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Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape.
J Comput Chem. 2016 Feb 5;37(4):437-47. doi: 10.1002/jcc.24249. Epub 2015 Nov 12.
J Comput Chem. 2016.
PMID: 26558715
Free PMC article.
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.
Schuepbach T, Pagni M, Bridge A, Bougueleret L, Xenarios I, Cerutti L.
Schuepbach T, et al.
Bioinformatics. 2013 May 1;29(9):1215-7. doi: 10.1093/bioinformatics/btt129. Epub 2013 Mar 16.
Bioinformatics. 2013.
PMID: 23505298
Free PMC article.
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Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.
Wells DK, van Buuren MM, Dang KK, Hubbard-Lucey VM, Sheehan KCF, Campbell KM, Lamb A, Ward JP, Sidney J, Blazquez AB, Rech AJ, Zaretsky JM, Comin-Anduix B, Ng AHC, Chour W, Yu TV, Rizvi H, Chen JM, Manning P, Steiner GM, Doan XC; Tumor Neoantigen Selection Alliance; Merghoub T, Guinney J, Kolom A, Selinsky C, Ribas A, Hellmann MD, Hacohen N, Sette A, Heath JR, Bhardwaj N, Ramsdell F, Schreiber RD, Schumacher TN, Kvistborg P, Defranoux NA.
Wells DK, et al.
Cell. 2020 Oct 29;183(3):818-834.e13. doi: 10.1016/j.cell.2020.09.015. Epub 2020 Oct 9.
Cell. 2020.
PMID: 33038342
Free PMC article.
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Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing.
Taylor AS, Barros D, Gobet N, Schuepbach T, McAllister B, Aeschbach L, Randall EL, Trofimenko E, Heuchan ER, Barszcz P, Ciosi M, Morgan J, Hafford-Tear NJ, Davidson AE, Massey TH, Monckton DG, Jones L, Network RIOTEHD, Xenarios I, Dion V.
Taylor AS, et al. Among authors: schuepbach t.
NAR Genom Bioinform. 2022 Dec 5;4(4):lqac089. doi: 10.1093/nargab/lqac089. eCollection 2022 Dec.
NAR Genom Bioinform. 2022.
PMID: 36478959
Free PMC article.
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The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.
SIB Swiss Institute of Bioinformatics Members.
SIB Swiss Institute of Bioinformatics Members.
Nucleic Acids Res. 2016 Jan 4;44(D1):D27-37. doi: 10.1093/nar/gkv1310. Epub 2015 Nov 28.
Nucleic Acids Res. 2016.
PMID: 26615188
Free PMC article.
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