CHARMM (Japanese Wikipedia)

Analysis of information sources in references of the Wikipedia article "CHARMM" in Japanese language version.

Last modified: 12:09:20, 20 May 2026 (UTC)

Ref.Un. Ref.Website

Global rank Japanese rank

1313doi.org

2^nd place

3^rd place

1111nih.gov

5^th place

11^th place

22adsabs.harvard.edu

14^th place

60^th place

11umaryland.edu

low place

11charmm.org

low place

adsabs.harvard.edu (Global: 14^th place; Japanese: 60^th place)

ui.adsabs.harvard.edu

Lamoureux G, Roux B (2003). “Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm”. J Chem Phys. 119 (6): 3025–3039. Bibcode:2003JChPh.119.3025L. doi:10.1063/1.1589749.
Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD (2006). “A polarizable model of water for molecular dynamics simulations of biomolecules”. Chem Phys Lett. 418: 245–249. Bibcode:2006CPL...418..245L. doi:10.1016/j.cplett.2005.10.135.

charmm.org (Global: low place; Japanese: low place)

“Versions”. CHARMM 2016. 2016年4月5日閲覧.

doi.org (Global: 2^nd place; Japanese: 3^rd place)

Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983). “CHARMM: A program for macromolecular energy, minimization, and dynamics calculations”. J Comp Chem. 4 (2): 187–217. doi:10.1002/jcc.540040211.
MacKerell AD Jr, Brooks B, Brooks CL 3rd, Nilsson L, Roux B, Won Y, Karplus M (1998). “CHARMM: The Energy Function and Its Parameterization with an Overview of the Program”. In Schleyer Pv, et al. (eds.). The Encyclopedia of Computational Chemistry. Vol. 1. Chichester: John Wiley & Sons. pp. 271–277. doi:10.1002/0470845015.cfa007.
Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (29 July 2009). “CHARMM: The biomolecular simulation program”. Journal of Computational Chemistry. 30 (10): 1545–1614. doi:10.1002/jcc.21287. PMC 2810661. PMID 19444816.
MacKerell AD Jr, et al. (1998). “All-atom empirical potential for molecular modeling and dynamics studies of proteins”. J Phys Chem B. 102 (18): 3586–3616. doi:10.1021/jp973084f.
MacKerell AD Jr, Feig M, Brooks CL 3rd (2004). “Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations”. J Comput Chem. 25 (11): 1400–1415. doi:10.1002/jcc.20065. PMID 15185334.
Brooks CL, Chen J, Im W (2006). “Balancing solvation and intramolecular interactions: toward a consistent generalized born force field (CMAP opt. for GBSW)”. J Am Chem Soc. 128 (11): 3728–3736. doi:10.1021/ja057216r. PMC 2596729. PMID 16536547.
MacKerell AD Jr, Banavali N, Foloppe N (2001). “Development and current status of the CHARMM force field for nucleic acids”. Biopolymers. 56 (4): 257–265. doi:10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W. PMID 11754339.
Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr (2009). “CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields”. J Comput Chem. 31 (4): 671–90. doi:10.1002/jcc.21367. PMC 2888302. PMID 19575467.
Patel S, Brooks CL 3rd (2004). “CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations”. J Comput Chem. 25 (1): 1–15. doi:10.1002/jcc.10355. PMID 14634989.
Patel S, Mackerell AD Jr, Brooks CL 3rd (2004). “CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model”. J Comput Chem. 25 (12): 1504–1514. doi:10.1002/jcc.20077. PMID 15224394.
Lamoureux G, Roux B (2003). “Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm”. J Chem Phys. 119 (6): 3025–3039. Bibcode:2003JChPh.119.3025L. doi:10.1063/1.1589749.
Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD (2006). “A polarizable model of water for molecular dynamics simulations of biomolecules”. Chem Phys Lett. 418: 245–249. Bibcode:2006CPL...418..245L. doi:10.1016/j.cplett.2005.10.135.
Karplus M (2006). “Spinach on the ceiling: a theoretical chemist's return to biology”. Annu Rev Biophys Biomol Struct. 35 (1): 1–47. doi:10.1146/annurev.biophys.33.110502.133350. PMID 16689626.

nih.gov (Global: 5^th place; Japanese: 11^th place)

pubmed.ncbi.nlm.nih.gov

Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (29 July 2009). “CHARMM: The biomolecular simulation program”. Journal of Computational Chemistry. 30 (10): 1545–1614. doi:10.1002/jcc.21287. PMC 2810661. PMID 19444816.
MacKerell AD Jr, Feig M, Brooks CL 3rd (2004). “Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations”. J Comput Chem. 25 (11): 1400–1415. doi:10.1002/jcc.20065. PMID 15185334.
Brooks CL, Chen J, Im W (2006). “Balancing solvation and intramolecular interactions: toward a consistent generalized born force field (CMAP opt. for GBSW)”. J Am Chem Soc. 128 (11): 3728–3736. doi:10.1021/ja057216r. PMC 2596729. PMID 16536547.
MacKerell AD Jr, Banavali N, Foloppe N (2001). “Development and current status of the CHARMM force field for nucleic acids”. Biopolymers. 56 (4): 257–265. doi:10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W. PMID 11754339.
Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr (2009). “CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields”. J Comput Chem. 31 (4): 671–90. doi:10.1002/jcc.21367. PMC 2888302. PMID 19575467.
Patel S, Brooks CL 3rd (2004). “CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations”. J Comput Chem. 25 (1): 1–15. doi:10.1002/jcc.10355. PMID 14634989.
Patel S, Mackerell AD Jr, Brooks CL 3rd (2004). “CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model”. J Comput Chem. 25 (12): 1504–1514. doi:10.1002/jcc.20077. PMID 15224394.
Karplus M (2006). “Spinach on the ceiling: a theoretical chemist's return to biology”. Annu Rev Biophys Biomol Struct. 35 (1): 1–47. doi:10.1146/annurev.biophys.33.110502.133350. PMID 16689626.

ncbi.nlm.nih.gov

Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (29 July 2009). “CHARMM: The biomolecular simulation program”. Journal of Computational Chemistry. 30 (10): 1545–1614. doi:10.1002/jcc.21287. PMC 2810661. PMID 19444816.
Brooks CL, Chen J, Im W (2006). “Balancing solvation and intramolecular interactions: toward a consistent generalized born force field (CMAP opt. for GBSW)”. J Am Chem Soc. 128 (11): 3728–3736. doi:10.1021/ja057216r. PMC 2596729. PMID 16536547.
Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr (2009). “CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields”. J Comput Chem. 31 (4): 671–90. doi:10.1002/jcc.21367. PMC 2888302. PMID 19575467.

umaryland.edu (Global: low place; Japanese: low place)

mackerell.umaryland.edu

“CHARMM Force Field Files”. MacKerell Lab. 2016年4月5日閲覧.