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Pathogenic Autoreactive T and B Cells Cross-React with Mimotopes Expressed by a Common Human Gut Commensal to Trigger Autoimmunity.

Ruff WE, Dehner C, Kim WJ, Pagovich O, Aguiar CL, Yu AT, Roth AS, Vieira SM, Kriegel C, Adeniyi O, Mulla MJ, Abrahams VM, Kwok WW, Nussinov R, Erkan D, Goodman AL, Kriegel MA.

Cell Host Microbe. 2019 Jul 10;26(1):100-113.e8. doi: 10.1016/j.chom.2019.05.003. Epub 2019 Jun 18.


Protein ensembles link genotype to phenotype.

Nussinov R, Tsai CJ, Jang H.

PLoS Comput Biol. 2019 Jun 20;15(6):e1006648. doi: 10.1371/journal.pcbi.1006648. eCollection 2019 Jun. Review.


Emerging Allosteric Mechanism of EGFR Activation in Physiological and Pathological Contexts.

Tsai CJ, Nussinov R.

Biophys J. 2019 Jul 9;117(1):5-13. doi: 10.1016/j.bpj.2019.05.021. Epub 2019 May 28. Review.


Author Correction: In vivo tropism of Salmonella Typhi toxin to cells expressing a multiantennal glycan receptor.

Yang YA, Lee S, Zhao J, Thompson AJ, McBride R, Tsogtbaatar B, Paulson JC, Nussinov R, Deng L, Song J.

Nat Microbiol. 2019 Jul;4(7):1242. doi: 10.1038/s41564-019-0505-7.


Correction: Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.

Nussinov R, Jang H, Tsai CJ, Cheng F.

PLoS Comput Biol. 2019 Jun 12;15(6):e1007114. doi: 10.1371/journal.pcbi.1007114. eCollection 2019 Jun.


A Systems Pharmacology Approach Uncovers Wogonoside as an Angiogenesis Inhibitor of Triple-Negative Breast Cancer by Targeting Hedgehog Signaling.

Huang Y, Fang J, Lu W, Wang Z, Wang Q, Hou Y, Jiang X, Reizes O, Lathia J, Nussinov R, Eng C, Cheng F.

Cell Chem Biol. 2019 May 30. pii: S2451-9456(19)30173-4. doi: 10.1016/j.chembiol.2019.05.004. [Epub ahead of print]


The structural basis for Ras activation of PI3Kα lipid kinase.

Zhang M, Jang H, Nussinov R.

Phys Chem Chem Phys. 2019 Jun 5;21(22):12021-12028. doi: 10.1039/c9cp00101h.


deepDR: A network-based deep learning approach to in silico drug repositioning.

Zeng X, Zhu S, Liu X, Zhou Y, Nussinov R, Cheng F.

Bioinformatics. 2019 May 22. pii: btz418. doi: 10.1093/bioinformatics/btz418. [Epub ahead of print]


The mechanism of PI3Kα activation at the atomic level.

Zhang M, Jang H, Nussinov R.

Chem Sci. 2019 Feb 20;10(12):3671-3680. doi: 10.1039/c8sc04498h. eCollection 2019 Mar 28.


Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.

Nussinov R, Jang H, Tsai CJ, Cheng F.

PLoS Comput Biol. 2019 Mar 28;15(3):e1006658. doi: 10.1371/journal.pcbi.1006658. eCollection 2019 Mar. Review. Erratum in: PLoS Comput Biol. 2019 Jun 12;15(6):e1007114.


A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications.

Peng H, Zeng X, Zhou Y, Zhang D, Nussinov R, Cheng F.

PLoS Comput Biol. 2019 Feb 19;15(2):e1006772. doi: 10.1371/journal.pcbi.1006772. eCollection 2019 Feb.


Computational Structural Biology: Successes, Future Directions, and Challenges.

Nussinov R, Tsai CJ, Shehu A, Jang H.

Molecules. 2019 Feb 12;24(3). pii: E637. doi: 10.3390/molecules24030637. Review.


Allostery in Its Many Disguises: From Theory to Applications.

Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T.

Structure. 2019 Apr 2;27(4):566-578. doi: 10.1016/j.str.2019.01.003. Epub 2019 Feb 7. Review.


Precision medicine review: rare driver mutations and their biophysical classification.

Nussinov R, Jang H, Tsai CJ, Cheng F.

Biophys Rev. 2019 Feb;11(1):5-19. doi: 10.1007/s12551-018-0496-2. Epub 2019 Jan 4. Review.


Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing.

Ozdemir ES, Halakou F, Nussinov R, Gursoy A, Keskin O.

Methods Mol Biol. 2019;1903:1-21. doi: 10.1007/978-1-4939-8955-3_1.


Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health.

Cheng F, Liang H, Butte AJ, Eng C, Nussinov R.

Pharmacol Rev. 2019 Jan;71(1):1-19. doi: 10.1124/pr.118.016253. Epub 2018 Dec 13. Review.


Conformational stability and dynamics of the cancer-associated isoform Δ133p53β are modulated by p53 peptides and p53-specific DNA.

Lei J, Qi R, Tang Y, Wang W, Wei G, Nussinov R, Ma B.

FASEB J. 2019 Mar;33(3):4225-4235. doi: 10.1096/fj.201801973R. Epub 2018 Dec 12.


Mutations in LZTR1 drive human disease by dysregulating RAS ubiquitination.

Steklov M, Pandolfi S, Baietti MF, Batiuk A, Carai P, Najm P, Zhang M, Jang H, Renzi F, Cai Y, Abbasi Asbagh L, Pastor T, De Troyer M, Simicek M, Radaelli E, Brems H, Legius E, Tavernier J, Gevaert K, Impens F, Messiaen L, Nussinov R, Heymans S, Eyckerman S, Sablina AA.

Science. 2018 Dec 7;362(6419):1177-1182. doi: 10.1126/science.aap7607. Epub 2018 Nov 15.


Developments in integrative modeling with dynamical interfaces.

Ozdemir ES, Nussinov R, Gursoy A, Keskin O.

Curr Opin Struct Biol. 2018 Nov 12;56:11-17. doi: 10.1016/ [Epub ahead of print] Review.


Interface-Based Structural Prediction of Novel Host-Pathogen Interactions.

Guven-Maiorov E, Tsai CJ, Ma B, Nussinov R.

Methods Mol Biol. 2019;1851:317-335. doi: 10.1007/978-1-4939-8736-8_18.


Autoinhibition in Ras effectors Raf, PI3Kα, and RASSF5: a comprehensive review underscoring the challenges in pharmacological intervention.

Nussinov R, Zhang M, Tsai CJ, Liao TJ, Fushman D, Jang H.

Biophys Rev. 2018 Oct;10(5):1263-1282. doi: 10.1007/s12551-018-0461-0. Epub 2018 Sep 29. Review.


Structural disorder in four-repeat Tau fibrils reveals a new mechanism for barriers to cross-seeding of Tau isoforms.

Weismiller HA, Murphy R, Wei G, Ma B, Nussinov R, Margittai M.

J Biol Chem. 2018 Nov 9;293(45):17336-17348. doi: 10.1074/jbc.RA118.005316. Epub 2018 Sep 21.


Antigen binding allosterically promotes Fc receptor recognition.

Zhao J, Nussinov R, Ma B.

MAbs. 2019 Jan;11(1):58-74. doi: 10.1080/19420862.2018.1522178. Epub 2018 Oct 5.


Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites.

Rangarajan S, He Y, Chen Y, Kerzic MC, Ma B, Gowthaman R, Pierce BG, Nussinov R, Mariuzza RA, Orban J.

J Biol Chem. 2018 Oct 12;293(41):15991-16005. doi: 10.1074/jbc.RA118.003832. Epub 2018 Aug 22.


Allosteric KRas4B Can Modulate SOS1 Fast and Slow Ras Activation Cycles.

Liao TJ, Jang H, Fushman D, Nussinov R.

Biophys J. 2018 Aug 21;115(4):629-641. doi: 10.1016/j.bpj.2018.07.016. Epub 2018 Jul 24.


Allosteric activation of RAF in the MAPK signaling pathway.

Tsai CJ, Nussinov R.

Curr Opin Struct Biol. 2018 Dec;53:100-106. doi: 10.1016/ Epub 2018 Jul 27. Review.


Calmodulin (CaM) Activates PI3Kα by Targeting the "Soft" CaM-Binding Motifs in Both the nSH2 and cSH2 Domains of p85α.

Zhang M, Li Z, Wang G, Jang H, Sacks DB, Zhang J, Gaponenko V, Nussinov R.

J Phys Chem B. 2018 Dec 13;122(49):11137-11146. doi: 10.1021/acs.jpcb.8b05982. Epub 2018 Aug 8.


Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδ.

Ozdemir ES, Jang H, Gursoy A, Keskin O, Nussinov R.

J Phys Chem B. 2018 Aug 2;122(30):7503-7513. doi: 10.1021/acs.jpcb.8b04347. Epub 2018 Jul 18.


Pharmacological inhibition of dihydroorotate dehydrogenase induces apoptosis and differentiation in acute myeloid leukemia cells.

Wu D, Wang W, Chen W, Lian F, Lang L, Huang Y, Xu Y, Zhang N, Chen Y, Liu M, Nussinov R, Cheng F, Lu W, Huang J.

Haematologica. 2018 Sep;103(9):1472-1483. doi: 10.3324/haematol.2018.188185. Epub 2018 Jun 7.


Correction to Familial Mutations May Switch Conformational Preferences in α-Synuclein Fibrils.

Xu L, Ma B, Nussinov R, Thompson D.

ACS Chem Neurosci. 2018 Jul 18;9(7):1866-1867. doi: 10.1021/acschemneuro.8b00240. Epub 2018 Jun 1. No abstract available.


The distinct structural preferences of tau protein repeat domains.

Li X, Dong X, Wei G, Margittai M, Nussinov R, Ma B.

Chem Commun (Camb). 2018 May 31;54(45):5700-5703. doi: 10.1039/c8cc01263f.


KRAS Activating Signaling Triggers Arteriovenous Malformations.

Cheng F, Nussinov R.

Trends Biochem Sci. 2018 Jul;43(7):481-483. doi: 10.1016/j.tibs.2018.04.007. Epub 2018 May 7.


Experimental and Computational Protocols for Studies of Cross-Seeding Amyloid Assemblies.

Ren B, Hu R, Zhang M, Liu Y, Xu L, Jiang B, Ma J, Ma B, Nussinov R, Zheng J.

Methods Mol Biol. 2018;1777:429-447. doi: 10.1007/978-1-4939-7811-3_27.


Oncogenic KRas mobility in the membrane and signaling response.

Nussinov R, Tsai CJ, Jang H.

Semin Cancer Biol. 2019 Feb;54:109-113. doi: 10.1016/j.semcancer.2018.02.009. Epub 2018 Feb 27. Review.


Interaction of Calmodulin with the cSH2 Domain of the p85 Regulatory Subunit.

Wang G, Zhang M, Jang H, Lu S, Lin S, Chen G, Nussinov R, Zhang J, Gaponenko V.

Biochemistry. 2018 Mar 27;57(12):1917-1928. doi: 10.1021/acs.biochem.7b01130. Epub 2018 Mar 19.


Raf-1 Cysteine-Rich Domain Increases the Affinity of K-Ras/Raf at the Membrane, Promoting MAPK Signaling.

Li S, Jang H, Zhang J, Nussinov R.

Structure. 2018 Mar 6;26(3):513-525.e2. doi: 10.1016/j.str.2018.01.011. Epub 2018 Feb 8.


Atomistic-level study of the interactions between hIAPP protofibrils and membranes: Influence of pH and lipid composition.

Qian Z, Zou Y, Zhang Q, Chen P, Ma B, Wei G, Nussinov R.

Biochim Biophys Acta Biomembr. 2018 Feb 9. pii: S0005-2736(18)30046-4. doi: 10.1016/j.bbamem.2018.02.005. [Epub ahead of print]


PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Corrigendum.

Kuzu G, Keskin O, Nussinov R, Gursoy A.

Acta Crystallogr D Struct Biol. 2018 Jan 1;74(Pt 1):65-66. doi: 10.1107/S2059798317017739. Epub 2018 Jan 1.


Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2.

Ozdemir ES, Jang H, Gursoy A, Keskin O, Li Z, Sacks DB, Nussinov R.

J Biol Chem. 2018 Mar 9;293(10):3685-3699. doi: 10.1074/jbc.RA117.001596. Epub 2018 Jan 22.


IKKα inactivation promotes Kras-initiated lung adenocarcinoma development through disrupting major redox regulatory pathways.

Song NY, Zhu F, Wang Z, Willette-Brown J, Xi S, Sun Z, Su L, Wu X, Ma B, Nussinov R, Xia X, Schrump DS, Johnson PF, Karin M, Hu Y.

Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):E812-E821. doi: 10.1073/pnas.1717520115. Epub 2018 Jan 8.


Is Nanoclustering essential for all oncogenic KRas pathways? Can it explain why wild-type KRas can inhibit its oncogenic variant?

Nussinov R, Tsai CJ, Jang H.

Semin Cancer Biol. 2019 Feb;54:114-120. doi: 10.1016/j.semcancer.2018.01.002. Epub 2018 Jan 5. Review.


Oncogenic Ras Isoforms Signaling Specificity at the Membrane.

Nussinov R, Tsai CJ, Jang H.

Cancer Res. 2018 Feb 1;78(3):593-602. doi: 10.1158/0008-5472.CAN-17-2727. Epub 2017 Dec 22. Review.


Structure and energetic basis of overrepresented λ light chain in systemic light chain amyloidosis patients.

Zhao J, Zhang B, Zhu J, Nussinov R, Ma B.

Biochim Biophys Acta Mol Basis Dis. 2018 Jun;1864(6 Pt B):2294-2303. doi: 10.1016/j.bbadis.2017.12.009. Epub 2017 Dec 12.


Local and global anatomy of antibody-protein antigen recognition.

Wang M, Zhu D, Zhu J, Nussinov R, Ma B.

J Mol Recognit. 2018 May;31(5):e2693. doi: 10.1002/jmr.2693. Epub 2017 Dec 8.


In vivo tropism of Salmonella Typhi toxin to cells expressing a multiantennal glycan receptor.

Yang YA, Lee S, Zhao J, Thompson AJ, McBride R, Tsogtbaatar B, Paulson JC, Nussinov R, Deng L, Song J.

Nat Microbiol. 2018 Feb;3(2):155-163. doi: 10.1038/s41564-017-0076-4. Epub 2017 Dec 4. Erratum in: Nat Microbiol. 2019 Jul;4(7):1242.


Phosphorylated Calmodulin Promotes PI3K Activation by Binding to the SH2 Domains.

Zhang M, Jang H, Gaponenko V, Nussinov R.

Biophys J. 2017 Nov 7;113(9):1956-1967. doi: 10.1016/j.bpj.2017.09.008.


Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer.

Guven-Maiorov E, Tsai CJ, Ma B, Nussinov R.

J Mol Biol. 2017 Dec 8;429(24):3925-3941. doi: 10.1016/j.jmb.2017.10.023. Epub 2017 Oct 26.


Calmodulin and IQGAP1 activation of PI3Kα and Akt in KRAS, HRAS and NRAS-driven cancers.

Nussinov R, Zhang M, Tsai CJ, Jang H.

Biochim Biophys Acta Mol Basis Dis. 2018 Jun;1864(6 Pt B):2304-2314. doi: 10.1016/j.bbadis.2017.10.032. Epub 2017 Oct 31. Review.


Structural host-microbiota interaction networks.

Guven-Maiorov E, Tsai CJ, Nussinov R.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005579. doi: 10.1371/journal.pcbi.1005579. eCollection 2017 Oct. Review.

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