User:Jaime Prilusky

From Proteopedia

Prof Jaime Prilusky, Ph.D.
R&D Bioinformatics and Data Management
Weizmann Institute of Science
76100 Rehovot - Israel

ORCID iD 0000-0002-7019-0191
email:
fax: 972-8-9344113
phone: 972-8-9344959

Links

Selected Publications

• Castro C, Johnson RJ, Kieffer B, Means JA, Taylor A, Telford J, Thompson LK, Sussman JL, Prilusky J, Theis K. A practical guide to teaching with Proteopedia. Biochem Mol Biol Educ. 2021 Jun 3. doi: 10.1002/bmb.21548. PMID:34080750 doi:http://dx.doi.org/10.1002/bmb.21548
• Zaidman D, Gehrtz P, Filep M, Fearon D, Gabizon R, Douangamath A, Prilusky J, Duberstein S, Cohen G, Owen CD, Resnick E, Strain-Damerell C, Lukacik P, Barr H, Walsh MA, von Delft F, London N. An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 M(pro) inhibitor. Cell Chem Biol. 2021 Jun 22. pii: S2451-9456(21)00263-4. doi:, 10.1016/j.chembiol.2021.05.018. PMID:34174194 doi:http://dx.doi.org/10.1016/j.chembiol.2021.05.018
• Daniel E, Maksimainen MM, Smith N, Ratas V, Biterova E, Murthy SN, Rahman MT, Kiema TR, Sridhar S, Cordara G, Dalwani S, Venkatesan R, Prilusky J, Dym O, Lehtio L, Koski MK, Ashton AW, Sussman JL, Wierenga RK. IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition. Acta Crystallogr D Struct Biol. 2021 Feb 1;77(Pt 2):151-163. doi:, 10.1107/S2059798320015223. Epub 2021 Jan 26. PMID:33559605 doi:http://dx.doi.org/10.1107/S2059798320015223
• Zaidman D, Prilusky J, London N. PRosettaC: Rosetta based modeling of PROTAC mediated ternary complexes. J Chem Inf Model. 2020 Sep 25. doi: 10.1021/acs.jcim.0c00589. PMID:32976709 doi:http://dx.doi.org/10.1021/acs.jcim.0c00589
• Gonzalez-Beltran AN, Masuzzo P, Ampe C, Bakker GJ, Besson S, Eibl RH, Friedl P, Gunzer M, Kittisopikul M, Devedec SEL, Leo S, Moore J, Paran Y, Prilusky J, Rocca-Serra P, Roudot P, Schuster M, Sergeant G, Stromblad S, Swedlow JR, van Erp M, Van Troys M, Zaritsky A, Sansone SA, Martens L. Community standards for open cell migration data. Gigascience. 2020 May 1;9(5). pii: 5836133. doi: 10.1093/gigascience/giaa041. PMID:32396199 doi:http://dx.doi.org/10.1093/gigascience/giaa041
• Lapidoth G, Parker J, Prilusky J, Fleishman SJ. AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains. Bioinformatics. 2019 May 1;35(9):1591-1593. doi: 10.1093/bioinformatics/bty822. PMID:30951584 doi:http://dx.doi.org/10.1093/bioinformatics/bty822
• Khersonsky O, Lipsh R, Avizemer Z, Ashani Y, Goldsmith M, Leader H, Dym O, Rogotner S, Trudeau DL, Prilusky J, Amengual-Rigo P, Guallar V, Tawfik DS, Fleishman SJ. Automated Design of Efficient and Functionally Diverse Enzyme Repertoires. Mol Cell. 2018 Oct 4;72(1):178-186.e5. doi: 10.1016/j.molcel.2018.08.033. Epub, 2018 Sep 27. PMID:30270109 doi:http://dx.doi.org/10.1016/j.molcel.2018.08.033
• Tickotsky N, Sagiv T, Prilusky J, Shifrut E, Friedman N. McPAS-TCR: A manually-curated catalogue of pathology-associated T cell receptor sequences. Bioinformatics. 2017 May 8. doi: 10.1093/bioinformatics/btx286. PMID:28481982 doi:http://dx.doi.org/10.1093/bioinformatics/btx286
• Elazar A, Weinstein JJ, Prilusky J, Fleishman SJ. Interplay between hydrophobicity and the positive-inside rule in determining membrane-protein topology. Proc Natl Acad Sci U S A. 2016 Aug 25. pii: 201605888. PMID:27562165 doi:http://dx.doi.org/10.1073/pnas.1605888113
• Goldenzweig A, Goldsmith M, Hill SE, Gertman O, Laurino P, Ashani Y, Dym O, Unger T, Albeck S, Prilusky J, Lieberman RL, Aharoni A, Silman I, Sussman JL, Tawfik DS, Fleishman SJ. Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability. Mol Cell. 2016 Jul 21;63(2):337-346. doi: 10.1016/j.molcel.2016.06.012. Epub 2016, Jul 14. PMID:27425410 doi:http://dx.doi.org/10.1016/j.molcel.2016.06.012
• Shoshanit Ohad, Shifra Ben-Dor, Jaime Prilusky, Valeria Kravitz, Bareket Dassa, Vered Chalifa-Caspi, Yechezkel Kashi and Efrat Rorman. The Development of a Novel qPCR Assay-Set for Identifying Fecal Contamination Originating from Domestic Fowls and Waterfowl in Israel. Front. Microbiol., 17 February 2016 doi:http://dx.doi.org/10.3389/fmicb.2016.00145
• Jaime Prilusky, Wayne Decatur, Eric Martz. Publishing in Proteopedia: The Guide, Advancing Methods for Biomolecular Crystallography NATO Science for Peace and Security Series A: Chemistry and Biology 2013, pp 277-295 doi:http://dx.doi.org/10.1007/978-94-007-6232-9_24
• Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
• Prilusky J, Hodis E. Proteopedia entry: "Tutorial: How we get the oxygen we breathe". Biochem Mol Biol Educ. 2012 Sep;40(5):339. doi: 10.1002/bmb.20646. PMID:22987558 doi:10.1002/bmb.20646
• Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R, Valencia A. Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts. Genome Res. 2012 Jun 4. PMID:22588898 doi:10.1101/gr.130062.111
• Tsvetkov P, Myers N, Moscovitz O, Sharon M, Prilusky J, Shaul Y. Thermo-resistant intrinsically disordered proteins are efficient 20S proteasome substrates. Mol Biosyst. 2012 Jan 1;8(1):368-73. Epub 2011 Oct 25. PMID:22027891 doi:10.1039/c1mb05283g
• Prilusky J, Hodis E and Sussman JL. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure. Chapter Macromolecular Crystallography, Part of the series NATO Science for Peace and Security Series A: Chemistry and Biology pp 149-161, 2011 doi:http://dx.doi.org/10.1007/978-94-007-2530-0_14
• Prilusky J, Hodis E, Canner D, Decatur W, Oberholser K, Martz E, Berchanski A, Harel M, Sussman JL. Proteopedia: A status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules. J Struct Biol. 2011 Apr 23. PMID:21536137 doi:10.1016/j.jsb.2011.04.011
• Hodis E, Prilusky J, Sussman JL. Proteopedia: A collaborative, virtual 3D web-resource for protein and biomolecule structure and function. Biochem Mol Biol Educ. 2010 Sep;38(5):341-2. doi: 10.1002/bmb.20431. PMID:21567857 doi:10.1002/bmb.20431
• Frenkel-Morgenstern M, Cohen AA, Geva-Zatorsky N, Eden E, Prilusky J, Issaeva I, Sigal A, Cohen-Saidon C, Liron Y, Cohen L, Danon T, Perzov N, Alon U. Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. Nucleic Acids Res. 2010 Jan;38(Database issue):D508-12. Epub 2009 Oct 9. PMID:19820112 doi:10.1093/nar/gkp808
• Noivirt-Brik O, Prilusky J, Sussman JL. Assessment of disorder predictions in CASP8. Proteins. 2009 Aug 21. PMID:19774619 doi:10.1002/prot.22586
• Ben-David M, Noivirt-Brik O, Paz A, Prilusky J, Sussman JL, Levy Y. Assessment of CASP8 structure predictions for template free targets. Proteins. 2009 Aug 21. PMID:19774550 doi:10.1002/prot.22591
• Prilusky J, Bibi E. Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs. Proc Natl Acad Sci U S A. 2009 Apr 6. PMID:19366666
• Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL. Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol. 2008;9(8):R121. Epub 2008 Aug 3. PMID:18673581 doi:http://dx.doi.org/10.1186/gb-2008-9-8-r121
• Graslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schutz A, Heinemann U, Yokoyama S, Bussow K, Gunsalus KC. Protein production and purification. Nat Methods. 2008 Feb;5(2):135-46. PMID:18235434 doi:http://dx.doi.org/10.1038/nmeth.f.202
• Tompa P, Prilusky J, Silman I, Sussman JL. Structural disorder serves as a weak signal for intracellular protein degradation. Proteins. 2008 May 1;71(2):903-9. PMID:18004785 doi:http://dx.doi.org/10.1002/prot.21773
• Felder CE, Prilusky J, Silman I, Sussman JL. A server and database for dipole moments of proteins. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W512-21. Epub 2007 May, 25. PMID:17526523 doi:http://dx.doi.org/10.1093/nar/gkm307
• Esnouf RM, Hamer R, Sussman JL, Silman I, Trudgian D, Yang ZR, Prilusky J. Honing the in silico toolkit for detecting protein disorder. Acta Crystallogr D Biol Crystallogr. 2006 Oct;62(Pt 10):1260-6. Epub 2006, Sep 19. PMID:17001103 doi:http://dx.doi.org/10.1107/S0907444906033580
• Albeck S, Alzari P, Andreini C, Banci L, Berry IM, Bertini I, Cambillau C, Canard B, Carter L, Cohen SX, Diprose JM, Dym O, Esnouf RM, Felder C, Ferron F, Guillemot F, Hamer R, Ben Jelloul M, Laskowski RA, Laurent T, Longhi S, Lopez R, Luchinat C, Malet H, Mochel T, Morris RJ, Moulinier L, Oinn T, Pajon A, Peleg Y, Perrakis A, Poch O, Prilusky J, Rachedi A, Ripp R, Rosato A, Silman I, Stuart DI, Sussman JL, Thierry JC, Thompson JD, Thornton JM, Unger T, Vaughan B, Vranken W, Watson JD, Whamond G, Henrick K. SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallogr D Biol Crystallogr. 2006 Oct;62(Pt 10):1184-95. Epub 2006, Sep 19. PMID:17001095 doi:http://dx.doi.org/10.1107/S090744490602991X
• Albeck S, Burstein Y, Dym O, Jacobovitch Y, Levi N, Meged R, Michael Y, Peleg Y, Prilusky J, Schreiber G, Silman I, Unger T, Sussman JL. Three-dimensional structure determination of proteins related to human health in their functional context at The Israel Structural Proteomics Center (ISPC). This paper was presented at ICCBM10. Acta Crystallogr D Biol Crystallogr. 2005 Oct;61(Pt 10):1364-72. Epub 2005, Sep 28. PMID:16204888 doi:http://dx.doi.org/10.1107/S0907444905023565
• Sobolev V, Eyal E, Gerzon S, Potapov V, Babor M, Prilusky J, Edelman M. SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W39-43. PMID:15980496 doi:http://dx.doi.org/33/suppl_2/W39
• Prilusky J, Felder CE, Zeev-Ben-Mordehai T, Rydberg EH, Man O, Beckmann JS, Silman I, Sussman JL. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics. 2005 Aug 15;21(16):3435-8. Epub 2005 Jun 14. PMID:15955783 doi:http://dx.doi.org/10.1093/bioinformatics/bti537
• Prilusky J, Oueillet E, Ulryck N, Pajon A, Bernauer J, Krimm I, Quevillon-Cheruel S, Leulliot N, Graille M, Liger D, Tresaugues L, Sussman JL, Janin J, van Tilbeurgh H, Poupon A. HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories. Acta Crystallogr D Biol Crystallogr. 2005 Jun;61(Pt 6):671-8. Epub 2005, May 26. PMID:15930618 doi:http://dx.doi.org/10.1107/S0907444905001290
• Jaakola VP, Prilusky J, Sussman JL, Goldman A. G protein-coupled receptors show unusual patterns of intrinsic unfolding. Protein Eng Des Sel. 2005 Feb;18(2):103-10. Epub 2005 Mar 24. PMID:15790574 doi:10.1093/protein/gzi004
• Prilusky J, (2004) Protein structure visualisation , BRIEFINGS IN BIOINFORMATICS, 5:89-90, doi:10.1093/bib/5.1.89
• Lin D, Manning NO, Jiang J, Abola EE, Stampf D, Prilusky J, Sussman JL. AutoDep: a web-based system for deposition and validation of macromolecular structural -information. Acta Crystallogr D Biol Crystallogr. 2000 Jul;56(Pt 7):828-41. PMID:10930830
• Sussman JL, Abola EE, Lin D, Jiang J, Manning NO, Prilusky J. The protein data bank. Bridging the gap between the sequence and 3D structure world. Genetica. 1999;106(1-2):149-58. PMID:10710721
• Sobolev V, Sorokine A, Prilusky J, Abola EE, Edelman M. Automated analysis of interatomic contacts in proteins. Bioinformatics. 1999 Apr;15(4):327-32. PMID:10320401
• Sussman JL, Lin D, Jiang J, Manning NO, Prilusky J, Ritter O, Abola EE. Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 1):1078-84. PMID:10089483
• Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics. 1998;14(8):656-64. PMID:9789091
• Rebhan M, Prilusky J. Rapid access to biomedical knowledge with GeneCards and HotMolecBase: implications for the electrophoretic analysis of large sets of gene products. Electrophoresis. 1997 Dec;18(15):2774-80. PMID:9504809 doi:10.1002/elps.1150181511
• Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. GeneCards: integrating information about genes, proteins and diseases. Trends Genet. 1997 Apr;13(4):163. PMID:9097728
• Abola EE, Sussman JL, Prilusky J, Manning NO. Protein Data Bank archives of three-dimensional macromolecular structures. Methods Enzymol. 1997;277:556-71. PMID:9379928
• Prilusky J. Computers in biology: the future is today. Arch Biol Med Exp (Santiago). 1986;19(3-4):323-8. PMID:8816081