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Noah Ollikainen, Ph.D. - Publications

Affiliations: 
Biological and Medical Informatics University of California, San Francisco, San Francisco, CA 
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13 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Perica T, Mathy CJP, Xu J, Jang GΜ, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, Kortemme T. Systems-level effects of allosteric perturbations to a model molecular switch. Nature. PMID 34646016 DOI: 10.1038/s41586-021-03982-6  0.587
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Ollikainen N, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.623
2019 Glasgow AA, Huang YM, Mandell DJ, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. Computational design of a modular protein sense-response system. Science (New York, N.Y.). 366: 1024-1028. PMID 31754004 DOI: 10.1126/Science.Aax8780  0.567
2017 Ollikainen N. Flexible Backbone Methods for Predicting and Designing Peptide Specificity. Methods in Molecular Biology (Clifton, N.J.). 1561: 173-187. PMID 28236238 DOI: 10.1007/978-1-4939-6798-8_10  0.524
2016 Engreitz JM, Ollikainen N, Guttman M. Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nature Reviews. Molecular Cell Biology. PMID 27780979 DOI: 10.1038/Nrm.2016.126  0.315
2015 Ollikainen N, de Jong RM, Kortemme T. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity. Plos Computational Biology. 11: e1004335. PMID 26397464 DOI: 10.1371/Journal.Pcbi.1004335  0.707
2015 Ó Conchúir S, Barlow KA, Pache RA, Ollikainen N, Kundert K, O'Meara MJ, Smith CA, Kortemme T. A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. Plos One. 10: e0130433. PMID 26335248 DOI: 10.1371/Journal.Pone.0130433  0.647
2014 Melero C, Ollikainen N, Harwood I, Karpiak J, Kortemme T. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition. Proceedings of the National Academy of Sciences of the United States of America. 111: 15426-31. PMID 25313039 DOI: 10.1073/Pnas.1410624111  0.709
2013 Jackson EL, Ollikainen N, Covert AW, Kortemme T, Wilke CO. Amino-acid site variability among natural and designed proteins. Peerj. 1: e211. PMID 24255821 DOI: 10.7717/Peerj.211  0.716
2013 Ollikainen N, Kortemme T. Computational protein design quantifies structural constraints on amino acid covariation. Plos Computational Biology. 9: e1003313. PMID 24244128 DOI: 10.1371/Journal.Pcbi.1003313  0.688
2013 Ollikainen N, Smith CA, Fraser JS, Kortemme T. Flexible backbone sampling methods to model and design protein alternative conformations. Methods in Enzymology. 523: 61-85. PMID 23422426 DOI: 10.1016/B978-0-12-394292-0.00004-7  0.698
2010 David DC, Ollikainen N, Trinidad JC, Cary MP, Burlingame AL, Kenyon C. Widespread protein aggregation as an inherent part of aging in C. elegans. Plos Biology. 8: e1000450. PMID 20711477 DOI: 10.1371/Journal.Pbio.1000450  0.419
2009 Ollikainen N, Sentovich E, Coelho C, Kuehlmann A, Kortemme T. SAT-based protein design Ieee/Acm International Conference On Computer-Aided Design, Digest of Technical Papers, Iccad. 128-135.  0.693
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