CHARMM (English Wikipedia)

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

refsWebsite

Global rank English rank

14nih.gov

4^th place

13doi.org

2^nd place

5semanticscholar.org

11^th place

8^th place

2academiccharmm.org

low place

2harvard.edu

18^th place

17^th place

1worldcat.org

5^th place

1umaryland.edu

low place

7,717^th place

1worldcommunitygrid.org

low place

academiccharmm.org

"Versions - CHARMM". CHARMM (Chemistry at HARvard Macromolecular Mechanics). Harvard University. Retrieved 2021-03-29.
"Installation". CHARMM (Chemistry at HARvard Macromolecular Mechanics). Harvard University. 2016. Retrieved 2021-03-29.

doi.org

Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983). "CHARMM: A program for macromolecular energy, minimization, and dynamics calculations". J. Comput. Chem. 4 (2): 187–217. doi:10.1002/jcc.540040211. S2CID 91559650.
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. PMID 24889800.
MacKerell AD Jr, Feig M, Brooks III CL (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. S2CID 11076418.
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.; MacKerell, A. D. (May 2015). "CHARMM additive and polarizable force fields for biophysics and computer-aided drug design". Biochimica et Biophysica Acta (BBA) - General Subjects. 1850 (5): 861–871. doi:10.1016/j.bbagen.2014.08.004. ISSN 0006-3002. PMC 4334745. PMID 25149274.
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. S2CID 19502363.
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. S2CID 39320318.
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. S2CID 16741310.
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 (1–3): 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.

harvard.edu

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 (1–3): 245–249. Bibcode:2006CPL...418..245L. doi:10.1016/j.cplett.2005.10.135.

nih.gov

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; 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. PMID 24889800.
MacKerell AD Jr, Feig M, Brooks III CL (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. S2CID 11076418.
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.; MacKerell, A. D. (May 2015). "CHARMM additive and polarizable force fields for biophysics and computer-aided drug design". Biochimica et Biophysica Acta (BBA) - General Subjects. 1850 (5): 861–871. doi:10.1016/j.bbagen.2014.08.004. ISSN 0006-3002. PMC 4334745. PMID 25149274.
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. S2CID 19502363.
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. S2CID 39320318.
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. S2CID 16741310.
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.; MacKerell, A. D. (May 2015). "CHARMM additive and polarizable force fields for biophysics and computer-aided drug design". Biochimica et Biophysica Acta (BBA) - General Subjects. 1850 (5): 861–871. doi:10.1016/j.bbagen.2014.08.004. ISSN 0006-3002. PMC 4334745. PMID 25149274.
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.

semanticscholar.org

api.semanticscholar.org

Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983). "CHARMM: A program for macromolecular energy, minimization, and dynamics calculations". J. Comput. Chem. 4 (2): 187–217. doi:10.1002/jcc.540040211. S2CID 91559650.
MacKerell AD Jr, Feig M, Brooks III CL (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. S2CID 11076418.
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. S2CID 19502363.
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. S2CID 39320318.
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. S2CID 16741310.

umaryland.edu

mackerell.umaryland.edu

Mackerell website

worldcat.org

Vanommeslaeghe, K.; MacKerell, A. D. (May 2015). "CHARMM additive and polarizable force fields for biophysics and computer-aided drug design". Biochimica et Biophysica Acta (BBA) - General Subjects. 1850 (5): 861–871. doi:10.1016/j.bbagen.2014.08.004. ISSN 0006-3002. PMC 4334745. PMID 25149274.

worldcommunitygrid.org

The Clean Energy Project