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LoopGrafter: Visual Support for the Grafting Workflow of Protein Loops.
Opaleny F, Ulbrich P, Planas-Iglesias J, Byska J, Pinto GP, Bednar D, FurmanovA K, KozlikovA B. Opaleny F, et al. IEEE Trans Vis Comput Graph. 2021 Sep 29;PP. doi: 10.1109/TVCG.2021.3114755. Online ahead of print. IEEE Trans Vis Comput Graph. 2021. PMID: 34587016
Computational design of enzymes for biotechnological applications.
Planas-Iglesias J, Marques SM, Pinto GP, Musil M, Stourac J, Damborsky J, Bednar D. Planas-Iglesias J, et al. Biotechnol Adv. 2021 Mar-Apr;47:107696. doi: 10.1016/j.biotechadv.2021.107696. Epub 2021 Jan 26. Biotechnol Adv. 2021. PMID: 33513434 Review.
Engineering the protein dynamics of an ancestral luciferase.
Schenkmayerova A, Pinto GP, Toul M, Marek M, Hernychova L, Planas-Iglesias J, Daniel Liskova V, Pluskal D, Vasina M, Emond S, Dörr M, Chaloupkova R, Bednar D, Prokop Z, Hollfelder F, Bornscheuer UT, Damborsky J. Schenkmayerova A, et al. Nat Commun. 2021 Jun 14;12(1):3616. doi: 10.1038/s41467-021-23450-z. Nat Commun. 2021. PMID: 34127663 Free PMC article.
Web-based tools for computational enzyme design.
Marques SM, Planas-Iglesias J, Damborsky J. Marques SM, et al. Curr Opin Struct Biol. 2021 Aug;69:19-34. doi: 10.1016/j.sbi.2021.01.010. Epub 2021 Mar 2. Curr Opin Struct Biol. 2021. PMID: 33667757 Review.
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.
Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium; Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Louis Bridges S Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM. Sieberts SK, et al. Nat Commun. 2016 Aug 23;7:12460. doi: 10.1038/ncomms12460. Nat Commun. 2016. PMID: 27549343 Free PMC article.
ArchDB 2014: structural classification of loops in proteins.
Bonet J, Planas-Iglesias J, Garcia-Garcia J, Marín-López MA, Fernandez-Fuentes N, Oliva B. Bonet J, et al. Nucleic Acids Res. 2014 Jan;42(Database issue):D315-9. doi: 10.1093/nar/gkt1189. Epub 2013 Nov 21. Nucleic Acids Res. 2014. PMID: 24265221 Free PMC article.
41 results