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Items: 1 to 50 of 635

1.

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.

2.

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.

3.

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 Jan 17. pii: S0969-2126(19)30003-6. doi: 10.1016/j.str.2019.01.003. [Epub ahead of print] Review.

PMID:
30744993
4.

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.

5.

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.

PMID:
30547433
6.

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.

7.

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.

PMID:
30540922
8.

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.

PMID:
30442762
9.

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/j.sbi.2018.10.007. [Epub ahead of print] Review.

PMID:
30439586
10.

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.

PMID:
30298406
11.

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.

12.

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.

PMID:
30242125
13.

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.

14.

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.

PMID:
30135211
15.

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.

PMID:
30097175
16.

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/j.sbi.2018.07.007. Epub 2018 Jul 27. Review.

PMID:
30059805
17.

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 Aug 8. doi: 10.1021/acs.jpcb.8b05982. [Epub ahead of print]

PMID:
30047727
18.

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.

PMID:
29961325
19.

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.

20.

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.

PMID:
29855185
21.

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.

PMID:
29774342
22.

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.

23.

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.

PMID:
29744852
24.

Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example.

Qi R, Wei G, Ma B, Nussinov R.

Methods Mol Biol. 2018;1777:101-119. doi: 10.1007/978-1-4939-7811-3_5.

PMID:
29744830
25.

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.

PMID:
29499269
26.

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.

PMID:
29494137
27.

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.

28.

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]

PMID:
29428499
29.

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.

PMID:
29372900
30.

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.

31.

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.

32.

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.

PMID:
29307569
33.

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.

34.

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.

PMID:
29241665
35.

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.

PMID:
29218757
36.

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.

37.

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.

38.

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.

PMID:
29106933
39.

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.

PMID:
29097261
40.

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.

41.

Network approaches and applications in biology.

Ideker T, Nussinov R.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005771. doi: 10.1371/journal.pcbi.1005771. eCollection 2017 Oct. No abstract available.

42.

Binding of protofibrillar Aβ trimers to lipid bilayer surface enhances Aβ structural stability and causes membrane thinning.

Dong X, Sun Y, Wei G, Nussinov R, Ma B.

Phys Chem Chem Phys. 2017 Oct 18;19(40):27556-27569. doi: 10.1039/c7cp05959k.

43.

How can computation advance microbiome research?

Nussinov R, Papin JA.

PLoS Comput Biol. 2017 Sep 21;13(9):e1005547. doi: 10.1371/journal.pcbi.1005547. eCollection 2017 Sep. No abstract available.

44.

Mechanisms of recognition of amyloid-β (Aβ) monomer, oligomer, and fibril by homologous antibodies.

Zhao J, Nussinov R, Ma B.

J Biol Chem. 2017 Nov 3;292(44):18325-18343. doi: 10.1074/jbc.M117.801514. Epub 2017 Sep 18.

45.

Nuclease activity gives an edge to host-defense peptide piscidin 3 over piscidin 1, rendering it more effective against persisters and biofilms.

Libardo MDJ, Bahar AA, Ma B, Fu R, McCormick LE, Zhao J, McCallum SA, Nussinov R, Ren D, Angeles-Boza AM, Cotten ML.

FEBS J. 2017 Nov;284(21):3662-3683. doi: 10.1111/febs.14263. Epub 2017 Sep 30.

46.

Energetic redistribution in allostery to execute protein function.

Liu J, Nussinov R.

Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):7480-7482. doi: 10.1073/pnas.1709071114. Epub 2017 Jul 10. No abstract available.

47.

Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.

Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizuguchi K, Ahmad S.

Sci Rep. 2017 Jun 22;7(1):4071. doi: 10.1038/s41598-017-03199-6.

48.

Flexible-body motions of calmodulin and the farnesylated hypervariable region yield a high-affinity interaction enabling K-Ras4B membrane extraction.

Jang H, Banerjee A, Chavan T, Gaponenko V, Nussinov R.

J Biol Chem. 2017 Jul 28;292(30):12544-12559. doi: 10.1074/jbc.M117.785063. Epub 2017 Jun 16.

49.

Graphite-Templated Amyloid Nanostructures Formed by a Potential Pentapeptide Inhibitor for Alzheimer's Disease: A Combined Study of Real-Time Atomic Force Microscopy and Molecular Dynamics Simulations.

Li N, Jang H, Yuan M, Li W, Yun X, Lee J, Du Q, Nussinov R, Hou J, Lal R, Zhang F.

Langmuir. 2017 Jul 11;33(27):6647-6656. doi: 10.1021/acs.langmuir.7b00414. Epub 2017 Jun 27.

PMID:
28605901
50.

Intrinsic protein disorder in oncogenic KRAS signaling.

Nussinov R, Jang H, Tsai CJ, Liao TJ, Li S, Fushman D, Zhang J.

Cell Mol Life Sci. 2017 Sep;74(17):3245-3261. doi: 10.1007/s00018-017-2564-3. Epub 2017 Jun 8. Review.

PMID:
28597297

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