Coarse-grained modeling (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Coarse-grained modeling" in English language version.

refsWebsite

Global rank English rank

18nih.gov

4^th place

14doi.org

2^nd place

4semanticscholar.org

11^th place

8^th place

3harvard.edu

18^th place

17^th place

1worldcat.org

5^th place

1rug.nl

2,779^th place

1,997^th place

1handle.net

102^nd place

76^th place

1figshare.com

5,893^rd place

3,320^th place

1arxiv.org

69^th place

59^th place

arxiv.org

Seiferth D, Sollich P, Klumpp S (December 2020). "Coarse graining of biochemical systems described by discrete stochastic dynamics". Physical Review E. 102 (6–1): 062149. arXiv:2102.13394. Bibcode:2020PhRvE.102f2149S. doi:10.1103/PhysRevE.102.062149. PMID 33466014. S2CID 231652939.

doi.org

Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A (July 2016). "Coarse-Grained Protein Models and Their Applications". Chemical Reviews. 116 (14): 7898–936. doi:10.1021/acs.chemrev.6b00163. PMID 27333362.
Ingólfsson HI, Lopez CA, Uusitalo JJ, de Jong DH, Gopal SM, Periole X, Marrink SJ (May 2014). "The power of coarse graining in biomolecular simulations". Wiley Interdisciplinary Reviews: Computational Molecular Science. 4 (3): 225–248. doi:10.1002/wcms.1169. PMC 4171755. PMID 25309628.
Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, et al. (April 2016). "SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction". Nucleic Acids Research. 44 (7): e63. doi:10.1093/nar/gkv1479. PMC 4838351. PMID 26687716.
Potoyan DA, Savelyev A, Papoian GA (2013-01-01). "Recent successes in coarse-grained modeling of DNA". Wiley Interdisciplinary Reviews: Computational Molecular Science. 3 (1): 69–83. doi:10.1002/wcms.1114. ISSN 1759-0884. S2CID 12043343.
Baron R, Trzesniak D, de Vries AH, Elsener A, Marrink SJ, van Gunsteren WF (February 2007). "Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models" (PDF). ChemPhysChem. 8 (3): 452–61. doi:10.1002/cphc.200600658. hdl:11370/92eedd39-1d54-45a4-bd8b-066349852bfb. PMID 17290360.
López CA, Rzepiela AJ, de Vries AH, Dijkhuizen L, Hünenberger PH, Marrink SJ (December 2009). "Martini Coarse-Grained Force Field: Extension to Carbohydrates". Journal of Chemical Theory and Computation. 5 (12): 3195–210. doi:10.1021/ct900313w. PMID 26602504.
Hadley KR, McCabe C (July 2012). "Coarse-Grained Molecular Models of Water: A Review". Molecular Simulation. 38 (8–9): 671–681. doi:10.1080/08927022.2012.671942. PMC 3420348. PMID 22904601.
Seiferth D, Sollich P, Klumpp S (December 2020). "Coarse graining of biochemical systems described by discrete stochastic dynamics". Physical Review E. 102 (6–1): 062149. arXiv:2102.13394. Bibcode:2020PhRvE.102f2149S. doi:10.1103/PhysRevE.102.062149. PMID 33466014. S2CID 231652939.
Hummer G, Szabo A (July 2015). "Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models". The Journal of Physical Chemistry B. 119 (29): 9029–37. doi:10.1021/jp508375q. PMC 4516310. PMID 25296279.
Liepelt S, Lipowsky R (June 2007). "Kinesin's network of chemomechanical motor cycles". Physical Review Letters. 98 (25): 258102. Bibcode:2007PhRvL..98y8102L. doi:10.1103/PhysRevLett.98.258102. PMID 17678059.
Levitt M, Warshel A (February 1975). "Computer simulation of protein folding". Nature. 253 (5494): 694–8. Bibcode:1975Natur.253..694L. doi:10.1038/253694a0. PMID 1167625. S2CID 4211714.
Warshel A, Levitt M (May 1976). "Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme". Journal of Molecular Biology. 103 (2): 227–49. doi:10.1016/0022-2836(76)90311-9. PMID 985660.
Levitt M (September 2014). "Birth and future of multiscale modeling for macromolecular systems (Nobel Lecture)". Angewandte Chemie. 53 (38): 10006–18. doi:10.1002/anie.201403691. PMID 25100216. S2CID 3680673.
Badaczewska-Dawid AE, Kolinski A, Kmiecik S (2020). "Computational reconstruction of atomistic protein structures from coarse-grained models". Computational and Structural Biotechnology Journal. 18: 162–176. doi:10.1016/j.csbj.2019.12.007. PMC 6961067. PMID 31969975.

figshare.com

López CA, Rzepiela AJ, de Vries AH, Dijkhuizen L, Hünenberger PH, Marrink SJ (December 2009). "Martini Coarse-Grained Force Field: Extension to Carbohydrates". Journal of Chemical Theory and Computation. 5 (12): 3195–210. doi:10.1021/ct900313w. PMID 26602504.

handle.net

hdl.handle.net

Baron R, Trzesniak D, de Vries AH, Elsener A, Marrink SJ, van Gunsteren WF (February 2007). "Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models" (PDF). ChemPhysChem. 8 (3): 452–61. doi:10.1002/cphc.200600658. hdl:11370/92eedd39-1d54-45a4-bd8b-066349852bfb. PMID 17290360.

harvard.edu

ui.adsabs.harvard.edu

Seiferth D, Sollich P, Klumpp S (December 2020). "Coarse graining of biochemical systems described by discrete stochastic dynamics". Physical Review E. 102 (6–1): 062149. arXiv:2102.13394. Bibcode:2020PhRvE.102f2149S. doi:10.1103/PhysRevE.102.062149. PMID 33466014. S2CID 231652939.
Liepelt S, Lipowsky R (June 2007). "Kinesin's network of chemomechanical motor cycles". Physical Review Letters. 98 (25): 258102. Bibcode:2007PhRvL..98y8102L. doi:10.1103/PhysRevLett.98.258102. PMID 17678059.
Levitt M, Warshel A (February 1975). "Computer simulation of protein folding". Nature. 253 (5494): 694–8. Bibcode:1975Natur.253..694L. doi:10.1038/253694a0. PMID 1167625. S2CID 4211714.

nih.gov

pubmed.ncbi.nlm.nih.gov

Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A (July 2016). "Coarse-Grained Protein Models and Their Applications". Chemical Reviews. 116 (14): 7898–936. doi:10.1021/acs.chemrev.6b00163. PMID 27333362.
Ingólfsson HI, Lopez CA, Uusitalo JJ, de Jong DH, Gopal SM, Periole X, Marrink SJ (May 2014). "The power of coarse graining in biomolecular simulations". Wiley Interdisciplinary Reviews: Computational Molecular Science. 4 (3): 225–248. doi:10.1002/wcms.1169. PMC 4171755. PMID 25309628.
Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, et al. (April 2016). "SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction". Nucleic Acids Research. 44 (7): e63. doi:10.1093/nar/gkv1479. PMC 4838351. PMID 26687716.
Baron R, Trzesniak D, de Vries AH, Elsener A, Marrink SJ, van Gunsteren WF (February 2007). "Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models" (PDF). ChemPhysChem. 8 (3): 452–61. doi:10.1002/cphc.200600658. hdl:11370/92eedd39-1d54-45a4-bd8b-066349852bfb. PMID 17290360.
López CA, Rzepiela AJ, de Vries AH, Dijkhuizen L, Hünenberger PH, Marrink SJ (December 2009). "Martini Coarse-Grained Force Field: Extension to Carbohydrates". Journal of Chemical Theory and Computation. 5 (12): 3195–210. doi:10.1021/ct900313w. PMID 26602504.
Hadley KR, McCabe C (July 2012). "Coarse-Grained Molecular Models of Water: A Review". Molecular Simulation. 38 (8–9): 671–681. doi:10.1080/08927022.2012.671942. PMC 3420348. PMID 22904601.
Seiferth D, Sollich P, Klumpp S (December 2020). "Coarse graining of biochemical systems described by discrete stochastic dynamics". Physical Review E. 102 (6–1): 062149. arXiv:2102.13394. Bibcode:2020PhRvE.102f2149S. doi:10.1103/PhysRevE.102.062149. PMID 33466014. S2CID 231652939.
Hummer G, Szabo A (July 2015). "Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models". The Journal of Physical Chemistry B. 119 (29): 9029–37. doi:10.1021/jp508375q. PMC 4516310. PMID 25296279.
Liepelt S, Lipowsky R (June 2007). "Kinesin's network of chemomechanical motor cycles". Physical Review Letters. 98 (25): 258102. Bibcode:2007PhRvL..98y8102L. doi:10.1103/PhysRevLett.98.258102. PMID 17678059.
Levitt M, Warshel A (February 1975). "Computer simulation of protein folding". Nature. 253 (5494): 694–8. Bibcode:1975Natur.253..694L. doi:10.1038/253694a0. PMID 1167625. S2CID 4211714.
Warshel A, Levitt M (May 1976). "Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme". Journal of Molecular Biology. 103 (2): 227–49. doi:10.1016/0022-2836(76)90311-9. PMID 985660.
Levitt M (September 2014). "Birth and future of multiscale modeling for macromolecular systems (Nobel Lecture)". Angewandte Chemie. 53 (38): 10006–18. doi:10.1002/anie.201403691. PMID 25100216. S2CID 3680673.
Badaczewska-Dawid AE, Kolinski A, Kmiecik S (2020). "Computational reconstruction of atomistic protein structures from coarse-grained models". Computational and Structural Biotechnology Journal. 18: 162–176. doi:10.1016/j.csbj.2019.12.007. PMC 6961067. PMID 31969975.

ncbi.nlm.nih.gov

Ingólfsson HI, Lopez CA, Uusitalo JJ, de Jong DH, Gopal SM, Periole X, Marrink SJ (May 2014). "The power of coarse graining in biomolecular simulations". Wiley Interdisciplinary Reviews: Computational Molecular Science. 4 (3): 225–248. doi:10.1002/wcms.1169. PMC 4171755. PMID 25309628.
Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, et al. (April 2016). "SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction". Nucleic Acids Research. 44 (7): e63. doi:10.1093/nar/gkv1479. PMC 4838351. PMID 26687716.
Hadley KR, McCabe C (July 2012). "Coarse-Grained Molecular Models of Water: A Review". Molecular Simulation. 38 (8–9): 671–681. doi:10.1080/08927022.2012.671942. PMC 3420348. PMID 22904601.
Hummer G, Szabo A (July 2015). "Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models". The Journal of Physical Chemistry B. 119 (29): 9029–37. doi:10.1021/jp508375q. PMC 4516310. PMID 25296279.
Badaczewska-Dawid AE, Kolinski A, Kmiecik S (2020). "Computational reconstruction of atomistic protein structures from coarse-grained models". Computational and Structural Biotechnology Journal. 18: 162–176. doi:10.1016/j.csbj.2019.12.007. PMC 6961067. PMID 31969975.

rug.nl

pure.rug.nl

Baron R, Trzesniak D, de Vries AH, Elsener A, Marrink SJ, van Gunsteren WF (February 2007). "Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models" (PDF). ChemPhysChem. 8 (3): 452–61. doi:10.1002/cphc.200600658. hdl:11370/92eedd39-1d54-45a4-bd8b-066349852bfb. PMID 17290360.

semanticscholar.org

api.semanticscholar.org

Potoyan DA, Savelyev A, Papoian GA (2013-01-01). "Recent successes in coarse-grained modeling of DNA". Wiley Interdisciplinary Reviews: Computational Molecular Science. 3 (1): 69–83. doi:10.1002/wcms.1114. ISSN 1759-0884. S2CID 12043343.
Seiferth D, Sollich P, Klumpp S (December 2020). "Coarse graining of biochemical systems described by discrete stochastic dynamics". Physical Review E. 102 (6–1): 062149. arXiv:2102.13394. Bibcode:2020PhRvE.102f2149S. doi:10.1103/PhysRevE.102.062149. PMID 33466014. S2CID 231652939.
Levitt M, Warshel A (February 1975). "Computer simulation of protein folding". Nature. 253 (5494): 694–8. Bibcode:1975Natur.253..694L. doi:10.1038/253694a0. PMID 1167625. S2CID 4211714.
Levitt M (September 2014). "Birth and future of multiscale modeling for macromolecular systems (Nobel Lecture)". Angewandte Chemie. 53 (38): 10006–18. doi:10.1002/anie.201403691. PMID 25100216. S2CID 3680673.

worldcat.org

Potoyan DA, Savelyev A, Papoian GA (2013-01-01). "Recent successes in coarse-grained modeling of DNA". Wiley Interdisciplinary Reviews: Computational Molecular Science. 3 (1): 69–83. doi:10.1002/wcms.1114. ISSN 1759-0884. S2CID 12043343.