De novo protein structure prediction (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "De novo protein structure prediction" in English language version.

refsWebsite

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11nih.gov

4^th place

10doi.org

2^nd place

3worldcat.org

5^th place

1newyorker.com

146^th place

110^th place

1psu.edu

207^th place

136^th place

1web.archive.org

1^st place

1washington.edu

1,067^th place

749^th place

1sciencedaily.com

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920^th place

1semanticscholar.org

11^th place

8^th place

1biorxiv.org

5,061^st place

5,698^th place

biorxiv.org

Lin, Zeming; Akin, Halil; Rao, Roshan; Hie, Brian; Zhu, Zhongkai; Lu, Wenting; dos Santos Costa, Allan; Fazel-Zarandi, Maryam; Sercu, Tom; Candido, Sal; Rives, Alexander (July 21, 2022). "Language models of protein sequences at the scale of evolution enable accurate structure prediction" (PDF). bioRxiv. doi:10.1101/2022.07.20.500902.

doi.org

"Editorial: So much more to know". Science. 309 (5731): 78–102. 2005. doi:10.1126/science.309.5731.78b. PMID 15994524.
Dill, Ken A.; et al. (2007). "The protein folding problem: when will it be solved?". Current Opinion in Structural Biology. 17 (3): 342–346. doi:10.1016/j.sbi.2007.06.001. PMID 17572080.
Samudrala, R; Moult, J (1998). "An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction". Journal of Molecular Biology. 275 (5): 893–914. CiteSeerX 10.1.1.70.4101. doi:10.1006/jmbi.1997.1479. PMID 9480776.
Samudrala, R; Xia, Y; Huang, ES; Levitt, M (1999). "Ab initio prediction of protein structure using a combined hierarchical approach". Proteins: Structure, Function, and Genetics. S3 (S3): 194–198. doi:10.1002/(SICI)1097-0134(1999)37:3+<194::AID-PROT24>3.0.CO;2-F. S2CID 1566472.
Xu D, Zhang Y (July 2012). "Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field". Proteins. 80 (7): 1715–35. doi:10.1002/prot.24065. PMC 3370074. PMID 22411565.
Xu D, Zhang J, Roy A, Zhang Y (Aug 2011). "Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement". Proteins. 79 (Suppl 10): 147–60. doi:10.1002/prot.23111. PMC 3228277. PMID 22069036.
Kmiecik, Sebastian; Gront, Dominik; Kolinski, Michal; Wieteska, Lukasz; Dawid, Aleksandra Elzbieta; Kolinski, Andrzej (2016-06-22). "Coarse-Grained Protein Models and Their Applications". Chemical Reviews. 116 (14): 7898–936. doi:10.1021/acs.chemrev.6b00163. ISSN 0009-2665. PMID 27333362.
Schmitz, Jonathan F; Bornberg-Bauer, Erich (2017-01-19). "Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA". F1000Research. 6: 57. doi:10.12688/f1000research.10079.1. ISSN 2046-1402. PMC 5247788. PMID 28163910.
Middendorf, Lasse; Eicholt, Lars A. (June 2024). "Random, de novo, and conserved proteins: How structure and disorder predictors perform differently". Proteins: Structure, Function, and Bioinformatics. 92 (6): 757–767. doi:10.1002/prot.26652. ISSN 0887-3585. PMID 38226524.
Lin, Zeming; Akin, Halil; Rao, Roshan; Hie, Brian; Zhu, Zhongkai; Lu, Wenting; dos Santos Costa, Allan; Fazel-Zarandi, Maryam; Sercu, Tom; Candido, Sal; Rives, Alexander (July 21, 2022). "Language models of protein sequences at the scale of evolution enable accurate structure prediction" (PDF). bioRxiv. doi:10.1101/2022.07.20.500902.

newyorker.com

https://www.newyorker.com/tech/annals-of-technology/the-promise-of-designer-protein-in-the-fight-against-covid-19#:~:text=William%20DeGrado%2C%20a%20biochemist%20at,from%20a%20sequence%20and%20also

nih.gov

pubmed.ncbi.nlm.nih.gov

"Editorial: So much more to know". Science. 309 (5731): 78–102. 2005. doi:10.1126/science.309.5731.78b. PMID 15994524.
Dill, Ken A.; et al. (2007). "The protein folding problem: when will it be solved?". Current Opinion in Structural Biology. 17 (3): 342–346. doi:10.1016/j.sbi.2007.06.001. PMID 17572080.
Samudrala, R; Moult, J (1998). "An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction". Journal of Molecular Biology. 275 (5): 893–914. CiteSeerX 10.1.1.70.4101. doi:10.1006/jmbi.1997.1479. PMID 9480776.
Xu D, Zhang Y (July 2012). "Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field". Proteins. 80 (7): 1715–35. doi:10.1002/prot.24065. PMC 3370074. PMID 22411565.
Xu D, Zhang J, Roy A, Zhang Y (Aug 2011). "Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement". Proteins. 79 (Suppl 10): 147–60. doi:10.1002/prot.23111. PMC 3228277. PMID 22069036.
Kmiecik, Sebastian; Gront, Dominik; Kolinski, Michal; Wieteska, Lukasz; Dawid, Aleksandra Elzbieta; Kolinski, Andrzej (2016-06-22). "Coarse-Grained Protein Models and Their Applications". Chemical Reviews. 116 (14): 7898–936. doi:10.1021/acs.chemrev.6b00163. ISSN 0009-2665. PMID 27333362.
Schmitz, Jonathan F; Bornberg-Bauer, Erich (2017-01-19). "Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA". F1000Research. 6: 57. doi:10.12688/f1000research.10079.1. ISSN 2046-1402. PMC 5247788. PMID 28163910.
Middendorf, Lasse; Eicholt, Lars A. (June 2024). "Random, de novo, and conserved proteins: How structure and disorder predictors perform differently". Proteins: Structure, Function, and Bioinformatics. 92 (6): 757–767. doi:10.1002/prot.26652. ISSN 0887-3585. PMID 38226524.

ncbi.nlm.nih.gov

Xu D, Zhang Y (July 2012). "Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field". Proteins. 80 (7): 1715–35. doi:10.1002/prot.24065. PMC 3370074. PMID 22411565.
Xu D, Zhang J, Roy A, Zhang Y (Aug 2011). "Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement". Proteins. 79 (Suppl 10): 147–60. doi:10.1002/prot.23111. PMC 3228277. PMID 22069036.
Schmitz, Jonathan F; Bornberg-Bauer, Erich (2017-01-19). "Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA". F1000Research. 6: 57. doi:10.12688/f1000research.10079.1. ISSN 2046-1402. PMC 5247788. PMID 28163910.

psu.edu

citeseerx.ist.psu.edu

Samudrala, R; Moult, J (1998). "An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction". Journal of Molecular Biology. 275 (5): 893–914. CiteSeerX 10.1.1.70.4101. doi:10.1006/jmbi.1997.1479. PMID 9480776.

sciencedaily.com

"Rosetta News Article".

semanticscholar.org

api.semanticscholar.org

Samudrala, R; Xia, Y; Huang, ES; Levitt, M (1999). "Ab initio prediction of protein structure using a combined hierarchical approach". Proteins: Structure, Function, and Genetics. S3 (S3): 194–198. doi:10.1002/(SICI)1097-0134(1999)37:3+<194::AID-PROT24>3.0.CO;2-F. S2CID 1566472.

washington.edu

depts.washington.edu

"The Baker Laboratory". Archived from the original on 2012-11-13.

web.archive.org

"The Baker Laboratory". Archived from the original on 2012-11-13.

worldcat.org

search.worldcat.org

Kmiecik, Sebastian; Gront, Dominik; Kolinski, Michal; Wieteska, Lukasz; Dawid, Aleksandra Elzbieta; Kolinski, Andrzej (2016-06-22). "Coarse-Grained Protein Models and Their Applications". Chemical Reviews. 116 (14): 7898–936. doi:10.1021/acs.chemrev.6b00163. ISSN 0009-2665. PMID 27333362.
Schmitz, Jonathan F; Bornberg-Bauer, Erich (2017-01-19). "Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA". F1000Research. 6: 57. doi:10.12688/f1000research.10079.1. ISSN 2046-1402. PMC 5247788. PMID 28163910.
Middendorf, Lasse; Eicholt, Lars A. (June 2024). "Random, de novo, and conserved proteins: How structure and disorder predictors perform differently". Proteins: Structure, Function, and Bioinformatics. 92 (6): 757–767. doi:10.1002/prot.26652. ISSN 0887-3585. PMID 38226524.