Backbone-dependent rotamer library (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Backbone-dependent rotamer library" in English language version.

refsWebsite

Global rank English rank

28nih.gov

4^th place

17doi.org

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3harvard.edu

18^th place

17^th place

3worldcat.org

5^th place

1nsf.gov

3,828^th place

2,823^rd place

1nature.com

234^th place

397^th place

1semanticscholar.org

11^th place

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1eyesopen.com

low place

1yasara.org

low place

1pymolwiki.org

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1ucsf.edu

5,479^th place

3,911^th place

doi.org

Huang, X; Pearce, R; Zhang, Y (2020). "Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries". Journal of Chemical Information and Modeling. 60 (1): 410–420. doi:10.1021/acs.jcim.9b00812. PMC 7938712. PMID 31851497. Retrieved 18 February 2021.
Dunbrack, RL Jr.; Karplus, M (1993). "Backbone-dependent rotamer library for proteins. Application to side-chain prediction". Journal of Molecular Biology. 230 (2): 543–74. doi:10.1006/jmbi.1993.1170. PMID 8464064.
Dunbrack, RL Jr.; Cohen, FE (1997). "Bayesian statistical analysis of protein side-chain rotamer preferences". Protein Science. 6 (8): 1661–81. doi:10.1002/pro.5560060807. PMC 2143774. PMID 9260279.
Bower, MJ; Cohen, FE; Dunbrack, RL Jr (1997). "Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool". Journal of Molecular Biology. 267 (5): 1268–82. doi:10.1006/jmbi.1997.0926. PMID 9150411.
Kuhlman, B; Baker, D (2000). "Native protein sequences are close to optimal for their structures". Proceedings of the National Academy of Sciences of the United States of America. 97 (19): 10383–8. Bibcode:2000PNAS...9710383K. doi:10.1073/pnas.97.19.10383. PMC 27033. PMID 10984534.
Dunbrack, RL Jr (2002). "Rotamer libraries in the 21st century". Current Opinion in Structural Biology. 12 (4): 431–40. doi:10.1016/s0959-440x(02)00344-5. PMID 12163064.
Alford, RF; Leaver-Fay, A; Jeliazkov, JR; O'Meara, MJ; DiMaio, FP; Park, H; Shapovalov, MV; Renfrew, PD; Mulligan, VK; Kappel, K; Labonte, JW; Pacella, MS; Bonneau, R; Bradley, P; Dunbrack, RL; Das, R; Baker, D; Kuhlman, B; Kortemme, T; Gray, JJ (13 June 2017). "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". Journal of Chemical Theory and Computation. 13 (6): 3031–3048. doi:10.1021/acs.jctc.7b00125. PMC 5717763. PMID 28430426.
Shapovalov, MV; Dunbrack, RL Jr (2011). "A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions". Structure. 19 (6): 844–58. doi:10.1016/j.str.2011.03.019. PMC 3118414. PMID 21645855.
Towse, Clare-Louise; Rysavy, Steven J.; Vulovic, Ivan M.; Daggett, Valerie (5 January 2016). "New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities". Structure. 24 (1): 187–199. doi:10.1016/j.str.2015.10.017. ISSN 0969-2126. PMC 4715459. PMID 26745530.
Levitt, Michael; Hirshberg, Miriam; Sharon, Ruth; Daggett, Valerie (1995). "Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution". Computer Physics Communications. 91 (1): 215–231. Bibcode:1995CoPhC..91..215L. doi:10.1016/0010-4655(95)00049-L.
Dunbrack, RL Jr.; Karplus, M (1994). "Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains". Nature Structural Biology. 1 (5): 334–340. doi:10.1038/nsb0594-334. ISSN 1545-9985. PMID 7664040. S2CID 9157373.
Waterhouse, A; Bertoni, M; Bienert, S; Studer, G; Tauriello, G; Gumienny, R; Heer, FT; de Beer, TAP; Rempfer, C; Bordoli, L; Lepore, R; Schwede, T (2018). "SWISS-MODEL: homology modelling of protein structures and complexes". Nucleic Acids Research. 46 (W1): W296–W303. doi:10.1093/nar/gky427. PMC 6030848. PMID 29788355.
Studer, G; Tauriello, G; Bienert, S; Biasini, M; Johner, N; Schwede, T (2021). "ProMod3-A versatile homology modelling toolbox". PLOS Computational Biology. 17 (1): e1008667. Bibcode:2021PLSCB..17E8667S. doi:10.1371/journal.pcbi.1008667. PMC 7872268. PMID 33507980.
Kelley, LA; Mezulis, S; Yates, CM; Wass, MN; Sternberg, MJ (2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols. 10 (6): 845–58. doi:10.1038/nprot.2015.053. PMC 5298202. PMID 25950237.
Heo, L; Park, H; Seok, C (2013). "GalaxyRefine: Protein structure refinement driven by side-chain repacking". Nucleic Acids Research. 41 (Web Server issue): W384-8. doi:10.1093/nar/gkt458. PMC 3692086. PMID 23737448.
Krivov, Georgii G.; Shapovalov, Maxim V.; Dunbrack, Roland L. (2009). "Improved prediction of protein side-chain conformations with SCWRL4". Proteins: Structure, Function, and Bioinformatics. 77 (4): 778–795. doi:10.1002/prot.22488. ISSN 1097-0134. PMC 2885146. PMID 19603484.
Huang, X; Pearce, R; Zhang, Y (2020). "EvoEF2: accurate and fast energy function for computational protein design". Bioinformatics. 36 (4): 1135–1142. doi:10.1093/bioinformatics/btz740. PMC 7144094. PMID 31588495.

eyesopen.com

docs.eyesopen.com

OpenEye Scientific Software. "Macromolecule Conformations — Toolkits -- Java". OEChem Toolkit 3.1.0.0. Retrieved 10 February 2021.

harvard.edu

ui.adsabs.harvard.edu

Kuhlman, B; Baker, D (2000). "Native protein sequences are close to optimal for their structures". Proceedings of the National Academy of Sciences of the United States of America. 97 (19): 10383–8. Bibcode:2000PNAS...9710383K. doi:10.1073/pnas.97.19.10383. PMC 27033. PMID 10984534.
Levitt, Michael; Hirshberg, Miriam; Sharon, Ruth; Daggett, Valerie (1995). "Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution". Computer Physics Communications. 91 (1): 215–231. Bibcode:1995CoPhC..91..215L. doi:10.1016/0010-4655(95)00049-L.
Studer, G; Tauriello, G; Bienert, S; Biasini, M; Johner, N; Schwede, T (2021). "ProMod3-A versatile homology modelling toolbox". PLOS Computational Biology. 17 (1): e1008667. Bibcode:2021PLSCB..17E8667S. doi:10.1371/journal.pcbi.1008667. PMC 7872268. PMID 33507980.

nature.com

Dunbrack, RL Jr.; Karplus, M (1994). "Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains". Nature Structural Biology. 1 (5): 334–340. doi:10.1038/nsb0594-334. ISSN 1545-9985. PMID 7664040. S2CID 9157373.

nih.gov

pubmed.ncbi.nlm.nih.gov

Huang, X; Pearce, R; Zhang, Y (2020). "Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries". Journal of Chemical Information and Modeling. 60 (1): 410–420. doi:10.1021/acs.jcim.9b00812. PMC 7938712. PMID 31851497. Retrieved 18 February 2021.
Dunbrack, RL Jr.; Karplus, M (1993). "Backbone-dependent rotamer library for proteins. Application to side-chain prediction". Journal of Molecular Biology. 230 (2): 543–74. doi:10.1006/jmbi.1993.1170. PMID 8464064.
Dunbrack, RL Jr.; Cohen, FE (1997). "Bayesian statistical analysis of protein side-chain rotamer preferences". Protein Science. 6 (8): 1661–81. doi:10.1002/pro.5560060807. PMC 2143774. PMID 9260279.
Bower, MJ; Cohen, FE; Dunbrack, RL Jr (1997). "Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool". Journal of Molecular Biology. 267 (5): 1268–82. doi:10.1006/jmbi.1997.0926. PMID 9150411.
Kuhlman, B; Baker, D (2000). "Native protein sequences are close to optimal for their structures". Proceedings of the National Academy of Sciences of the United States of America. 97 (19): 10383–8. Bibcode:2000PNAS...9710383K. doi:10.1073/pnas.97.19.10383. PMC 27033. PMID 10984534.
Dunbrack, RL Jr (2002). "Rotamer libraries in the 21st century". Current Opinion in Structural Biology. 12 (4): 431–40. doi:10.1016/s0959-440x(02)00344-5. PMID 12163064.
Alford, RF; Leaver-Fay, A; Jeliazkov, JR; O'Meara, MJ; DiMaio, FP; Park, H; Shapovalov, MV; Renfrew, PD; Mulligan, VK; Kappel, K; Labonte, JW; Pacella, MS; Bonneau, R; Bradley, P; Dunbrack, RL; Das, R; Baker, D; Kuhlman, B; Kortemme, T; Gray, JJ (13 June 2017). "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". Journal of Chemical Theory and Computation. 13 (6): 3031–3048. doi:10.1021/acs.jctc.7b00125. PMC 5717763. PMID 28430426.
Shapovalov, MV; Dunbrack, RL Jr (2011). "A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions". Structure. 19 (6): 844–58. doi:10.1016/j.str.2011.03.019. PMC 3118414. PMID 21645855.
Towse, Clare-Louise; Rysavy, Steven J.; Vulovic, Ivan M.; Daggett, Valerie (5 January 2016). "New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities". Structure. 24 (1): 187–199. doi:10.1016/j.str.2015.10.017. ISSN 0969-2126. PMC 4715459. PMID 26745530.
Dunbrack, RL Jr.; Karplus, M (1994). "Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains". Nature Structural Biology. 1 (5): 334–340. doi:10.1038/nsb0594-334. ISSN 1545-9985. PMID 7664040. S2CID 9157373.
Waterhouse, A; Bertoni, M; Bienert, S; Studer, G; Tauriello, G; Gumienny, R; Heer, FT; de Beer, TAP; Rempfer, C; Bordoli, L; Lepore, R; Schwede, T (2018). "SWISS-MODEL: homology modelling of protein structures and complexes". Nucleic Acids Research. 46 (W1): W296–W303. doi:10.1093/nar/gky427. PMC 6030848. PMID 29788355.
Studer, G; Tauriello, G; Bienert, S; Biasini, M; Johner, N; Schwede, T (2021). "ProMod3-A versatile homology modelling toolbox". PLOS Computational Biology. 17 (1): e1008667. Bibcode:2021PLSCB..17E8667S. doi:10.1371/journal.pcbi.1008667. PMC 7872268. PMID 33507980.
Kelley, LA; Mezulis, S; Yates, CM; Wass, MN; Sternberg, MJ (2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols. 10 (6): 845–58. doi:10.1038/nprot.2015.053. PMC 5298202. PMID 25950237.
Heo, L; Park, H; Seok, C (2013). "GalaxyRefine: Protein structure refinement driven by side-chain repacking". Nucleic Acids Research. 41 (Web Server issue): W384-8. doi:10.1093/nar/gkt458. PMC 3692086. PMID 23737448.
Krivov, Georgii G.; Shapovalov, Maxim V.; Dunbrack, Roland L. (2009). "Improved prediction of protein side-chain conformations with SCWRL4". Proteins: Structure, Function, and Bioinformatics. 77 (4): 778–795. doi:10.1002/prot.22488. ISSN 1097-0134. PMC 2885146. PMID 19603484.
Huang, X; Pearce, R; Zhang, Y (2020). "EvoEF2: accurate and fast energy function for computational protein design". Bioinformatics. 36 (4): 1135–1142. doi:10.1093/bioinformatics/btz740. PMC 7144094. PMID 31588495.

ncbi.nlm.nih.gov

Huang, X; Pearce, R; Zhang, Y (2020). "Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries". Journal of Chemical Information and Modeling. 60 (1): 410–420. doi:10.1021/acs.jcim.9b00812. PMC 7938712. PMID 31851497. Retrieved 18 February 2021.
Dunbrack, RL Jr.; Cohen, FE (1997). "Bayesian statistical analysis of protein side-chain rotamer preferences". Protein Science. 6 (8): 1661–81. doi:10.1002/pro.5560060807. PMC 2143774. PMID 9260279.
Kuhlman, B; Baker, D (2000). "Native protein sequences are close to optimal for their structures". Proceedings of the National Academy of Sciences of the United States of America. 97 (19): 10383–8. Bibcode:2000PNAS...9710383K. doi:10.1073/pnas.97.19.10383. PMC 27033. PMID 10984534.
Alford, RF; Leaver-Fay, A; Jeliazkov, JR; O'Meara, MJ; DiMaio, FP; Park, H; Shapovalov, MV; Renfrew, PD; Mulligan, VK; Kappel, K; Labonte, JW; Pacella, MS; Bonneau, R; Bradley, P; Dunbrack, RL; Das, R; Baker, D; Kuhlman, B; Kortemme, T; Gray, JJ (13 June 2017). "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". Journal of Chemical Theory and Computation. 13 (6): 3031–3048. doi:10.1021/acs.jctc.7b00125. PMC 5717763. PMID 28430426.
Shapovalov, MV; Dunbrack, RL Jr (2011). "A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions". Structure. 19 (6): 844–58. doi:10.1016/j.str.2011.03.019. PMC 3118414. PMID 21645855.
Towse, Clare-Louise; Rysavy, Steven J.; Vulovic, Ivan M.; Daggett, Valerie (5 January 2016). "New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities". Structure. 24 (1): 187–199. doi:10.1016/j.str.2015.10.017. ISSN 0969-2126. PMC 4715459. PMID 26745530.
Waterhouse, A; Bertoni, M; Bienert, S; Studer, G; Tauriello, G; Gumienny, R; Heer, FT; de Beer, TAP; Rempfer, C; Bordoli, L; Lepore, R; Schwede, T (2018). "SWISS-MODEL: homology modelling of protein structures and complexes". Nucleic Acids Research. 46 (W1): W296–W303. doi:10.1093/nar/gky427. PMC 6030848. PMID 29788355.
Studer, G; Tauriello, G; Bienert, S; Biasini, M; Johner, N; Schwede, T (2021). "ProMod3-A versatile homology modelling toolbox". PLOS Computational Biology. 17 (1): e1008667. Bibcode:2021PLSCB..17E8667S. doi:10.1371/journal.pcbi.1008667. PMC 7872268. PMID 33507980.
Kelley, LA; Mezulis, S; Yates, CM; Wass, MN; Sternberg, MJ (2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols. 10 (6): 845–58. doi:10.1038/nprot.2015.053. PMC 5298202. PMID 25950237.
Heo, L; Park, H; Seok, C (2013). "GalaxyRefine: Protein structure refinement driven by side-chain repacking". Nucleic Acids Research. 41 (Web Server issue): W384-8. doi:10.1093/nar/gkt458. PMC 3692086. PMID 23737448.
Krivov, Georgii G.; Shapovalov, Maxim V.; Dunbrack, Roland L. (2009). "Improved prediction of protein side-chain conformations with SCWRL4". Proteins: Structure, Function, and Bioinformatics. 77 (4): 778–795. doi:10.1002/prot.22488. ISSN 1097-0134. PMC 2885146. PMID 19603484.
Huang, X; Pearce, R; Zhang, Y (2020). "EvoEF2: accurate and fast energy function for computational protein design". Bioinformatics. 36 (4): 1135–1142. doi:10.1093/bioinformatics/btz740. PMC 7144094. PMID 31588495.

nsf.gov

par.nsf.gov

Huang, X; Pearce, R; Zhang, Y (2020). "Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries". Journal of Chemical Information and Modeling. 60 (1): 410–420. doi:10.1021/acs.jcim.9b00812. PMC 7938712. PMID 31851497. Retrieved 18 February 2021.

pymolwiki.org

Kulp, Daniel W. "Rotamer Toggle - PyMOLWiki". pymolwiki.org. SBGrid Consortium. Retrieved 10 February 2021.

semanticscholar.org

api.semanticscholar.org

Dunbrack, RL Jr.; Karplus, M (1994). "Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains". Nature Structural Biology. 1 (5): 334–340. doi:10.1038/nsb0594-334. ISSN 1545-9985. PMID 7664040. S2CID 9157373.

ucsf.edu

cgl.ucsf.edu

Pettersen, EF; Goddard, TD; Huang, CC; Meng, EC; Couch, GS; Croll, TI; Morris, JH; Ferrin, TE. "Rotamer Tools (ChimeraX)". The ChimeraX User Guide. Regents of the University of California. Retrieved 9 February 2021.

worldcat.org

search.worldcat.org

Towse, Clare-Louise; Rysavy, Steven J.; Vulovic, Ivan M.; Daggett, Valerie (5 January 2016). "New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities". Structure. 24 (1): 187–199. doi:10.1016/j.str.2015.10.017. ISSN 0969-2126. PMC 4715459. PMID 26745530.
Dunbrack, RL Jr.; Karplus, M (1994). "Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains". Nature Structural Biology. 1 (5): 334–340. doi:10.1038/nsb0594-334. ISSN 1545-9985. PMID 7664040. S2CID 9157373.
Krivov, Georgii G.; Shapovalov, Maxim V.; Dunbrack, Roland L. (2009). "Improved prediction of protein side-chain conformations with SCWRL4". Proteins: Structure, Function, and Bioinformatics. 77 (4): 778–795. doi:10.1002/prot.22488. ISSN 1097-0134. PMC 2885146. PMID 19603484.

yasara.org

Krieger, E. "Protein side-chain modeling in YASARA". www.yasara.org. Yasara Biosciences. Retrieved 10 February 2021.