropic interactions
    • Paramonov, L.; Yaliraki, S. N. The directional contact distance of two ellipsoids: Coarse-grained potentials for anisotropic interactions J. Chem. Phys. 2005, 123, 194111
    • (2005) J. Chem. Phys. , vol.123 , pp. 194111
    • Paramonov, L.1    Yaliraki, S.N.2
  • 32
    • 84870860843 scopus 로고    scopus 로고
    • Quasi-Continuous Interpolation Scheme for Pathways between Distant Configurations
    • Wales, D. J.; Carr, J. M. Quasi-Continuous Interpolation Scheme for Pathways between Distant Configurations J. Chem. Theory Comput. 2012, 8, 5020-5034
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 5020-5034
    • Wales, D.J.1    Carr, J.M.2
  • 33
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li, Z.; Scheraga, H. A. Monte Carlo-minimization approach to the multiple-minima problem in protein folding Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 6611-6615
    • (1987) Proc. Natl. Acad. Sci. U.S.A. , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 34
    • 0000732463 scopus 로고
    • A Limited Memory Algorithm for Bound Constrained Optimization
    • Byrd, R. H.; Lu, P.; Nocedal, J.; Zhu, C. A Limited Memory Algorithm for Bound Constrained Optimization SIAM J. Sci. Comput. 1995, 16, 1190
    • (1995) SIAM J. Sci. Comput. , vol.16 , pp. 1190
    • Byrd, R.H.1    Lu, P.2    Nocedal, J.3    Zhu, C.4
  • 37
    • 0022095776 scopus 로고
    • Animating rotation with quaternion curves
    • Shoemake, K. Animating rotation with quaternion curves SIGGRAPH Comput. Graph. 1985, 19, 245-254
    • (1985) SIGGRAPH Comput. Graph. , vol.19 , pp. 245-254
    • Shoemake, K.1
  • 39
    • 41949085799 scopus 로고    scopus 로고
    • Optimization methods for finding minimum energy paths
    • Sheppard, D.; Terrell, R.; Henkelman, G. Optimization methods for finding minimum energy paths J. Chem. Phys. 2008, 128, 134106
    • (2008) J. Chem. Phys. , vol.128 , pp. 134106
    • Sheppard, D.1    Terrell, R.2    Henkelman, G.3
  • 40
    • 84884183187 scopus 로고    scopus 로고
    • OPTIM: A program for optimizing geometries and calculating pathways.
    • Wales, D. J. OPTIM: A program for optimizing geometries and calculating pathways. http://www-wales.ch.cam.ac.uk/software.html.
    • Wales, D.J.1
  • 42
    • 0037145606 scopus 로고    scopus 로고
    • Discrete path sampling
    • Wales, D. J. Discrete path sampling Mol. Phys. 2002, 100, 3285-3305
    • (2002) Mol. Phys. , vol.100 , pp. 3285-3305
    • Wales, D.J.1
  • 43
    • 31544439918 scopus 로고    scopus 로고
    • Equilibrium thermodynamics from basin-sampling
    • Bogdan, T. V.; Wales, D. J.; Calvo, F. Equilibrium thermodynamics from basin-sampling J. Chem. Phys. 2006, 124, 044102
    • (2006) J. Chem. Phys. , vol.124 , pp. 044102
    • Bogdan, T.V.1    Wales, D.J.2    Calvo, F.3
  • 44
    • 33751283977 scopus 로고    scopus 로고
    • Potential Energy and Free Energy Landscapes
    • Wales, D. J.; Bogdan, T. V. Potential Energy and Free Energy Landscapes J. Phys. Chem. B 2006, 110, 20765-20776
    • (2006) J. Phys. Chem. B , vol.110 , pp. 20765-20776
    • Wales, D.J.1    Bogdan, T.V.2
  • 45
    • 84990689301 scopus 로고
    • On coordinate transformations in steepest descent path and stationary point locations
    • Banerjee, A.; Adams, N. P. On coordinate transformations in steepest descent path and stationary point locations Int. J. Quantum Chem. 1992, 43, 855-871
    • (1992) Int. J. Quantum Chem. , vol.43 , pp. 855-871
    • Banerjee, A.1    Adams, N.P.2
  • 47
    • 0001048852 scopus 로고
    • Use of the histogram and jump- walking methods for overcoming slow barrier crossing behavior in Monte Carlo simulations: Applications to the phase transitions in the (Ar)13 and (H2O)8 clusters
    • Tsai, C. J.; Jordan, K. D. Use of the histogram and jump- walking methods for overcoming slow barrier crossing behavior in Monte Carlo simulations: Applications to the phase transitions in the (Ar)13 and (H2O)8 clusters J. Chem. Phys. 1993, 99, 6957-6970
    • (1993) J. Chem. Phys. , vol.99 , pp. 6957-6970
    • Tsai, C.J.1    Jordan, K.D.2
  • 48
    • 0141959762 scopus 로고    scopus 로고
    • Parallel-Tempering Monte Carlo Study of (H2O)n = 6-9
    • Tharrington, A. N.; Jordan, K. D. Parallel-Tempering Monte Carlo Study of (H2O)n = 6-9 J. Phys. Chem. A 2003, 107, 7380-7389
    • (2003) J. Phys. Chem. A , vol.107 , pp. 7380-7389
    • Tharrington, A.N.1    Jordan, K.D.2
  • 49
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 2008, 4, 435-447
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 50
    • 33846957776 scopus 로고    scopus 로고
    • Energy landscapes for water clusters in a uniform electric field
    • James, T.; Wales, D. J.; Hernández Rojas, J. Energy landscapes for water clusters in a uniform electric field J. Chem. Phys. 2007, 126, 054506
    • (2007) J. Chem. Phys. , vol.126 , pp. 054506
    • James, T.1    Wales, D.J.2    Hernández Rojas, J.3
  • 51
    • 33645683978 scopus 로고    scopus 로고
    • Global optimization and folding pathways of selected α -helical proteins
    • Carr, J. M.; Wales, D. J. Global optimization and folding pathways of selected α -helical proteins J. Chem. Phys. 2005, 123, 234901
    • (2005) J. Chem. Phys. , vol.123 , pp. 234901
    • Carr, J.M.1    Wales, D.J.2
  • 52
    • 49149126925 scopus 로고    scopus 로고
    • Folding Pathways and Rates for the Three-Stranded β -Sheet Peptide Beta3s using Discrete Path Sampling
    • Carr, J. M.; Wales, D. J. Folding Pathways and Rates for the Three-Stranded β -Sheet Peptide Beta3s using Discrete Path Sampling J. Phys. Chem. B 2008, 112, 8760-8769
    • (2008) J. Phys. Chem. B , vol.112 , pp. 8760-8769
    • Carr, J.M.1    Wales, D.J.2
  • 53
    • 65349189938 scopus 로고    scopus 로고
    • Refined kinetic transition networks for the GB1 hairpin peptide
    • Carr, J. M.; Wales, D. J. Refined kinetic transition networks for the GB1 hairpin peptide Phys. Chem. Chem. Phys. 2009, 11, 3341-3354
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 3341-3354
    • Carr, J.M.1    Wales, D.J.2
  • 55
    • 84884179941 scopus 로고    scopus 로고
    • GMIN: A program for basin-hopping global optimization, basin-sampling, and parallel tempering.
    • Wales, D. J. GMIN: A program for basin-hopping global optimization, basin-sampling, and parallel tempering. http://www-wales.ch.cam.ac.uk/software. html.
    • Wales, D.J.1
  • 56
    • 84884171310 scopus 로고    scopus 로고
    • Python Energy Landscape Explorer.
    • Python Energy Landscape Explorer. http://github.com/ pele-python/pele.
  • 58
    • 0004122714 scopus 로고
    • In; Kirk, D. Academic Press: New York - 132
    • Shoemake, K. In Graphics Gems III; Kirk, D., Ed.; Academic Press: New York, 1992; pp 124-132.
    • (1992) Graphics Gems III , pp. 124
    • Shoemake, K.1
  • 59
    • 0004122714 scopus 로고
    • In; Kirk, D. Academic Press: New York - 120
    • Arvo, J. In Graphics Gems III; Kirk, D., Ed.; Academic Press: New York, 1992; pp 117-120.
    • (1992) Graphics Gems III , pp. 117
    • Arvo, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.